Home

"user manual"

1. J3 12VDC HV Pwr 12VDC when Pwr is Enabled 12V Enable Pwr Relay Vertica Switch J4 risen venis Vertical 010500V Polarity Polarity 0 to 500V DAC Adjust Bm DC DC Reverse J39 Reverse en Input 12V to 500V Relay Relay D V Vertical p V Output J1 Horizontal Output gt H Horiz Horizontal Polarity Polarity H Adjust eB DC DC gt Reverse p Reverse 12V to 500V 0 to 500V Relay Relay Pw On Horizontal Switch J2 HV Enb Polarity Change amp Polarity Legend Signal Lines Control Lines PB100836 2 34 Figure 2 22 Beam Steering Board Block Diagram This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments The X Y plates are positioned early in the ion flight path They interface to the outside via a 4 wire high voltage vacuum feedthrough Two twisted pair of 600 V wire connect the feedthrough to the board assembly The voltage applied to each plate is proportional to the ion acceleration voltage A polarity switch anda trim pot trimmer potentiometer tailor each beam axis control to the individual instrument The deflection voltages are automatically reversed when the instrument is reconfigured from positiv
2. eU U U U oes Pulse generator E U Flight tube Cable distribution power supply Control board I Laser switch Left cabinet Right cabinet Figure 2 31 Housing of Electronics Only in Instruments with SN 4153 and Earlier 2 59 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics 2 4 1 Flight Tube Drift Tube Power Supply V750061 Overview Voyager DE STR instruments with serial numbers 4153 and earlier have a guide wire strung along the center axis of the flight tube to organize the stream of ions into a narrow straight beam The V750061 Flight Tube Power Supply is a programmable dual polarity power supply board Figure 2 32 that provides a programmable potential to the wire Ground Guide Wire when Pwr is not Enabled J3 12VDC 12V Enable 12VDC to OpAmps when Pwr is Pwr Relay Enabled DC DC 12V 0 to 100V l Pos lon Mode J4 PAG Oui I t Invert 0 to 10V nver 0 to 10V Out nve DAC OpAmp gt OpAmp i Aven H Output Input Gain 1 Gain 10 7N 0 to 100V Neg Pos Neg lon Mode Offset Offset Neg lon Input Neg Pos Pos lon Input Pela 0 to 10V J
3. Computer Video External digitizer monter monitor Mass Control stick spectrometer 29 1a components f EX l Computer Data system f I inside cabinet Electronics p inside cabinets NM Figure B 1 Voyager DE STR Biospectrometry Workstation BA1 location BA1 is not visible is this drawing the gauge is within a mesh bag Voltage divider box not visible along side the DE switch box DE switch box PB100853 Figure B 2 Voyager DE STR Left Cabinet Rear View This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Appendix B TIS assembly CID High voltage quick Foreline switch box disconnect Valve 2 EL Boe f jk j qq r th 56 LT PH SN se l Lee Loue ied Mirror turbo controller L B KUTT P S N CIS E ut hs PB100854 Mechanical sieve Fore rough pump Figure B 3 Voyager DE STR Center Rear View B 4 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Computer rear view 7 SCS SSS 15 kV power
4. Dooo00000000000_0 I L fmm PB100852 Front View Side View Figure 2 1 Electronics in Left Cabinet Low mass gate linear detector Mirror Linear detector positive driver is HVPS power supply Reflector detector power supply Low mass gate mirror detector FS negative driver D Low mass gate ey delay timer board pA 7 Beam steering board C amp 7 Linear detector and reflector detector power supplies positions may be reversed PB100851 Mirror 16 bit Beam guide wire or DAC board Beam steering DAC 2 2 Figure 2 2 Electronics in Right Cabinet Bottom Drawer This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Theory Overview Two circuit boards the 48 bit I O board and stepper motor board are within the computer Figure 2 3 The computer is housed on the top drawer of the right cabinet Computer boards Stepper not shown motor board Internal digitizer card Network cards k SCSI board Optional CPIB 48 bit I O board PB100867 Figure 2 3 Circuit Boards in the Computer Right Cabinet Top Drawer Rear View Circuit Board Descriptions The circuit board descriptions in this chapter detail the Logic Specifications Connections Switches and Test points
5. i tee ol ele elle role HOTTE Left cabinet drawer B a Side view i p DD ODD DORD 0 AC distribution board PB100852 Main J1 J11 J13 transformer Fore Vacuum Mirror rough multigauge reflector rbo pump controller turbo controller controller power 110 V power J14 Source Figure C 2 Electronics in the Left Cabinet Side View This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Locations of Electronic Components Computer boards Stepper p r card motor board o iiio Network cards SCSI board Optional CPIB Computer PB100867 Figure C 3 Electronics in the Right Cabinet Top Drawer Rear View Low mass gate linear detector Mirror Linear detector positive Driver bo HVPS power supply Reflector detector power supply Low mass gate mirror detector negative driver D Low mass gate delay timer board LA F Beam steering board C amp EM LY Note Linear detector and reflector detector power supplies positions may be reversed PB100851 Mirror 16 bit Beam guide wire or DAC board Beam steering DAC Figure C 4 Electronics in the Right Cabinet Bottom Drawer Front View C 3 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized
6. O O o o O o o O Q J17 4 000000000000000000090 6L0O000000000000000000 J22 J18 JO 1 H0000000000000000 oooooooo 000000 0000000000000 O000000000000 LJOOOOOOOOOOOO OOOOOOOOOO x CL 0000000000 O000000000 0000000000 NEL J N A U O O0000000 O000000 O0000000000000 OOOOOOOOOOCOOO O0000000000000 O0000000000000 00000000000000 00000000000000 00000000000000 00000000000000 a gU 2S A D Xo D XV A e MOL egt OSL Gh S p ne OS 00 OO OOOOOOO zl qq 13 1 majaa aaan Ores JO J14 WP wmm 4999999999990 J4 ENABLED OK AN9 H3MOd pieog jonuo2 1e6e on SL OO Oloooo looo 4 Uu N eo c COLO OO c 2 OO c _ PB100859 Figure C 2 Consolidated MALDI Control Board J25 J25 J17 tloooooooo0oo0o000 7 4 000000000000000000007 iIDoooooooooooot 6LOOOOOOOOOOOOOOOOOO0UL ocaaaaoaog R51 J22 J18 JO o oL 00000000 OOOOO00 OOOOOOOOO0000l lcz o of CO 2 x goo L D000 000 z 0000000000000 sus wooo che QR EE JU3 JU5 J1
7. Low Mass Gate Enable Voltages Delays Section 5 3 8 Set start delay Voltages Delays Section 5 3 9 Direct Bus Access Mirror DAC DAC Section 5 3 6 voltage Set output voltage Section 5 3 8 Direct Bus Access Voltage Set values Voltages Delays Test high voltages DE Switch Box Polarity Set Voltages Delays Section 5 3 8 Positive Section 6 1 1 negative Reflector mode Set mode Voltages Delays Section 5 3 6 Section 6 1 1 Sample loading Initiate load eject cycles Section 5 2 4 and ejecting Mechanical Section 5 2 5 single or multiple iteration cycles Source DAC DAC Section 5 3 7 voltage Set output voltage Direct Bus Section 5 3 8 Access Section 6 1 1 Voltage Set values Voltages Delays Test high voltages DE Switch Box Sample Stage X Set Load position X Y Table Section 5 2 4 Y table Section 5 2 5 Initiate load eject cycles Mechanical See also X and Y feedthroughs Timed lon Enable Voltages Delays Section 5 3 8 Selector Set start and end delay Voltages Section 5 3 9 Delays Direct Bus Access Section 5 5 1 Variable grid Section 5 3 4 Section 5 3 5 Section 5 3 8 Section 5 3 10 5 5 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components Table 5 1 Matching Components with Control Page and Troubleshooting Information mponent or Com
8. Switch Driver Optical Coupler e 95 J1 5 12 V dc Pwr In Common 12VDC Mode DC DC Isolation Float Inductor 12 V de Pwr In 12 V dc Float Out 412 V dc Rtn oi uiui 7 a Gnd Jmpr JPR1 d d Signal N Z HV Gnd l Gnd Low Voltage High Voltage Input Side Output Side Legend High Voltage Control amp Power Jx y PCB Pin Assign Jx y Assy Pin Assign High Current Detector Programmable 0 to 3kV PSS HV in HV Negative Gnd Rs 4 7 Mohm III HV Pulse out Pulse in Rd 300 J2 kv Rf1 4 7 Mohm ask electrons Scintillator photons Photomultiplier gt Rf2 4 7 Mohm Digitizer Input Signal r V700643 DVD LMG Positive Box Assy V750066 PCA LMG Positive V107049 PCB LMG Pos Neg V775029 Cbl Assy DVD LMG N s JUBWNIJSU H1S Fq 4abeAOA JSOW ui uouiuo Ss31u01 98 9 penuueg Buikdo2 pazisoyineun on AJUO esr jeusajuy 404 suiejsAsoig parjddy jo JeW TVLLN3GIJNOO Sulejuog jueunoog SIYL AAA es nd 9ANeDEN 9129 sseyj mo7 au jo weibeig 420 g L 2 ainbl4 D en Detector Filter Bias Board V750032 PCA Det Fitr V107025 PCB Det Fitr I I RH 4 7M I HV Pulse out Pulse in Dual MCP Rd 300 Chevron f Switch ions
9. Fore pump PB100854 Figure 5 33 Thermocouple TC2 Gauge Voyager STR Workstation Rear View Because factors other than pressure affect the thermocouple reading the thermocouple gauge provides an indication of the vacuum pressure rather than an accurate measurement of it In general the true pressure is within approximately 30 of the measured value Inaccuracies in pressure readings result when the dissipation of heat occurs at a different rate than expected Factors affecting the thermocouple accuracy are Presence of a gas other than air The system is calibrated for air If the residual gas in the vacuum system is a different gas the dissipation of heat occurs at a different rate For example hydrogen or helium in the system causes the heat to be conducted away from the thermocouple more rapidly than air resulting in a higher than actual pressure reading e Contaminants on the surface of the thermocouple and heater Calibrating the Thermocouple Gauge Before using the thermocouple select TC2 using the CHAN key Set the atmosphere and vacuum by using the ATM and VAC keys Table 5 9 5 52 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Vacuum System Table 5 9 Setting Atmosphere and Vacuum To Set Do This Atmosphere 1 Expose TC2 to atmospheric pressure 2 Press the ATM key The main display read
10. Beam steering plate To sample loading chamber Figure 1 5 Typical Voltages of Source Chamber Components For more information see the following sections in the Voyager User Guide Optimizing Acquisition Settings Setting Accelerating Voltage and Optimizing Grid Voltage This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager DE STR Workstation Components For Voyager DE STR instruments with a serial number of 4154 and later the main source chamber includes a Sample plate and sample stage The source of ions The sample plate and sample stage Figure 1 3 on page 1 7 are supplied with voltage source up to 25 000 V for acceleration of ions into the flight tube Variable voltage grid A grid supplied with voltage to fine tune ion acceleration Typical voltage settings are shown in the following table Mode Typical Variable Voltage Grid Settings Percent of Source Voltage Linear Delayed Extraction mode 94 to 9596 Reflector mode 65 to 75 higher with PSD When the Delayed Extraction switch is open in Delayed Extraction mode the source plate and variable voltage grid have approximately the same voltage When the Delayed Extraction switch is closed the sample source plate has higher voltage than the variable voltage grid This causes ions of the same polarity to accelerate out of the main
11. Filters out neutral molecules Corrects time dispersion due to initial kinetic energy distribution Provides greater mass accuracy and resolution The reflector Figure 1 13 on page 1 18 is a series of parallel equally spaced disks with coaxial holes separated by insulators Figure 1 14 on page 1 18 shows the time focusing of ions of identical mass and energy within the mirror Time focusing results in improved resolution This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 1 System Overview W M Hen nn Figure 1 13 Reflector Reflector detector TI Faster ion takes longer path Linear detector Slower ion takes shorter path I 20 25 kV Figure 1 14 Reflector Cross Section Diagram The disk potentials are determined by the reflector voltage and series resistor network such that their potentials gradually increase as the ions penetrate farther into the mirror The final disk has a potential that is slightly higher than the source accelerating voltage so that all charged ions are forced to reverse direction before they reach the back of the mirror Neutral molecules are not deflected The Voyager DE STR workstation reflector is tilted down one degree off axis The slight tilt allows the reflector detector to be placed off axis to avoid blocking incoming ions and minimize inci
12. m z Figure 1 15 Time of Flight Analysis Video System The Voyager DE STR video monitor displays a black and white real time sample image 100 times magnification of the sample spot in the sample chamber as viewed through the video camera The camera turns on when the vacuum system is started 1 4 Voyager DE STR Workstation Supporting Systems Electronics Electronics including circuit boards and power supplies are described in Chapter 2 Voyager DE STR Workstation Electronics Theory Power Supplies The Voyager DE STR workstation operates with two power supply systems low voltage and high voltage For more information see Chapter 2 Voyager DE STR Workstation Electronics Theory Vacuum System The vacuum system uses multiple pumps and valves to create and maintain a sealed vacuum environment See Section 6 1 5 Vacuum System for more information Voyager Software The Voyager DE STR software is bidirectional and communicates with the hardware and software Through the control stick and mouse the Voyager control software to allows you to Align a sample plate in the path of the laser Start and stop acquisition Save and transfer data to the processing software Voyager software and computer systems have evolved from using Microsoft Windows 3 11 to Microsoft Windows NT 4 0 platforms 32 bit structure 1 20 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthoriz
13. Component Comment Source power The source power supply is always set higher than the grid power supply The source voltage appears across the adjacent 4700 pF capacitor Behlke switch The Behlke switch is an extremely fast HV electronic switch Grid power supply The grid power supply provides a potential to the grid The forward biased diode also provides the same grid rest potential to the source Source the sample The source and the control grid are both plate represented as small capacitances of approximately 40 pF The series of events are as follows 1 Immediately after the laser ionizes the sample the Behlke input receives a 2 uS TTL level pulse then the output closes for 10 uS 10 uS is enough time to launch all the ions generated by the laser pulse 2 The 4700 pF capacitance is briefly placed in parallel with the source capacitance The voltage across the source quickly jumps to a value only slightly less than the initial value across the 4700 pF capacitor 3 The diode is reversed biased to disconnect the source from the grid power supply 4 The Behlke switch opens The elevated source voltage exponentially decays through the parallel 200 Mohm resistor 5 When it decays to the original grid rest voltage level the diode again conducts and the grid power supply again maintains the source at the grid rest voltage 2 39 This Document Contains CONFIDENTIAL Material of Ap
14. 2 Turn off both BA1 and BA2 ion gauges from the multigauge controller 3 Onthe rear panel of the instrument turn off the Voyager STR workstation main power switch 4 Onthe AC distribution board Figure 3 1 disconnect unplug AC power to the following components Source turbo controller J14 Mirror reflector turbo controller J13 Fore roughing pump power J1 Lf X j UU il B Left cabinet drawer 000000000000000 0 1 S S PB J1 J13 J14 100852 Fore Mirror Source rough reflector turbo pump turbo controller controller power Figure 3 1 AC Power Connectors 5 To prevent possible damage to the turbo pump balanced blades allow the turbos to spin down for 5 to 10 minutes 3 4 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted 3 2 2 Venting to Air Venting the Voyager DE STR Workstation Allow air to flow into the chamber slowly as described in the following table As air flows into the vacuum chamber you hear a slight hissing indicating atmosphere is seeping into the vacuum chamber Step Newer Systems Older Systems 1 Locate the filter mounted on the vent valve of Locate the small knurled vent screw on the the source turbo and mirror turbo side of the tur
15. Verifying Parity in the Voyager Registry To verify parity in the Voyage registry setting 1 Access the Voyager computer registry Voyager vacuum monitor baud as described in Accessing the Voyager Computer Registry Keys on page 48 2 Checkthe Voyager vacuum monitor parity setting in the registry by selecting the following path in the Registry Editor window left panel HKEY LOCAL MACHINE SOFTWARE PerSeptiveBiosystems Maldi Server HiVolt Vacuum Monitor Vacuum Monitor Parity 3 Inthe Registry Editor window right panel select default The DWORD Editor box is displayed 4 In the DWORD Editor box select Decimal 5 If the parity setting is a value other than 1 type 1 in the Data field 6 Click OK Thermocouple Gauge High pressures such as those found in the fore pumping of a vacuum system are generally measured with a thermocouple gauge The thermocouple gauge Figure 5 33 on page 4 52 measures the heat transfer rate from a heated wire at approximately 350 C Heat transfer and pressure are directly proportional As gas is removed from the system less heat is removed The changes in temperature are measured by a thermocouple junction and its output is displayed as changes in pressure 5 51 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components gr TC2
16. 8 With the multimeter set for Ohms measure resistance from the high voltage feedthrough to the shaft of the Linear 1 actuator 9 If open infinite resistance is observed the internal high voltage connection cable is defective or dislodged Vent the system then replace or reconnect the cable Using the 32 Bit Diagnostic Software To test the HV cable using the 32 bit diagnostics software 1 Load the sample plate into the sample plate holder 2 Exit Voyager Control software and manually turn off the ion gauge tubes 5 30 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Main Source Chamber 3 Shut down the Instrument Hardware Controller and start the 32 bit diagnostics software For information see Chapter 4 Voyager Diagnostics Software Select the XY tab Initialize the autosampler by clicking Home Click Move to Load Select the Mechanical tab Close Foreline Valve 1 o N o s Open Flap Door 1 and extend the Linear 1 actuator This completes the circuit As you extend the Linear 1 actuator watch the video monitor If you see movement of the plate the grabber assembly is touching the plate 9 Connect a small feeler gauge to the shaft of the Linear 1 actuator and the high voltage feedthrough Measure resistance Ohm flows from the high voltage feedthrough to the shaft of the Linear 1 actuator 10 If open infinite resistance
17. At Limit Home position is the position where the attenuation strength is maximum Laser Pulse Detection Circuit The beam splitter directs a part of the laser beam onto the photodiode CR1 The photodiode turns On when the beam hits it When CR1 turns ON Q1 and Q2 also turn On This produces a positive signal at the input of the buffers U1 and U2 The signal is buffered by these chips and output to J4 J5 then sent to the pulse generator The signal stays high until the laser stops firing AT Limit Feedback Circuit The attenuator wheel has reflective tape at the position where the attenuation strength is maximum the position where minimum laser energy passes The limit switch consists of an LED and a phototransistor When the attenuator wheel is in the Home position the light from the LED is reflected off the reflector tape onto the phototransistor This causes the phototransistor to turn on and subsequently turns on Q3 This signal is then sent to the Autosampler Control PCA Connectors Table 2 7 Connectors on the TTL Output Opto Trigger PCA Name Function Type J1 Power input 5 V 15 V and 4 pin Mini Fit 15V J2 At Limit sensor power and 4 pin Mini Fit read back J3 At Limit read back to stepper 2 pin Mini Fit motor control board J4 Laser detected pulse to control SMA board J5 Laser detected pulse spare SMA 2 31 This Document Contains CONFIDENTIAL Material of App
18. Bin XXXX XXxx 0000 0000 to Xxxx xxxx 1111 1111 Where 0 8000 and 255 65000 You must interpolate all values between the min max Bits 8 15 are ignored P This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Data Values for Direct Access Table D 1 Direct Access Data Values continued Component Parameter Bit values 6 DE delay Delayed Extraction delay time Bits 0 14 represent 10 to 32 768 ns Values entered represent the target time divided by the TIS clock frequency in ns 10 ns Bit 15 selects start end time 0 start 1 5 end Valid start times correspond to values ranging from 10 to 32 767 are Dec 0 to 32767 Hex 0000 to 7FFF Bin 0000 0000 0000 0000 to 0111 1111 1111 1111 Where 0 10 ns and 32767 327670 ns at the DAC You must interpolate all values between the min max Valid end times correspond to values ranging from 10 to 32 768 are Dec 32768 to 65535 Hex 8000 to FFFF Bin 1000 0000 0000 0000 to 1111 1111 1111 1111 Where 32768 10 ns and 65535 327680 ns at the DAC You must interpolate all values between the min max 7 TIS delay Timed lon Selector delay time Bits 0 14 represent 10 to 32 768 ns Values entered represent the target time TIS clock frequency ns 10 ns Bit 15 Sets start end time 0 start k end Valid start times corresp
19. PB100855 Figure B 9 Sample Loading Chamber B 8 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronic Drawings This appendix contains the following Locations of Electronic Components C 2 Pin 1 Connector Locations C 4 Interconnects saata dd NER INIRE RU EI etes C 5 MALDI Consolidated Control Board C 7 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Appendix C Locations of Electronic Components Use the following figures to locate electronic components For more information about Voyager workstation electronics see the circuit board schematics posted on the MALDI knowledge database and review Chapter 2 Voyager DE STR Workstation Electronics Theory in this manual LI gt glo Grid HVPS H 2 s 5 Source HVPS o NY EX y KE MALDI contro N h 2 W DC distribution AC 7 Q ogogo CAH Oo Vacuum Don multigauge controller PB100848 Figure C 1 Electronics in Left Cabinet Front View F11B F11A wine
20. desired position conversions automatically The micron is used in the counts or microns NT Registry editor Move to Limit switches NA desired home home load load Set load position NA NOTE The SET Load Position button on the X Y Table control page initiates a data write to the Registry file The next time it is accessed the Voyager Instrument Control Panel reads the new X Y coordinates from the Registry file to determine the sample stage load position Record the old coordinates in case you need to revert to them DE Switch Box Control Checks the control wiring on the DE switch box Check control wiring Check Control Before you begin assemble your voltmeter and meter test Wiring test steps probes and access the DE switch box through expected voltage readings This test checks the operative states of the three high and instructions voltage kilovac relays by looking at resistance between J2 and J4 and the admittance between J3 and J2 Gnd DE Switch Box type NA V725059 Three connector high voltage switch box in Voyager DE STR workstation with serial numbers 4147 and earlier V725115 Four connector high voltage switch box in systems with serial numbers 4148 through 4160 V725125 Four connector fast DE switch box in systems with serial numbers 4161 and later continued 4 9 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Intern
21. Camera Mechanical Laser Voltages Dela XY Table J iE Switch Box Direct Bus Access r XY Table 15633 y FE r Units Limit Switches al Current Position 0 Counts Home iv Load Position 15000 8000 Microns C Load r Desired Position 0 z 0 Y Position i Move to Load Move to Desired SET Load Position X Position o gt 16688 Figure 5 7 X Y Table Control Page Homing the Sample Stage Before you can access the functions on this control page you must click sample stage to its Home position 0 0 This initializes the diagnostics so software to calculate all other positions including load position to move the is enabling the The limit switches are microswitches located on each feedthrough Figure 5 8 on page 5 20 at the Home position These microswitches are position sensitive and detect when the feedthroughs are Home or are within the load region The Home microswitches detects the 0 0 position The Load microswitches because of their orientation on the feedthrough arms sense position within a range of points This range of points is referred to as the load region The load switch for both the X and Y position must be enabled closed before the air compressor will run If only one load switch is enabled closed the air compressor remains off The limit switches Figure 5 8 are Home Indicates the sample stage has reached the Ho
22. Sequazyme C Peptide Sequencing Kit Sequazyme Oligonucleotide Sequencing Kit This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter1 System Overview 1 2 Voyager DE STR Laser Safety Laser Classification The Voyager DE Biospectrometry Workstation uses a standard nitrogen laser and an optional Nd YAG laser Under normal operating conditions the instrument laser is categorized as a Class laser Under certain conditions during servicing when interlocks have been circumvented the lasers fall into the following categories and can cause permanent eye damage Nitrogen Class IIIb Nd YAG Class IV The Voyager DE Biospectrometry Workstation complies with Title 21 U S Government DHEW BRH Performance Standards Chapter 1 Subchapter J Section 1040 as applicable Laser Safety Features The following safety features are included on the Voyager DE Biospectrometry Workstation Cabinet is designed to prevent access to collateral laser radiation exceeding the accessible emission limits in Performance Standards for Laser Products 21 CFR 1040 10 Top front back and side panels have interlock switches that disable the laser when panels are opened or removed Safety labels for Class standards are affixed to the unit WARNING ELECTRICAL SHOCK AND LASER HAZARD In External Trigger mode the nitrogen laser energ
23. sss 2 2 4 Low Mass Gate Delay Timer Board V750069 V750073 2 2 5 Low Mass Gate Driver Boxes V700635 V700643 and Detector Filter Bias V750032 inii eat ced Aa FETTERE 2 2 6 Timed lon Selector TIS Assembly V700471 sse 2 2 7 TTL Output Opto Trigger Board V750065 2 3 Electronics Only in Newer Model Instruments sssssseeennn 2 3 1 Beam Steering Board V750091 sss 2 3 2 DE Switch Box V725115 V725125 sss 2 3 3 Einzel Lens Electronics Voltage Divider Box 4317251 2 3 4 48 Bit I O Board with Game Port V750033 esseere 2 3 5 MALDI Control Board V750082 and V750102 001 V750102 002 N 75027003 xctl putate ter tebet td ida eet ee lil This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Table of Contents 2 4 Electronics Only in Earlier Instruments 2 59 2 4 1 Flight Tube Drift Tube Power Supply V750061 sess 2 60 2 4 2 Pulse Generator Board V750063 sssssssssssssse ee 2 63 Chapter 3 Before Servicing the Workstation 3 1 3 2 3 3 Voyager Laser Safety audiant o OU n iiia Gn edt deti dete 3 2 3 1 1 Overview of Laser Safety ss 3 2 3 1 2 Required Customer Provided YAG Laser Safety Measures 3 3 Venting the Voyager DE
24. Fuse OK LEDs LED 2 8 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Common in Most Voyager DE STR Instruments 2 2 2 DAC Digital to Analog Converter Board V750025 Overview This DAC circuit board converts a digital code from the computer to an analog output voltage Each DAC Digital to Analog Converter board has a unique address that is set by its DIP switches eti PB100851 Mirror 16 bit Beam guide wire or DAC board Beam steering DAC Figure 2 7 DAC Board Locations Theory Adaress The computer address is compared to the board address by U3 If the address is correct the Chip Select CS on the DAC chip is asserted and the chip is selected Data Data is loaded on the bus sometime after the address is loaded The 16 bit data is buffered through U2 and U5 and passed to the DAC chip Load and Latch The computer sends a Load Data LD and a Latch pulse that are buffered through U6B When the load and latch are asserted the DAC loads the data from the bus 2 9 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics DAC The DAC uses a 5 V reference generated by the U4 regulat
25. Home position see Microswitch see Sample stage How to use this guide xvii pot source voltage power supply setting of 3 turns ccw 5 32 ICP see Instrument Control Panel IHC see Instrument Hardware Controller Init fault diagnostics software and lon gauge 5 16 overriding warning 5 16 Instrument Hardware Controller function 1 21 restarting 4 4 Intensity signal definition 1 20 Interconnect Diagram 2 3 Interlocks avoiding errors and warnings 5 9 status bar display 4 11 Interlocks defeated LED nitrogen laser 1 12 Interlocks internal error message 5 9 hazard control 5 9 potential damage if compromised 5 9 prerequisites 5 9 warning message 5 9 Internal high voltage cable see high voltage cable Internal external trigger adjustment nitrogen laser 1 13 lon beam path in linear mode 1 1 lon gauge see also BA gauge 5 5 BA gauge 5 45 Bayard Alpert 5 45 components 5 53 conditions damaging to 5 16 conditions potential damaging to 5 16 factors affecting accuracy 5 54 function 5 45 5 53 ion emission and pressure 5 54 pressure bursts shuts down 5 10 process when faults during a load eject cycle 5 15 range 5 45 restarting 5 10 restarting after a fault 5 16 restarting during load eject cycles 5 15 safely ignoring 5 15 shuts down due to over pressure 5 15 theory 5 54 when irrelevant 5 15 lon Gauge Controller not responding error possible causes 6 15 lon source see Source D Co Index 6 This Document Contain
26. Open the vent valve Close Flap Door 1 Error Close Foreline Valve 1 Close the vent valve Close Flap Door 2 Warning Linear 1 actuator Extend Linear 1 actuator When under vacuum Error Open Flap Door 1 Retract Linear 2 actuator Have the sample stage in Load position In addition No error message occurs Close Flap Door 2 if these conditions are not Close the vent valve masl bul gomrols ara disabled This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Sample Loading Chamber Table 5 2 Internal Interlock Hazard Control Continued Load position AND retract the Linear 1 actuator To perform this operation Do this first Otherwise this occurs Retract Linear 1 actuator When vented open Flap Error Door 1 When under vacuum Open Flap Door 1 Close Flap Door 2 Close the vent valve Linear 2 actuator Extend Linear 2 actuator Retract Linear 1 actuator Error Open Flap Door 2 Retract Linear 2 actuator Open Flap Door 2 Error Grabber Grabber off Move the sample stage to Warning 5 2 3 Camera The camera enables you to see on the external monitor the sample spot and location where the laser is striking The Diagnostics Software Camera control page Section 5 6 Computer and Video Systems shows the status of the camera 5 2 4 Grabber Linear Actua
27. Trigger Input The external trigger requires a TTL signal of 1 microsecond or longer The input of the trigger is protected with an opto isolator that minimizes EMI RF interferences The cable is an RG58C U BNC cable 4 feet 1 2 m or shorter Fan Moderates the temperature of the nitrogen laser unit WARNING LASER BURN HAZARD An overheated laser can cause severe burns if it contacts skin DO NOT operate the laser when it cannot be cooled by its cooling fan Always wear laser safety goggles This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter1 System Overview Nitrogen Laser Beam Path Figure 1 9 shows the path of the laser beam through the Voyager DE STR mass spectrometer Optical trigger board Gradient optical disk splitter lens Nitrogen laser unit Attenuator housing Sample plate Main source chamber Laser beam PB100832 Figure 1 9 Nitrogen Laser Beam Path When the laser is triggered the emitted laser beam strikes the beam splitter lens A small part of the beam is reflected to the optical trigger board providing timing signals for the following components Digitizer Delayed Extraction pulse delay Timed lon Selector pulse delay Low Mass Gate The remaining part of the laser beam passes through the beam splitter lens to a laser attenuator The laser attenuator is a 0 to
28. be lt J Jas LASER y A CONTROL TRIG QUT EI a VIT AI TRIG Je 7 jN Digitizer TDS Tektronix gt LASER TRIG BD 50 60 HZ PJe3 CA CONTROL TRIG IN z J exe 1x2 CA DIGITIZER TRIG pes sua ab ELU us PF V 2A Top Jie Je7 TIS CONTRDL CABLE Assy Bottom Jl s Co NTISTOR JP14 amp V700471 Assy DE BOX Power Supply Sv 24V V700723 CA HV DeBox to S Distribution Ca HCD Power BERTAN GRID IVPS CA Mirror Dut 775070 Lin ACD sig Dut 700635 Assy High Current ReflectorDetect Ca CA Buss Right Drawer HV Mirror v7T9048 V775848 CA Beam Steering PCA A Y VITSE Qu Bean Steering Steering PUR V750091 CA STEPPER m MOTOR CA Right Drawer Harness ole Blk Diagram Voyager S EE Eze Docanent Nune Re MT el ee Corry th a mand x 7 Date Tuesday June 27 2000 Sheet of 1 A 3 T T E Figure C 1 Voyager STR Interconnect MALDI Consolidated Control Board c N oo0oo0o0 000 6cr C000 rer ZA O 0000o lo OO OOOOO0 oer Oo o O o O OO O O O 4 3 B B N eer cer J25 vy ooooooooooooSs 1D000000000000OE k Iooooooooo R51 J26 Ju4 JU3 JUS S2 Reset fe exe SN R46
29. control Voltage select Electronics Common in Most Voyager DE STR Instruments Fuse OK Output Fuses LEDs Connectors F1 DSi AB J Fore roughing pump fe gies J2 Fans AB Mrd iens J3 Not used B E J4 Laser AB F5 DS5 l AB p Optional turbo E Qs E Computer F7 D87 AB p Y 12 V power supply F8 gta y Not used AB m DS9 Ms gt J Not used E DS10 AR p Quad power supply pt St z 110 V power AB Vacuum gauge control DS12 A6 p 2 24 V power supply ae ea z3 Turbo mirror controller BL Pa as ee 34 Turbo source controller BILL F15 DS15 AB 45 Compressor K1 Compressor Relay PB100838 Figure 2 6 AC Distribution Board Block Diagram This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Connectors and LEDs Table 2 1 Connectors and LEDs on the AC Distribution Board Item Name Function Type Connectors J1 J14 Output connectors 3 position MATE N LOK J15 Compressor power 3 position MATE N LOK J16 Terminal block 2 x 8 terminal block J17 Load Position in out 4 position Mini Fit LEDs DS1 DS15
30. following IBM9 compatible computer hardware components Minimum computer configuration of Pentium III 500 MHz CPU with a 6 4 GB hard disk and 128 MB random access memory RAM 3 5 inch HD high density 1 44 MB floppy disk drive CD ROM drive integrated sound card Integrated 10 100 MB 3COM Ethernet adapter card on the motherboard VGA compatible color monitor e WIN95 Spacesaver Quiet Key 104 key keyboard Microsoft compatible mouse Control stick Optional laser printer NOTE The manufacturer installed integrated sound card is disabled before the Voyager workstation is shipped The sound card can interfere with the loading of drivers and the functioning of the Voyager stepper motors Also screen savers may interfere with Voyager system performance This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter1 System Overview Computer monitor To produce the spectral trace displayed on the computer monitor m z values are plotted against 1 intensity Figure 1 15 The Voyager software calculates m z from the measured drift time Intensity is calculated from the number of ions reaching the detector at a given time Intensity is referred to as ion intensity abundance or signal intensity Heavier Lighter Lighter Heavier ions ions gt one ions 9 2 Go Q o9 5 e OO Qe SS Relative Distance Time
31. oO IIS oo OJ O ol o 5 099 R4e oL lo oL Jo N 0000 sen 0000 o Li c c N E amp O o o Ox co m ojlo 6 ooo Oo Ooo0 HE ter cer paeog jouog sabekon STOO TP22 ES naa TP18 e 2g TP9 TP20 oo g 8 o 8 8 8 e OOJ OJ O OJ o OJ o OJ o J21 55 lo ol fe al oo a e e a o 8 e TP17 s a lo ol S lo ol o OJ O O o OJ o OJ o OJ O OJ U27 o OJ o OJ o OJ O OJ o OJ o OJ o OJ O OJ o OJ o OJ o OJ O OJ o OJ lO OJ o OJ iO OJ o OJ o OJ o fo C a mj O a L1 C oO O D o 9 S amp P lt SR e Uu es Y oe Pg LE e a e ee Ground ASAA J14 T LILILILILILILILI OEO Qo OO000000 b G a aa nes OEO J12 PB100859 Figure 2 30 MALDI Control Board 2 58 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Earlier Instruments 2 4 Electronics Only in Earlier Instruments Overview The electronics only in instruments with serial numbers 4153 and earlier described in this section are Flight tube drift tube power supply V750061 Pulse Generator board V750063 In addition the earlier instruments have the following electronics Cable Distribution V750003 Control board V750015 DC power supplies 412 V 24 V Quad 5 V 15 V 5 2 V Laser switch board Figure 2 31 shows the housing of these electronics
32. 19 Ethernet adapter card 1 1 minimum requirements 1 19 screen saver interference 1 1 software shipped with 1 21 sound card interference 1 1 troubleshooting tables 6 9 Connectors see also Circuit board connectors andLEDs 2 8 Control pages Diagnostics software Camera 4 6 5 11 5 43 DE switch box 4 9 5 36 Direct Bus Access 4 10 D 2 function summary 4 6 Laser 4 7 5 39 Mechanical 4 6 5 12 5 16 5 31 overview 4 5 resources Summary 4 5 troubleshooting summary 5 2 Voltages Delays 4 8 5 33 5 43 X Y Table 4 9 5 19 Control stick description 1 2 Counters 2 17 2 64 Customer training information A 11 Index 2 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted D DAC setting voltages using diagnostics software 5 34 DAC board calculating grid expected output voltage 5 32 calculating source expected output voltage 5 32 connectors 2 10 location 2 9 theory 2 9 DAC voltages ramping 5 33 Data bus setting values in binary decimal or hexadecimal D 3 writing to D 3 Data bus control page entering values D 4 Data Explorer Software function 1 21 Database MALDI knowledge 5 6 A 3 DC Distribution board connectors 2 12 LEDs 2 14 location 2 11 overview 11 test points 2 1 theory 2 11 DE switch box component of source 5 18 components 2 37 connectors 2 42 firmware configuration 2 43 input output 2 42 LEDs 2 43
33. 2 1 Preparing to Vent eeeeseseessess 3 4 3 2 2 Venting to Air sse 3 5 3 2 8 Purging the System to N2 3 5 3 8 Powering Up After Venting 3 6 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 3 Before Servicing the Workstation 3 1 Voyager Laser Safety 3 1 1 Overview of Laser Safety Laser Classification The Voyager DE Biospectrometry Workstation uses a standard nitrogen laser and an optional Nd YAG laser Under normal operating conditions the instrument laser is categorized as a Class laser Under certain conditions during servicing when interlocks have been circumvented the lasers fall into the following categories and can cause permanent eye damage Nitrogen Class IIIb Nd YAG Class IV The Voyager DE Biospectrometry Workstation complies with Title 21 U S Government DHEW BRH Performance Standards Chapter 1 Subchapter J Section 1040 as applicable Laser Safety Features The following safety features are included on the Voyager DE Biospectrometry Workstation Cabinet is designed to prevent access to collateral laser radiation exceeding the accessible emission limits in Performance Standards for Laser Products 21 CFR 1040 10 Top front back and side panels have interlock switches that disable the laser when panels are o
34. 2 on b3 off 4 position address b1 2 on DIP switch SW3 Configuration b0 1 off b0 1 off 4 position address 3 b2 3 on b2 3 on DIP switch Test Points TP1 15 V dc Not used Not used Not used TP2 5 2 V dc Not used Not used Not used TP3 24 V dc Not used Not used Not used TP4 15 V dc Not used Not used Not used TP5 5 V dc Not used Not used Not used TP6 Ground Not used Not used Not used TP7 Delayed pulse DE trigger TIS trigger TTL out TP8 Trigger input Laser opto Laser opto TTL trigger trigger Diodes D2 15 V dc LED 15VdcLED 15VdcLED 15 V dc LED D4 5 2VdcLED 5 2VdcLED 5 2VdcLED 5 2 Vdc LED D5 5 V dc LED 5 V dc LED 5 V dc LED 5 V dc LED D7 15 V dc LED 15 V de LED 15 V dc LED 15 V de LED D9 24 V de LED 24 V dc LED 24 V de LED 24 V de LED D11 Pulse out LED Pulse out LED Pulse out LED Pulse out LED Configurable address and board function DE TIS settings 2 66 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted 3 Before Servicing the Workstation This chapter contains the following sections 3 1 Voyager Laser Safety 3 2 3 1 1 Overview of Laser Safety 3 2 3 1 2 Required Customer Provided YAG Laser Safety Measures sese 3 3 3 2 Venting the Voyager DE STR Workstation 3 4 3
35. 3 OD optical density gradient optical disk that decreases or increases the intensity of the laser beam As the laser is firing you adjust the attenuation by pressing the Control Page Up and Control Page Down keys on the computer keyboard The Control window must be active The attenuated beam passes through a prism which directs the laser beam through a focusing ring a lens assembly and into the ion source The output beam exiting the nitrogen laser unit is approximately 250 uJ Depending on the attenuation setting approximately 2 to 8 uJ enters the main source chamber and is allowed to strike the sample This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager DE STR Workstation Components 1 3 4 Flight Tube Drift Tube Overview The flight tube is free of electromagnetic fields no accelerating forces are present allowing ions to drift at a velocity inversely proportional to the square root of their masses That is the lighter an ion the faster it drifts the heavier an ion the slower it drifts The flight tube is also referred to as the drift tube At the entrance to the flight tube of an instrument with a serial number of 4154 and later there are an einzel lens Figure 1 10 and four beam steering plates Voltage applied to the einzel lens and beam steering plates focuses the beam and directs the ions to the detector 7 Beam
36. 5 21 troubleshooting symptoms 6 4 Source clips checking for damage 5 23 imperfections 5 23 Source DAC calculating expected output voltage 5 32 Source pedestal aligning 5 24 and grabber alignment 5 24 Source turbo controller reconnecting 3 6 Source voltage and grid voltages 5 34 diagnostics software values 5 34 effect on beam steering plates einzel lens 5 34 setting using diagnostics software 5 3 testing using diagnostics software 5 3 Spectra how trace produced 1 20 instrument error 6 15 troubleshooting symptoms 6 2 Stability fault 5 15 Start register Low Mass Gate Delay Timer board 2 17 Status bar diagnostics software display 4 11 see also BA TC2 gauge component states shown 4 11 high voltage status 4 11 Interlocks status 4 11 Laser status 4 11 mirror BA2 pressure 4 11 sample loading chamber TC2 pressure 4 11 sample stage X coordinate 4 11 sample stage Y coordinate 4 11 source BA1 pressure 4 11 Status load and eject cycles 5 14 Stepper motor feedthroughs adjusting 6 8 binding 5 28 grinding noise 5 28 home switches adjusting ifloose 6 8 interconnects 5 27 lubricating 5 28 microswitches 5 26 troubleshooting 5 26 5 28 Switch box see DE switch box o amp Index 12 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted T TC1 TC3 TC4 5 46 TC2 see also thermocouple gauge calibrating 5 52 high reading 6 11 6 12
37. 65 firing pulse O OO OO J5 External laser trigger 4 je LQ cer cer Figure C 4 Consolidated MALDI Control Board View B C 10 J32 Interlock E s A Switches Jue J7 DE Switch box control 24 V Relay Control J8 DE switch box trigger J9 Digitizer trigger TP18 TP20 J21 O O O Ol O O O o J10 DVDT trigger J11 TIS trigger TP17 O O O O O O O O 00000000000000 00000000000000 TP19 J34 5 24 15 15 V D12 PM ooo0o0o0o0 000000 e amp amp 7 0 B O Ki amp es ee 3 e Sag Ki TP21 J27 OOOOOOOL D10 D9 e CA e GROUND alsjnim siee e SNS F eg lo lo OEO 2f n2 mE 4 control J27 Turbo controllers gt J14 p 8 DAC control monitors p 8 HVPS enables 3 PTS poqj R24 TP20 TP9 z 00000000 iL O0000000 s u22 u19 0000000000000 c eo o 00000000000000 00000000000000 00000000000000 R 4 Kid p 4 00 4 Pd zi e P s GES 4 ON we ea oococoon D10 Ga e eee e P Trp 2 RE apes EN Cr eu J12 ae oo a LED PB100869 Figure C 5 Consolidated MALDI Control Board View C C 11 C 12 This page intentionally left blank Isolating Components Us
38. B Wrong Com port is selected In the computer use Com Port 2 for the vacuum gauge controller see Voyager User Guide 7 Vacuum initialization error BA1 and or BA2 pressure Check vacuum system readings exceed the normal performance and ensure the operational pressure limits pumps are pumping properly When the system reaches appropriate pressures re initialize the gauges if necessary 8 When system re starts aftera System pressure has not Check system pressure power outage the Voyager control panel shows an instrument error when acquiring data been pumping down sufficiently before the computer boots up and IHC starts to initialize the system Stop and restart the IHC if system is under normal operating pressures 6 15 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 6 Troubleshooting by Symptoms 6 2 Multigauge Controller Common Error Codes Table 6 6 Multigauge Controller Common Error Codes Error Pose Piero Possible Cause Action Code Source E02 Microburst Wet sample plate Recalibrate microburst tolerance setting to the default by pressing F Vac then A52 E03 lon gauge No current If resetting the Voyager software connection clears the error the problem was broken or between the software and the disconnected multigauge controller The Voyager If the error per
39. Cable sussssss 5 30 5 3 6 Operation Mode sseenn 5 31 5 3 7 Delayed Extraction lon Source suus 5 32 5 3 8 Source Grid and Mirror Voltages 5 33 5 3 9 Delayed Extraction Low Mass Gate and Timed lon Selector Delay Times 5 35 5 3 10 DE Switch Box Control ssseseeess 5 36 5 4 Laser System unitas ie nement 5 38 5 4 1 Laser Firing Repetition Rate and Reinitialization Zspirit e 5 38 5 4 2 Laser Attenuation eeeeeen 5 40 5 5 Flight Tube and Mirror Chamber seeeeeeeeeeeeeeneees 5 42 5 5 1 Timed lon Selector 5 42 5 5 2 Flight Tube Drift tube Power Supply 5 43 5 6 Computer and Video Systems 5 43 5 7 Vacuum System e a Res REC RE 5 44 5 7 1 Vacuum Gauges and Pumps sseessss 5 44 5 7 2 Multigauge Controller seeeseeess 5 45 5 7 8 Multigauge Controller Computer and Workstation Interaction eee 5 47 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components 5 1 Troubleshooting Overview This manual describes troubleshooting using The Voyager Diagnostic software introduced in Section 4 4 1 Control Pages and detai
40. Flap Door 1 Error Linear 1 actuator is Extended Open Flap Door 2 Warning Flap Valve 1 is Open Warning Foreline Valve 1 is Open Warning Vent valve is Closed Close Flap Door 2 Error Linear 2 actuator is Extended 5 16 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Sample Loading Chamber Table 5 4 Diagnostics Software Mechanical Control Page Warning and Error Conditions Continued Action Selected in the Message eis Mechanical Control Page Type Condition Causing the Message Extend Linear 1 actuator Error Flap Door 1 is Closed OR Linear 2 actuator is Sample Stage is NOT at the Load Position Retract Linear 1 actuator Error Flap Door 1 is Closed Extend Linear 2 actuator Error Flap Valve 2 is Closed OR Linear 1 actuator is Extended Retract Linear 2 actuator Error Flap Door 2 is Closed Open Vent Valve Error Flap Door 1 OR Foreline Valve 1 is Open Close Vent Valve Warning Flap Door 2 is Open Open Foreline 1 Error Flap Door 2 OR Vent Valve is Open Open Foreline 2 Warning Vent valve AND Foreline Valve 1 are Open Warning Flap Door 2 AND Foreline Valve 1 are Open Close Foreline 2 Warning Flap Door 1 AND Vent Valve are Open Warning Flap Door 1 AND Flap Door 2 are Open Grabber OFF Warning Linear 1 actuator is Extended AND the X Y Stage is NOT at the Load Position 5 17 This Document Contains CONFIDENTIAL Ma
41. Gate Start Delay and Timed lon Selector Start and End Delays See Section 5 3 9 5 6 Computer and Video Systems The camera allows you to see on the external monitor the sample spot and location where the laser is striking The Camera control page Figure 5 28 shows the status of the camera By default the Camera control page appears and powers on the camera and video lamps when you start the Voyager diagnostics software for NT platform Camera Mecharica Laser Voltages Delays X Y Table DE Switch Box Direct Bus Access Camera OFF ON Figure 5 28 Camera Control Page 5 43 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 5 Troubleshooting by Components 5 7 Vacuum System This section includes a description of the vacuum gauges and multigauge controller Additional information is provided in Section 3 Before Servicing the Workstation A procedure for venting the system to air A procedure for purging the system to No A procedure for powering up the workstation after venting 5 7 1 Vacuum Gauges and Pumps The vacuum system Figure 5 2 on page 5 8 uses multiple pumps to create and maintain a sealed high vacuum environment for unobstructed ion drift The Voyager DE STR has three vacuum chambers and three pumps as described in the following table Vacuum Chamber Vacuum Range Typical Pr
42. I O Board Continued Connector Function Type J4 Not used NA J5 Not used NA J6 Game port 16 pin ribbon LEDs The I O Board has one LED the 5 V LED The function is Buffered 5 V 2 3 5 MALDI Control Board V750082 and V750102 001 V750102 002 V7502 003 Overview The MALDI consolidated control board consolidates discrete logic functions previously found on the Pulse Generator Timed lon Selector Board DAC source grid reflector and Beam Guide Boards Old style TTL MALDI Control and Distribution Boards MALDI z control Bz el A board i Figure 2 29 MALDI Control Board Location 2 47 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Table 2 17 on page 2 52 and Figure 2 30 on page 2 58 present the highlights of the MALDI control board Systems controlled by this board include the pumps voltages and vacuum system MALDI consolidated control board functions to controls the DE switch box High voltage power supply DAC control and enable polarity Timed lon Selector Delayed pulse generator Laser trigger Interlock sensor Functions not controlled by the MALDI Control Board are listed in Table 2 16 Table 2 16 Functions Excluded from
43. Interconnect Diagram An overall cable connection diagram that shows how the electronics interact with each other is available in Appendix C Electronic Drawings Additional Electronics Information Additional information is available on the MALDI Product Support web site of the Applied Biosystems intranet The MALDI Product Support web site path is https gene peintranet net login to the intranet is needed Departments Product Support Voyager Support The table below provides paths to electronic schematics bulletins and recently encountered problems Information Path from Voyager Support Web Site Home Page Circuit board schematics Service Documentation Service Training Schematics Service bulletins Alerts Bulletins Notes Voyager Electronics Electronics problems recently encountered Link to the MALDI Knowledge database by field service engineers At the MALDI Knowledge database select Electronics This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics 2 2 Electronics Common in Most Voyager DE STR Instruments Most Voyager DE STR instruments have the following electronics AC Distribution V750053 DAC Board V750025 DC Distribution Board V750034 Low Mass Gate positive negative and detector filter bias Timed lon Selector TIS Assembly V700471 TTL Output Opto Trigger PCA V75
44. J15 ES aa N Ole QN9 u3MOd 1 1 4 4 1 1 1 4 4 1 1 1 1 1 4 J17 cd sSTR DAC control S low mass gate J25 J17 Detector 24 V switched 24 V switching LMG enable VAC gauge to workstation 4 000000000oooooooooo0 OOOOOOOOOOOOOOOOOOLL J18 JO 6L Hooooo090999 R51 J22 Hoooo0O0 2 00000000000000000 d l N 0O000000OO OOOO OO L LIOOOOOOOO00000lsz J26 E OOOO 0000000000000 J23 run al R40 Jl 0000000000000lls JU3 JU5 J1 vl ooooooooooooSe IOooooooooooO amp l J26 J23 J22 J15 J1 JO Linear Linear Camera grabber Vacuum gauge Workstation flap and flap vent solenoid serial connection 48 Bit I O load position actuator foreline solenoid to MGC controller sensors solenoid control control PB100867 Mirror beam steering 5 m E 2 Os O J2 y Power NO ground S lt Figure C 3 Consolidated MALDI Control Board View A C 9 R51 J22 J18 J0 ay oo Hooooooo 9000 0 2 00000000000000000 z 5000000000000 SU D0000000000000000 m o of oooooooo 299099 3 3 000000
45. Overview Nitrogen Laser Structure Components of the nitrogen laser module include the 1 Shutter manual slide mechanism Plasma cartridge module Low voltage power supplies High voltage power supplies Trigger transformer board All controls for the laser unit are on the rear panel of the laser unit Figure 1 8 Interlocks Laser On Defeated LED LED _ Key Control On Off switch Internal external trigger adjustment manual repetition rate control normally set to External Fan i AN Power J receptacle BNC connector trigger input Remote interlock connector control for repetition rate cable connection Figure 1 8 Nitrogen Laser Control Panel The components of the nitrogen laser control panel and their functions are as follows Interlocks Defeated LED When lit green indicates that the laser is ready to fire When dim the cover or remote interlock is open and the laser will not fire Laser On Radiation Emission LED When lit red indicates that the laser is powered on and may emit radiation Key Control On Off Switch Turns on or off the electrical power to the laser You can remove the key only in the Off position The Laser On LED indicates the state Power Receptacle Receives a grounded standard three wire power plug for 110 20 V 3A operation The power cord must not be longer than 6 feet 1 8 m
46. Pulse Out End Counter 13 bit Down Counter reset i reset PB100842 s lu01 99 7 Z s4ajdeyo Electronics Common in Most Voyager DE STR Instruments 18 MHz Clock and Divide by Four The clock generates a 220 ns 4 5 MHz timbales used by the counters synchronizer and address decoder Trigger Buffer The trigger buffer takes a 3 to 12 V asynchronous pulse event buffers it to 5 V synchronizes it to the 4 5 MHz clock then presents it as an enable signal to the three counters The pulse event is the DE Trigger Start Register The start register contains the 8 bit delay loaded off the data bus Counters There are three down counters Offset delay Hard coded Offsets the delay by 8 us Programmable delay Loaded off the data bus Provides 8 bit value corresponding to the desired delay after the 8 usecond offset End delay Hard coded Ends the delayed pulse and resets the circuit at approximately 1 s When a trigger signal is received from the Trigger Buffer 1 The first counter counts off an 8 us offset 2 After the 8 us the delay counter and the reset counter begin counting down 3 When the start counter reaches zero a latch is set high as the start of the delayed pulse 4 When the reset counter reaches zero the latch is reset as the end of the delayed pulse The rest of the circuit is also reset and counters are reloaded in preparation for the next input trigge
47. STR Workstation 3 4 3 2 1 Preparing to Vert itte eau ent e tus 3 4 3 2 2 Vaning OA ea chit ieee th re po aet meii e res 3 5 3 2 3 Purging the System to N2 ou eeeceeceeeeeeeeeeecee ce eae ea eeeeeeeeeeeeeeeeeaeeaaaaaaaeeseeeeeeess 3 5 Powering Up After Venting sisi 3 6 Chapter 4 Diagnostics Software 4 1 4 2 4 3 4 4 Overview e se Ede P o LA terra ie arin ro br eeu aes 4 2 Voyager Software Compatibility sus 4 2 Accessing the Diagnostics Software ssssssssssssssseese eee 4 3 Diagnostics Software Features ss 4 5 4 1 1 Gontro Pages eed tede pet eval dh ee vta ERR Re EROR 4 5 4 1 2 Status Bar teta etiem A EL de nn e 4 11 Chapter 5 Troubleshooting by Components 5 1 5 2 5 3 Troubleshooting Overview sisi 5 2 Sample Loading Chamber sissies ni ee e d terr Pl e pere ten 5 7 5 2 1 Vacuum System Interaction sess nennen 5 7 5 2 2 Internal Interlocks Operation ssssssseeeeeneeenn emen enne 5 9 5 2 3 Camera 5 11 5 2 4 Grabber Linear Actuators and Valves ssssse eee 5 11 5 2 5 Load Eject Cycles est et eO ea eei te ne da Ren e kkdE CER 5 13 5 2 6 VacuurmvFaults ens eec bed teer ce e Ute ted re eect e oo Eod teet ant 5 15 5 2 7 Mechanical Control Page Errors and Warnings cccccceceeeeeeeeeeeeeeeeeeeees 5 16 Main Source Chamber ire 5 18 5 3 1 SOULCE GIIPS e ee nda Bel ee Poe ee ek Rs 5 23 5 3 2 Source Pedestal riiin li
48. The power cord is factory installed Remote Interlock Connector Connects a cable to a remote location from which you can interrupt operation of the laser This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager DE STR Workstation Components Internal External Trigger Adjustment Provides control of internal manual and external trigger pulse repetition rate Internal Trigger mode allows you to manually vary the pulse repetition rate continuously from 0 to 20 pulses per second To increase the pulse repetition rate you turn the knob clockwise Use Internal Trigger mode for diagnostic purposes only External Trigger mode is the standard mode for Voyager workstation operation In this mode external electrical signals are sent through the BNC trigger input connector to set the pulse repetition rate up To set External Trigger mode turn the knob fully counterclockwise until you feel a switch action WARNING ELECTRICAL SHOCK AND LASER HAZARD In External Trigger mode the nitrogen laser energy storage capacitors are charged and the laser is ready to fire at any time When you perform service on the laser in External Trigger mode remove jewelry and other items that can reflect the beam into your eyes or the eyes of others Wear laser safety goggles and protect others from exposure to the beam Post a laser warning sign BNC Connector
49. Turbo fault Unplug the turbo pump and plug it in again If the fault persists check the Turbo pump for turbo failure Turbo pump for turbo controller failure Vacuum system for a severe vacuum leak 6 18 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Technical Support and Training This appendix contains the following Technical Service Resources A 2 Contacting Technical Support ai oe ve rcu rna A 5 Obtaining Technical Documents A 10 Obtaining Customer Training Information A 11 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Appendix A Technical Service Resources Overview Figure A 1 shows the available chain of resources to obtain Voyager service and troubleshooting assistance Immediate Resources Pri See Primary access Ao mode on page A 3 administered by PSE s Knowledge Database available 24 7 Additional Resources response lt 2 hours Also Field Service Technical Specialist Figure A 1 Resource Chain This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager Support Database Field service engineers can review the Voyager MALDI Product Support w
50. Turn grabber on pressure 11 Open Flap Door 2 11 Extend Linear 1 actuator 12 Extend Linear 2 actuator 12 Turn grabber off 13 Retract Linear 1 actuator 14 Close Flap Door 1 15 Check source chamber pressure 16 Move sample stage to default position Monitoring the Progress of Load Eject Cycles The status field Figure 5 5 displays which operation in the load or eject cycle is currently executing Status EJECT CYCLE gt Sample Plate Ejected Figure 5 5 Load or Eject Cycle Status Display This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Sample Loading Chamber Aborting Load Eject Cycles You can abort load eject operations while they are executing but doing so could place the system in an unsafe state You can return the system to a safe state by clicking the appropriate radio buttons to open or close the affected components flap doors foreline valves and linear actuators To abort the currently executing load eject operation click ABORT 5 2 6 Vacuum Faults When testing the system using the Diagnostics Software Mechanical control page you develop a vacuum fault Options for responding to vacuum faults depend on whether the system is in a load eject cycle If not in a load eject cycle and the ion gauges shut down due to a stability fault a message is displayed that allows you to choose to restart the gauges or not If the system
51. appliedbiosystems com techsupp training html provides course descriptions schedules and other training related information A 11 Appendix A AE This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Assembly Drawings This appendix contains the following Finding Components B 2 Relative Assembly Locations B 3 B 1 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Appendix B Finding Components Table B 1 provides figure numbers showing the listed component Table B 1 Component Diagrams Component See Figure Beam steering plates and voltage connections Figure B 5 Figure B 6 Einzel lens assembly and voltage connection Figure B 5 Figure B 6 Figure B 7 Feedthroughs Figure B 8 Flap doors Figure B 9 Flap valve block Figure B 9 lon exit aperture Figure B 5 Linear actuators Figure B 9 Sample loading chamber Figure B 9 Stage X Y table load position Figure B 8 Variable grid Figure B 6 X and Y feedthroughs home and load positions Figure B 8 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Relative Assembly Locations
52. at the external terminals This energy may remain stored in the capacitors for some time after all external connectors have been removed The DE switch box is comprised of A625 in x 6 25 in x 12 5 in Lexan enclosure An HV solid state switch Associated components necessary to provide the sample plate with voltage pulses to accelerate ions Three HV relays are included which in conjunction with reversible power supplies permit operation in either positive ion or negative ion mode 2 37 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Figure 2 24 shows two basic versions of the DE switch 400 d 300K 1M Behlke Source Switch Grid Power 4700 pF Source 200M 4700 pF Grid Power Supply Supply N7 N7 FAST DE SWITCH V725125 BLOCK DIAGRAM 400 401M 3M 1M Behlke Source Switch Grid Power 4700 pF Source 2000M 4700 pF Grid Power Supply Supply NM NZ DE SWITCH V725115 V725059 BLOCK DIAGRAM Figure 2 24 DE Switch Box Block Diagrams 2 38 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments
53. displayed in Mechanical control page 5 17 when to replace 5 24 GRAMS software 1 21 Grid DAC incorrect voltage 6 10 Grid voltage and source voltage 5 34 diagnostics software values 5 34 enabling using diagnostics software 5 34 setting using diagnostics software 5 33 5 34 testing high voltage 5 36 Grids in source 1 9 Grids in source measuring voltage 5 30 Guide wire voltage enabling using diagnostics software 5 34 invalid in some systems 5 34 setting using diagnostics software 5 33 5 34 testing using diagnostics software 5 36 Index 5 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted dui ES Index H High Current detector LMG 2 25 High voltage direct measurement 5 30 disabling 5 42 indirect measurement 5 30 Measuring at sample plate and grid 5 30 off 6 10 status bar display 4 11 High voltage interlock error possible causes 6 10 High voltage source pot setting of 3 turns ccw 5 32 troubleshooting 5 32 when to replace power supply 5 32 High voltages powering on off using diagnostics software 5 34 verifying 5 34 High current detector components of 1 17 description 1 17 High voltage cable testing internal 5 30 testing with 32 bit Diagnostics Software 5 31 testing with system under vacuum 5 30 high voltage cable using 16 bit Diagnostics Software to test 5 30 High voltage cables 5 18 High voltage power supplies nitrogen laser 1 12
54. electrons v HV Bias out Bias in l J4 Le J1 15 I I Jmpr for ON Ra 10 9 J1 14 D Digitizer Rb 1M Input e J3 5 Signal 43 5 42VDC Pwr In Common 12VDC l Mode DC DC Isolation Float LL Inductor 12VDC Pwr In gt 12VDC FI i Sam dc EE 12VDC Rin C Foar Out PEDE HV in HV Gnd Jmpr JPR1 al Ji NV dis cil Programmable Signal NZ HV Oto3kVP S Gnd Gnd Positive Gnd Low Voltage High Voltage E Input Side i Output Side Legend V700635 DVD LMG Negative Box Assy l V750060 PCA LMG Negative High Voltage V107049 PCB LMG Pos Neg Control amp Power Jx y PCB Pin Assign Jx y Assy Pin Assign V775029 Cbl Assy DVD LMG S91U01198 7 Z sajdeyo Electronics Common in Most Voyager DE STR Instruments A configurable PCB is used to assemble both the positive and the negative LMG units Both boxes also use the same internal cable The following chart relates the part numbers for these three options LMG Positive LMG Negative Detector Filter Bias V700643 DVD LMG Box Assembly Positive contains 2 MHV connectors V700635 DVD LMG Box Assembly Negative contains 3 MHV connectors N A V750066 PCA LMG Positive V750060 PCA LMG Negative V750032 PCA Detector Filter Bias Board V107049 PCB LMG V107049 PCB LMG V107025 PCB PCA Detector Filter Bias Board V775029 CBL Assembly DVD LMG internal to box assembly V775029 C
55. flight path allows greater sensitivity This flight path is appropriate for analyzing high mass greater than 5 to 15 kDa and other samples such as DNA This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager DE STR Workstation Components The linear detector Measures ion abundance over time e Is used in Linear mode only it is not used in Reflector or PSD mode s the most sensitive mode Fragments neutral molecules and molecular ions arrive at the detector at the same time and less sample fragmentation is observed s a hybrid high current detector HCD The HCD Figure 1 12 consists of a single microchannel plate a fast scintillator and a photomultiplier Earlier instruments serial numbers 4115 4114 4111 and earlier can be upgraded with HCD Bottom View Top View Figure 1 12 High Current Detector Reflector Mode In Reflector mode the ion beam travels approximately 2 meters down the flight tube to the reflector mirror where the beam is reflected an additional meter to the reflector detector Reflector mode offers higher resolution and greater mass accuracy because of the longer flight path and action of the reflector Reflector mode is commonly used for analyzing lower mass ions and in PSD analysis The reflector is a single stage gridded mirror that focuses energy and reverses the direction of the ions lon reflection
56. for continuity through grabber coils B X coordinate needs adjusting To adjust the X load coordinate while the system is under vacuum 1 Extend the magnetic grabber attached to Linear 1 actuator see the Voyager diagnostics software Mechanical Control page 2 Observe the deflection of a sample plate when the grabber turned off The stage deflects 1 to 2 mm when the grabber pushes on it There is some play between the sample plate and source when the plate is mounted in the source When the X load coordinate is set correctly the plate should deflect slightly more than the source continued This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Troubleshooting Tables Table 6 2 Source and Sample Loading Chamber Troubleshooting Continued Item Symptom Possible Cause Action During sample plate ejection the sample plate either occasionally or consistently cannot be pulled off the stage by the grabber continued C Source pedestal is not rotationally aligned with the grabber Place a known good plate in the source Verify the grabber poles are of equal length If necessary replace the grabber poles When extending the grabber check that both poles of the grabber touch the sample plate simultaneously If not adjust alignment For information see Aligning the Source Pedes
57. function operates with the High Voltage Enable on the Voyager software menu and is disabled by the Voyager hardware interlock See Section 5 5 Flight Tube and Mirror Chamber for the steps to set the output to zero An earlier version of the Flight Tube Power board has the same functionality and cable connections as the V750061 PCA The earlier board has two relays and two programmable 100 V DC DC power supplies One relay provides High Voltage Enable and the other relay selects the output from either the Positive 100 V converter or the Negative 100 V converter This PCA also has a potentiometer to adjust scale and can be replaced by the newer V750061 PCA Specifications Power Power specifications are 424 V dc at approximately 20 mA to power the two relays e 412 V dc at approximately 250 mA to power the two DC DC converters and associated operational amplifiers The guide wire is essentially a no load device Input Input impedance load presented to the DAC is approximately 10 K resistive Output The guide wire receives 0 0 to 100 V dc in positive ion mode and 0 0 to 100 V dc in negative ion mode The output OpAmp is protected by an 100 ohm series resistor and by an internal thermal shutdown circuit Ripple consists of approximately 5 mV peak to peak switching noise that can be measured with a coax cable directly connected to an oscilloscope 2 61 This Document Contains CONFIDENTIAL Material of Applied Biosystems For In
58. greater attenuation of beam Lower intensity strikes the sample Less density less attenuation of beam Higher intensity strikes the sample of the original beam intensity that passes through to the sample Figure 5 26 Internal Laser Attenuator When the laser pulse passes through an area of greater optical density the intensity of the laser beam is proportionally blocked and lower intensity reaches the sample When the laser pulse passes through an area of less optical density a smaller proportion of the laser beam is blocked Therefore the laser beam reaching the sample is of higher intensity more energy when the attenuator is set at a low density than when set to a greater density Adjusting the Attenuator Position To set the attenuation using the Diagnostics Software Laser Control page 1 Select or enter a value in the Attenuator Desired 96 Position spin box Values range from 0 to 100 A value of 0 Home position allows the minimum intensity laser beam to strike the sample a value of 10096 allows the maximum intensity to strike the sample f 2 Click Apply to rotate the attenuator to the new position or click Home to rotate the attenuator to its Home position 0 0 When the attenuator reaches its new position the value in Current 96 changes to match the value in Desired 96 When the attenuator reaches Home position the value in Current 96 changes to 0 0 and a check appe
59. is in a load eject cycle during most cycle steps no message is displayed Faults are displayed in the status bar However in some cycle steps the cycle cannot progress until the vacuum pressures are below a safe threshold pressure Under these conditions an error condition may occur where the ion gauges shut down and a message is displayed that allows you to choose to restart the gauges or not If an error condition continues and the safe threshold is not attained before a Registry specified timeout period expires the load or eject cycle will stop A message is displayed indicating you can recover from the error by backtracking the cycle steps You backtrack until the instrument is back to a safe initial state Overriding Vacuum Faults Checking the IGNORE VACUUM FAULTS check box allows the system to ignore all vacuum gauge faults and continue the load eject cycle even if gauge errors or high pressures present The system continues on to the next step once the safe threshold pressure is attained or the Registry specified timeout period expires You should ignore vacuum faults only when the system is vented operating at atmosphere When vented ion gauge and BA2 values are irrelevant After you ve started to bring the system back up under vacuum you can restart the gauges when TC2 Smp Pres in the system status bar reaches 8 x 107 torr Under normal operation when vacuum gauges TC2 BA1 or BA2 reports a fault during a load or an
60. is observed the internal high voltage connection cable is defective or dislodged Vent the system then replace or reconnect the cable 5 3 6 Operation Mode The Voyager DE STR workstation offers two flight path modes of operation Linear and Reflector When set to Linear and Reflector mode Linear The mirror voltage is inoperative and the Timed lon Selector delay time ignored Reflector All voltages and delay times apply To set the instrument mode using the Diagnostics Software Voltage and Delays control page 1 click the Linear or Reflector radio button next to Mode of Operation and apply 2 Click APPEVALL Ramp Voltages Set Delays If you leave the Voltage and Delays control page without applying the changes you will lose the changes The values revert to the last applied settings 5 3 7 Delayed Extraction lon Source To troubleshoot the ion source in Delayed Extraction mode do the following 1 When the laser is not firing Verify source voltage is less than the grid voltage Verify all switch box relay LEDs are off when the system is in positive ion mode See the schematic for appropriate LED states for other modes 2 Fire the laser 3 Observe the source voltage and the DE Timer switch box for pulses If pulses are present or the source voltage is not pulsing replace the switch box 5 31 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Co
61. leave permanent blind spots Never look directly into the laser beam Remove jewelry and other items that can reflect the beam into your eyes Wear laser safety goggles during laser alignment Protect others from exposure to the beam Post a laser warning sign while performing the alignment This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 6 Troubleshooting by Symptoms 6 1 4 Power Supplies and Circuit Boards Table 6 4 Power Supply and Circuit Board Troubleshooting Item Symptom Possible Cause Action 1 High voltage interlock error Cover is open front side Close and secure all Voyager and rear panels workstation covers Insert interlock service tag 2 High voltage interlock error A Fuse is blown Check the 5 V fuse Replace occurs with covers and service interlock tag are in B Cable connection is faulty Verify the 5 V cable place connection to the 48 bit I O board is properly connected Verify the cable connections between the control board and 48 bit I O card are secure 3 High voltage is off DAC voltage is not present Replace DAC 4 After replacing the 30 kV I pot needs adjusting Turn I pot counter clockwise power supply voltage less three turns than 30 kV is observed 5 5 V reference is less than or Reference pot needs Adjust the DAC reference pot greater than 5
62. location 2 37 overview 2 37 power needed 2 42 safety warning 2 37 triggered by DE pulse generator 2 50 types of and partnumbers 5 36 DE switch box control page before beginning the Check Control Wiring Test 5 37 checking high voltages with 5 36 function 4 9 running the Check Control Wiring Test 5 37 switch box types 5 36 test not available 5 36 Index DEGAS multigauge controller key 5 46 Degassing ion gauges 5 54 see DEGAS multigauge controller key 5 54 Delayed Extraction see also DE switch box see also DE switch box control page delay time clock cycle 5 35 disabling D 11 enabling using diagnostics software 5 33 setting start delay time using diagnostics software 5 33 setting start end delay times D 10 timing signal pulse delay 1 14 Delayed Extraction ion source preliminary troubleshooting 5 32 Delayed extraction ion source troubleshooting 5 32 verifying source voltage 5 32 Detector Linear detector 1 17 reflector 1 18 Detector filter bias board LMG 2 25 Diagnostics software accessing 4 3 and the Instrument Control Panel 1 21 4 2 and the Instrument Hardware Controller 1 21 4 2 before accessing 4 3 before setting output voltages and Low Mass Gate D 3 Camera control page 4 6 5 11 5 43 compatible Voyager software versions 4 2 control page summary 4 6 data bus 16 bit values D 5 DE switch box control page 4 9 5 36 Direct Bus Access control page 4 10 D 2 forNT 1 21 4 2 interface 3 1 4 1 Laser control
63. norme CSA 1010 Sp cifications de s curit du mat riel lectrique utilis pour les mesures les contr les et dans les laboratoires Partie 1 Sp cifications g n rales et il est conforme cette norme C est un produit homologu par les ETL Testing Laboratories EMC This Class A digital apparatus meets all requirements of the Canadian Interference Causing Equipment Regulations Cet appareil num rique de la classe A respecte toutes les exigences du R glement sur le materiel brouilleur du Canada xiii This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Safety and Compliance Information European Safety and EMC Standards C Safety This instrument meets European requirements for safety EMC Directive 73 23 EEC This instrument has been tested to and complies with standard EN61010 1 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use EMC This instrument meets European requirements for emission and immunity EMC Directive 98 336 EEC This product has been evaluated to the EN55011 1992 Group 1 Class B Radiated Emissions and EN50082 1 1992 Generic Immunity Laser Safety Laser Classification The Voyager DE Biospectrometry Workstation uses a standard nitrogen laser and an optional Nd YAG laser Under normal operating conditions the instrument laser is categoriz
64. on the ac distribution circuit board Replace if necessary If the turbo controller is working properly but the turbo cannot be restarted to normal speed replace the turbo Check that the corresponding turbo controller is working properly See the Varian Turbocontroller Instruction Manual C Failure of Foreline Valve 1 Check the functioning of or 2 Foreline Valves 1 and 2 Replace if faulty 4 Fore pump is not running A Fuse is blown Replace the fuse on the Voyager AC distribution board B Oil level too low or oil is Refill oil to appropriate level too dirty or replace oil completely Use designated oil for each type of pump C Pump is inoperable Replace the pump 5 Multigauge controller A The ion gauge filament is Check the continuity of the displays E05 error on BA1 or open filament If the filament is BA2 gauges open replace the gauge B The connection from the Reseat cable connections ion gauge to the multi gauge controller is loose or malfunctioning continued 6 14 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Troubleshooting Tables Table 6 5 Vacuum System Troubleshooting Continued Item Symptom Possible Cause Action lon Gauge Controller not responding error occurs during vacuum initialization A BA1 and or BA2 are not on Turn on BA1 and BA2 before starting vacuum initialization
65. overview 2 31 theory 2 31 Turbo pump fault 6 18 function 5 44 LED states 6 18 MALDI control board LEDs 3 6 status when powering up 3 6 typical pressure 5 44 workstation top panel LEDs 3 6 Types of signals 2 18 2 64 U Up key multigauge controller key 5 47 V VAC multigauge controller key 5 46 5 52 Vacuum faults conditions for safely overriding 5 15 conditions that trigger 5 15 ignoring 5 16 over pressure 5 15 overriding during load eject cycles 5 15 overriding in diagnostics software 5 15 persistent over pressure 5 15 potential sources of 5 16 Vacuum gauge panel see also Multigauge controller Vacuum pumps conditions damaging to 5 16 Index 13 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Index Vacuum system see also Multigauge controller chambers 5 44 description 5 44 gauge 5 44 initialization error 6 15 overriding vacuum faults in diagnostics software 5 15 powering up after venting 3 6 pressure ranges 5 46 pumping baffle to maintain differential pressure 5 44 pumps 5 44 purging with nitrogen 3 5 typical pressures 5 44 valves to isolate chambers 5 44 venting 3 4 venting to air 3 5 Voyager DE STR 1 8 Valves see also Flap valves see Flap valves Vent valve diagnosing using Mechanical control page 5 11 Variable voltage grid and Delayed Extraction 1 9 component of source 5 18 description 1 9 typical voltage applied
66. page 5 38 list of control pages 4 6 Mechanical control page 5 11 no pressure requirement 1 21 overview 4 2 overwriting load position in the NT Registry 5 20 Sample Stage control 5 18 setting data bus values in binary decimal or hexadecimal D 3 continued Index 3 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted lt xmMmo2 Index Diagnostics software continued setting laser attenuation with 5 41 setting Linear or Reflector mode 5 31 setting output voltages and Low Mass Gate 4 10 D 2 status bar indicators described 4 11 testing high voltages 5 36 uses of 4 2 Voltages Delays control page 5 33 5 35 5 43 writing to data bus with D 2 X Y Table control page 5 18 Digitizer Acqiris 1 19 description function 1 LeCroy 1 19 minimum 2 GH supported 1 Tektronix 1 19 timing signal 1 14 triggered by DE pulse generator 2 50 Direct Bus Access control page see also Diagnostics software comparing output to set values D 4 data bus 16 bit values D 5 disabling Delayed Extraction D 11 format of values D 3 function 4 10 overview D 2 procedure for writing to the data bus D 3 setting Delayed Extraction start end times D 10 setting Low Mass Gate delay time D 9 setting Timed lon Selector start end times D 12 19 Doors see flap doors Down key multigauge controller key 5 47 Drift Tube see Flight tube 2 6
67. pedestal Magnetic v grabber Linear 1 actuator PB100866 Figure 5 4 Grabber and Extended Linear 1 Actuator Rotated View 5 2 5 Load Eject Cycles After you replace or repair parts in the main source chamber and while the main source chamber is dismantled you may need to verify that all mechanical parts involved in loading and ejecting sample plates are aligned and operating properly Using the Diagnostics Software Mechanical Control page you can perform single load and single eject cycles to fine tune alignment To test the alignment under simulated working conditions you can set up multiple dual load eject cycles that run automatically and consecutively For both single cycles and multiple dual cycles you can Monitor the progress of operations as they execute Abort operations at any point during execution Force the diagnostics software to ignore vacuum faults when the system is operating at atmosphere Runload eject cycles without moving the sample stage Keeping the Sample Stage Stationary During Load Eject Cycles You can override the normal sequence of load eject cycles and keep the sample stage stationary when you need to test the pneumatics of the linear actuators and flap doors or to test the grabber To do so 1 If you haven t already done so open the X Y Table control page and move the sample stage to Load position 2 Return to the Mechanical control page and check Do Not Move X
68. pressure range 5 45 5 46 reading normal but BA gauge shuts down 6 14 Technical documents obtaining A 10 Technical Support contacting through the Technical Support web site A 9 Technical support contacting Eastern Asia China Oceania A 7 e mail A 5 Japan A 8 Latin America A 8 telephone or fax in North America A 5 telephone or fax outside North America A 7 Tektronix digitizer 1 19 Testing high voltage cable function 5 30 Thermocouple gauge see also TC2 calibrating 5 52 expected accuracy 5 52 factors affecting accuracy 5 52 function 5 45 5 51 heat transfer and pressure 5 51 junction 5 51 location 5 51 output display 5 51 range 5 45 TC2 5 45 wire temperature 5 51 Timed lon Selector adjusting voltage 5 42 disabling high voltage 5 42 enabling using diagnostics software 5 33 function 1 15 location 2 26 setting start end delay times D 12 setting start end delay times using diagnostics software 5 33 theory 2 26 timing signal 1 14 triggered by DE pulse generator 2 50 uses 1 15 voltage 1 15 5 42 Index Timing delays setting using diagnostics software 5 33 5 35 5 43 Timing signals nitrogen laser 1 14 TIS see Timed lon Selector Triangle multigauge controller key 5 47 Trigger buffer 2 17 2 64 Trigger input nitrogen laser 1 13 Trigger transformer board nitrogen laser 1 12 Troubleshooting source 5 23 Source flowchart 5 21 with system under vacuum 5 30 TTL Output Opto Trigger board connectors 2 31
69. register and presets the corresponding counter with the value on the data bus Drivers The line drivers take the delayed pulse from the programmable logic circuit and provide enough current to drive the cabling to devices Types of Signals The input signals to the pulse generator are A trigger event Data and address lines from the Voyager bus Power The output signals to the pulse generator are Adelayed pulse Configuration and control lines for relays and devices 2 64 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Connectors Headers Jumpers Test Points and DIP Switches Table 2 20 Functions of Pulse Generator Connectors Electronics Only in Earlier Instruments Headers Jumpers Test Points and DIP Switches 15 V 15 V 415 V 15 V 415 V 15 V Item Name Generic DE Function TIS Function Type Function Connectors JO Trigger in Laser opto Laser opto 2 position 0 1 inch header J1 Voyager bus Voyager bus Voyager bus 34 position ribbon J2 Auxiliary power Auxiliary power Auxiliary power 10 position out out out 0 1 inch header J3 24 V in 24 V in 24 V in 3 position 0 1 inch header J4 Power in 5 V Powerin 5 V Power in 5 V 9 position 15 V 15 V 15 V 15 V 15 V 0 1 inch header 15 V J5 TIS control Not used TIS co
70. steering internal connections Einzel lens Variable grid Figure 1 10 lon Exit Flange Showing the Einzel Lens Assembly Timed lon Selector TIS for PSD and CID Applications The flight tube contains a Timed lon Selector TIS The TIS is a Bradbury Nielson gate a device that allows ions only of a selected mass range and associated fragments to pass through to the detector The TIS deflects other ions When the TIS is turned on voltage 950 V is applied to the selector to deflect unwanted ions At the time that corresponds to the ions of interest voltage is turned off and the ions of interest pass to the detector Figure 1 11 on page 1 16 After the ions pass through the selector voltage is turned on again to deflect ions of non interest The TIS is used during post source decay PSD applications to selectively allow the precursor ion and associated fragments to reach the mirror chamber The TIS deflects other ions This feature allows one molecule species to be analyzed without interference from others present in the original sample This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter1 System Overview Approximately 950 V 0 Volts low m z m z of interest high m z ooo Voltage off lons of interest pass to the detector undeflected Approximately 950 V PB100835 Figure 1 11 D
71. steering plates Two pairs of parallel plates that maintain the correct path horizontal and vertical for the beam to strike the detector You tune the beam voltage to optimize ion focusing This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager DE STR Workstation Components 1 3 3 Laser System Laser System Overview The standard laser is a 337 1 nm beam nitrogen laser It produces 3 ns wide pulses at up to 20 pulses per second For Voyager workstation with serial numbers 4154 and later an optional 355 nm wavelength Nd YAG laser unit can be purchased When all the Voyager workstation covers top front side back and rear covers are installed no detectable radiation is present and the nitrogen laser is classified as a Class 1 laser Similarly if all Voyager workstation covers and the YAG laser unit covers are installed the YAG laser unit is classified as a Class 1 laser The Voyager workstation covers have interlock switches that disable the laser when the covers are removed When maintenance requires a field service engineer to defeat the interlock protection system the radiation may be present in excess of Class 1 limits Under certain conditions during servicing when interlocks have been circumvented the lasers can cause permanent eye damage and therefore are classified in the following categories Nitrogen laser Class llIb Nd
72. switch selectable firmware for compatibility with the old and new DE switches In these systems the laser pulse rate is further limited by the digitizer speed and the maximum pulse rate of the laser itself 2 40 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments Figure 2 25 illustrates operation on the V725125 operating at a pulse rate of 100 Hz VOLTAGE source V A grid DISTANCE source grid ground VOLTAGE source B grid TTL Pulse f gt 5 mS per division TIME Figure B VOLTAGE AN source C V TTL Pulse l l L 1 uS per division gt TIME Figure C Figure 2 25 DE Switch Waveforms Figure 2 25 A illustrates voltage vs distance Note that the grid potential remains fixed while the source or sample potential is pulsed above the grid potential to launch the ions Figure 2 25 B illustrates source voltage vs time Each time the Behlke switch receives a TTL level pulse the source voltage pulses to the higher level then exponentially decays to the grid rest voltage level Figure 2 25 C is an expanded voltage vs time diagram showing the leading edge of a single source pulse Approximately 120 ns after the leading edge of the TTL level control pulse the source voltage pulses from the rest grid leve
73. that must be connected to earth ground before any other electrical connections are made to the instrument 6 60o A terminal marked with this symbol either receives or delivers alternating current or voltage Viii This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Safety and Compliance Information A terminal marked with this symbol can receive or supply an alternating and a direct current or voltage This symbol appears next to the values of the fuses required by the system WARNING This symbol indicates the presence of high voltage and warns the user to proceed with caution WARNING This symbol alerts you to consult the manual for further information and to proceed with caution gt e a Non electrical Symbols The following is an illustrated glossary of non electrical safety alert symbols that may be displayed on your instrument WARNING This symbol illustrates a heater hazard Proceed with caution when working around these areas to avoid being burned by hot components This symbol indicates that a laser is present inside the instrument pe Symboles des Alertes de S curit Les symboles suivants peuvent tre affich s sur le systeme Dans ce document ces symboles peuvent aussi apparaitre c t des avertissements auxquels ils s associent Symboles Electriques Le tablea
74. the MALDI Control Board Functions Excluded from MALDI Control Board Voyager STR Voyager DE or DE Pro Stepper control Stepper control DVDT Low Mass Gate timer functions DVDT low mass gate timer functions Reflector DAC Beam guide or beam steering DAC To provide use of an external laser the MALDI Control Board is connected directly to the 48 bit IO PCA in the system computer and the stepper motor signals for the laser attenuator are switched through the Control Board Theory All the MALDI Control Board logic functions are in Altera complex programmable logic devices CPLDs All signals to and from the CPLDs are isolated by buffers or drivers The buffer section receives 40 bits of control from the computer 48 bit I O card and supplies 8 bits back All 48 bits to and from the 48 bit I O card are immediately buffered U1 U2 U3 U13 U14 U17 The 40 bits designated as inputs to the control board are further divided into the Voyager Bus and Discrete IO Voyager Bus The unidirectional Voyager Bus consists of 2 48 A 16 bit data bus Either a 3 or 5 bit address bus Two control bits Load and Latch This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments The bus is capable only of receiving data from the computer it cannot be read from the computer The Voyager B
75. the plasma cartridge because it must be aligned by the manufacturer The beam steering plates work in conjunction with the laser position After adjusting the laser position beam steering plates often require re optimization 5 4 1 Laser Firing Repetition Rate and Reinitialization Use the Diagnostics Software Laser control page Figure 5 25 to fire the internal or external if present laser set its repetition rate re initialize it and adjust its attenuator intensity You cannot use the joystick to control either the internal or the external laser Instead you must use the Fire Laser button on the control page WARNING ELECTRICAL SHOCK AND LASER HAZARD In External Trigger mode the nitrogen laser energy storage capacitors are charged and the laser is ready to fire at any time When you perform service on the laser in External Trigger mode remove jewelry and other items that can reflect the beam into your eyes or the eyes of others Wear laser safety goggles and protect others from exposure to the beam Post a laser warning sign WARNING ELECTRICAL SHOCK AND LASER HAZARD When instrument covers are removed high voltage contacts are exposed and the laser emits ultraviolet radiation Wear laser safety goggles and post a laser warning sign at the entrance to the laboratory when you remove covers for service WARNING LASER HAZARD Exposure to direct or reflected laser light can burn the reti
76. to 1 9 Vent valve conditions to meet before opening closing 5 10 diagnosing using Mechanical control page 5 11 error message in Mechanical control page 5 17 manually opening closing 5 12 Mechanical control page error and warning messages 5 17 warning message in Mechanical control page 5 17 lt xmMmo2 Venting see Vacuum system Video camera monitor initialization 1 20 magnification 1 20 Video monitor description 1 2 Voltage 5 voltage low or high 6 10 see also high voltage continued Voltage continued adjusting Timed lon Selector 5 42 calculating expected Grid DAC voltage 5 32 Grid DAC voltage incorrect 6 10 low 30 kV power supply measurement 6 10 measuring directly 5 30 measuring indirectly 5 30 see also high voltage setting component using diagnostics software 5 33 5 43 setting using diagnostics software 5 35 source DAC voltage incorrect 6 10 testing cable with system under vacuum 5 30 Voltage Divider box einzel lens location 2 44 theory 2 44 Voltage source DAC calculating expected output voltage 5 32 Voltages see also Grid Guide wire Mirror Source voltage controlling using Voltages Delays control page 5 34 diagnosing using Voltages Delays control page 5 34 grabber 5 13 setting DAC using diagnostics software 5 34 setting polarity using diagnostics software 5 34 typical main source chamber 1 8 Voltages Delays control page 5 33 5 35 5 43 see also Diagnostics software applying delay ti
77. 0 E E09 multigauge controller error 6 14 Einzel lens see also Voltage Divider Box 2 44 description 1 10 Electrical shock warning 5 38 Electromagnetic compatibility compliance xiii Electronics see Voyager electronics E mail contacting technical support A 5 EMC standards xiii EMIS multigauge controller key primary function 5 45 5 46 secondary function 5 45 5 46 Errors acquisition error 6 9 high voltage interlock 6 10 lon gauge not responding 6 15 vacuum initialization 6 15 Extend orifice valve adjustment range for Linear 1 actuator 5 25 location on Linear 1 actuator 5 24 F F multigauge controller key 5 47 Fan nitrogen laser 1 13 Field Service in North America contacting A 5 Field service resources accessing A 2 Firing the laser 5 39 Flap Door 1 see also Flap doors conditions to meet before opening closing 5 9 description 1 7 Flap Door 2 see also Flap doors conditions to meet before opening closing 5 9 description 1 7 Flap doors conditions to meet before opening closing 5 9 diagnosing using Mechanical control page 5 11 error message in Mechanical control page 5 16 indicators 5 11 keeping stationary when testing 5 13 loss of operating pressure 5 20 manually opening closing 5 12 operating pressure 5 20 warning message displayed in Mechanical control page 5 16 Warning messages Mechanical control page 5 16 Index 4 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Onl
78. 0 to 20 kV range Set as a percentage of the source voltage it must be within 10 kV of the source voltage typically about 6596 to 9596 of source voltage The grid voltage defaults to 15000 0 when the Voltage and Delays control page opens You must set and apply the source and grid voltages at the same time Mirror 0 to 30 kV range Reflector mode only ignored in linear mode The mirror voltage defaults to 22000 0 when the Voltage and Delays control page opens When changing from reflector to linear mode diagnostics software waits 5 seconds for the mirror high voltage supply to fully discharge Guide Wire Ignored in Voyager DE STR workstation with serial numbers 4154 and later Resetting All Voltages and Delay Times Click Reset All to disable all high voltages reset all DAC voltage values to 0 0 V and disable all delay timing options 5 84 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Main Source Chamber 5 3 9 Delayed Extraction Low Mass Gate and Timed lon Selector Delay Times Use the Diagnostics Software Voltages Delays control page Figure 5 19 timing delays To enable DE the LMG or the TIS click the radio button of the function you want to enable To set delay times defined in Table 5 5 increase or decrease the counter start and end delay times to set the delay Table 5 5 DE LMG and TIS Delay Times Par
79. 000 to 65 000 ns Click Write The remaining steps are optional Because you cannot enable the Low Mass Gate timers it makes no difference whether the delay time you write is the start or end time From the Address pulldown menu select 4 Control Register Enter a 16 bit value in Data Value text field Clear bit 15 LMG enable to specify that the data value previously written is the start time for the delay The remaining bits do not affect the Low Mass Gate circuitry Remember you must write the entire sixteen bits of the control register so enter a value that sets all components the control register configures including TIS and DE parameters appropriately C i ck White i Repeat steps 1 through 6 but specify the end delay time in step 5 by setting bit 15 to 1 For Internal Use Only No Unauthorized Copying Permitted Appendix D Isolating Components Using Direct Bus Access Setting and Disabling Delayed Extraction Setting Delayed Extraction To set and invoke delayed extraction you Set the start and end times for the delay Write to the control register to select and enable DE mode Write to the control register to enable the DE counter which starts the DE timer counters The procedure is as follows 1 From the Address pulldown menu select 6 DE delay 2 Enter a 16 bit value in the Data Value text field for the start delay time Values range from 0 to 32 767 decimal and represent 0 to
80. 0000000 s X See ue mo o HUS Regeo 0000000000000 EE J23 PT R40 NE J L2000000000000 o NS JU4 0000 eo D s oo ES JU3 JUS J15 J1 E oo s s s a o br ool 8 8 k e ol pi b I 9 s oo S X ooje 9 Ed oolgo x oof Ss mage w S2 Reset o ol a o o0 on S8 a g a Do S o Go jo eo a s O io o Dti abeaeb s c 00 e So Aq jo J b im D ole o 9 ol o3 8 s ol o ME lo o j x a9 m o off e R x 9 o Pog Ras sie sis ES 3 ofele m o o S o j JU2 M 9 8jo TP5 a D cl OL jo J3 Ko k 9 dx s i m EE TP4 s ol 1 3 s ao J4 FS N TP6 IN TP1 A a 9 e e s o o 9 528 S vas U5 M o ol E 5600 J5 FO x o o TP25 5 i m c e e R51 J22 J18 JO OOOO0 2 00000000000000000 Q LE EE ii Ol F Stepper motor Goooal s J2 PCBA Span 5553 0 EIE pe wee J15 J1 i ground o J29 3 Internal laser 8 1 attenuator g J30 E d External laser 2 5 8 attenuator o jo ol fo 2 Ol O Ol o so LEE Internal laser RAR J3 interlock dk sie From Opto trigger R46 TP5 board 3 Hz adjustment detected Old laser trigger pulse Direct monitor at J4 U39 Pin 3 q From YAG Q switch
81. 0065 Figure 2 4 shows the housing of these electronics In rear Low Mass Gate detector filter bias TIS assembly TTL output opto trigger board EU U U Seo AC Distribution q Low Mass Gate positive DC Distribution Low Mass Gate negative DAC boards Left cabinet Right cabinet 2 4 Figure 2 4 Housing of Electronics Common in Most Instruments This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Common in Most Voyager DE STR Instruments 2 2 1 AC Distribution Board V750053 Overview The AC Distribution board Figure 2 5 Selects the proper auto transformer tap Fuses both sides of the power line Provides a Fuse OK LED for each output Gates the compressor AC power with the autosampler Load position AC distribution PB100852 Side view of left cabinet Figure 2 5 AC Distribution Board Theory Terminal Block J16 This terminal block connects the auto transformer to the PCA and allows you to connect the auto transformer taps to select the
82. 1 4 1 13 3 2 5 38 Laser intensity nitrogen energy striking the sample 1 14 Laser Pulse Detection Circuit 2 31 Laser trigger malfunctioning 6 9 LeCroy digitizer 1 19 LEDs 2 5 2 47 48 bit I O 2 47 AC Distribution board 2 5 2 7 MALDI control board 6 18 Voyager workstation top panel 6 18 Limit switches see Microswitches 5 19 Line voltages AC Distribution board 2 5 Linear 1 actuator bleed screw 5 24 conditions to meet before extending or retracting 5 10 description 1 7 extend orifice valve 5 24 extend orifice valve adjustment range 5 25 see also Linear actuators 5 11 Linear 2 actuator conditions to meet before extending or retracting 5 11 description 1 7 Linear actuators conditions to meet before extending or retracting 5 10 diagnosing using Mechanical control page 5 11 error message displayed in Mechanical control page 5 17 extending or retracting 5 12 function 1 7 Home microswitch 5 29 indicators 5 11 continued Index 7 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Index Linear actuators continued keeping stationary when testing 5 13 Load microswitch 5 29 loss of operating pressure 5 20 Mechanical control page error and warning messages 5 17 microswitches 5 29 operating pressure 5 20 troubleshooting 5 29 warning message displayed in Mechanical control page 5 17 Linear detector description 1 17 function 1 16 5 31 h
83. 2 1 start register 2 17 switches 2 18 2 19 test points 2 18 2 19 theory 2 15 Low Mass Gate Delay timer board triggered by DE pulse generator 2 50 Low Mass Gate driver boxes configurations 2 23 connectors 2 25 detector filter bias board 2 25 input output 2 25 negative 2 20 positive 2 20 power 2 25 pulse diagrams 2 24 switches 2 23 types of 2 23 Low voltage power supplies nitrogen laser 1 12 Index 8 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted M Main source chamber diagram of 1 8 diagram of typical voltages 1 8 Over pressure vacuum fault 5 15 overview 1 8 performing load eject cycles 5 13 tools to troubleshooting 5 23 typical voltages applied to 1 8 MALDI Control board bus 2 48 connectors 2 52 functions 2 47 input output 2 50 LEDs 2 55 location 2 47 overview 2 47 pots 2 53 simplified drawing 2 58 switches 2 57 test points 2 53 MALDI knowledge database 5 6 A 3 MALDI product support web site 5 6 A 3 MALDI TOF definition 1 2 Mass spectrometer see also Voyager DE STR Biospectrometry Workstation components of Voyager DE STR overview 1 6 diagram of Voyager DE STR components 1 6 5 18 parts of Voyager DE STR 1 2 1 6 Mass standards kit 1 3 Mechanical control page 4 6 5 11 5 13 see also Diagnostics software 4 6 error messages 5 16 function 4 6 warning messages 5 16 Microchannel plate in linear detector 1 17 Microswitche
84. 2 Pos lon Mode HV Enb si 0 i Mcd amp Polarity Change SO ONN Dee Polarity Legend Signal Lines gt Control Lines PB100841 2 60 Figure 2 32 Flight Drift Tube Power Supply Block Diagram This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Earlier Instruments Theory lons of polarity opposite to the wire potential are drawn to the center of the flight tube by their attraction to the wire Polarity applications are summarized in the following table Mode lons Attracted to Wire Wire Potential Positive ion Negative Negative ion Positive The Neg Pos relay controlled by J2 directs the 0 to 10 V signal from the guide wire DAC output to the power amplifier The power amplifier amplifies the signal by a factor of 10 providing 0 to 100 V Connector J2 also provides a signal to activate the HV Power Enable relay This relay has two outputs High Voltage disabled output Connects the guide wire to ground when high voltage is not enabled High Voltage enabled output Provides 12 V dc power to the two operational amplifiers when high voltage is enabled The gain 1 OpAmp receives 12 V directly from the relay and receives 12 V from a small DC DC converter The gain 10 OpAmp receives 100 V and 100 V from a DC DC converter powered by the same 12 V line The High Voltage Enable
85. 327 670 ns at the DAC 4 Enter a 16 bit value in the Data Value text field for the end delay time The most significant bit MSB is a select bit defined in the table below Data Value MSB Represents 0 Start 1 End Values range from 32 768 to 65 535 decimal and represent 0 to 327 680 ns at the DAC 5b Click Wiite 6 From the Address pulldown menu select 4 Control Register 7 Enter a 16 bit value in the Data Value text field Setbit 3 DE counter enable to enable the counter Setbit 7 DE mode enable to enable DE mode Clear bits 8 through 10 DE mode select for positive ion mode or set them to 110 for negative ion mode Remember you must write the entire sixteen bits of the control register so enter a value that sets all components the control register configures including TIS and LMG parameters appropriately This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Setting and Disabling Delayed Extraction Disabling Delayed Extraction To disable delayed extraction you must disable the DE counter select non DE mode and disable DE mode 1 2 From the Address pulldown menu select 4 Control Register Enter a 16 bit value in the Data Value text field Clear bit 3 DE counter enable to disable the counter Clear bit 7 DE mode enable to disable DE mode Setbits 8 thr
86. 4 2 Laser Attenuation Section 6 1 1 Spectral Problems Beam guide wire Set output voltage NA DAC Direct Bus Access Appendix D Beam steering Set observe values Voltages Section 5 3 8 Source Grid and Mirror plates and Delays source Voltages voltage connections Camera Turn camera off on Camera Section 5 6 Computer and Video Systems 5 2 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Troubleshooting Overview Table 5 1 Matching Components with Control Page and Troubleshooting Information Component or Parameter Task Control Page Troubleshooting Section Control Register high frequency counter and ion source pulsar Set values Direct Bus Access Appendix D NA Delayed extraction Enable Voltages Delays Set start delay Voltages Delays Direct Bus Access Section 5 3 7 Delayed Extraction lon Source Section 5 3 10 DE Switch Box Control Section 6 1 1 Spectral Problems DE switch box Test voltages DE Switch Box Section 5 3 7 Delayed Extraction lon Source Section 6 1 1 Spectral Problems Einzel lens Set observe values Voltages Section 5 3 8 Source Grid and Mirror assembly and Delays source Voltages voltage Section 6 1 1 Spectral Problems connection Feedthroughs Observe coordinates status Section 5 3 3 Window Status bar X Y X Y Status Stepp
87. 46 3 Hz adjust old laser trigger direct Potentiometer monitor at pin 3 U39 Test Points TP1 External laser in NA TP2 DE box trigger NA TP3 TIS trigger NA TP4 Internal laser in NA TP5 Internal laser in Comparator Signal NA TP6 External laser in Comparator Signal NA TP7 Source DAC command NA TP8 Source DAC monitor Test point TP9 5 V reference Test point 2 53 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Table 2 17 MALDI Control Board Connectors Resistors and Test Points Continued Item Name Function Type Test Points TP10 Source DAC Return Test point continued TP11 Spare DAC monitor Test point TP12 Grid DAC command Test point TP13 Grid DAC monitor Test point TP14 Grid DAC Return Test point TP15 Spare DAC command Test point TP16 Spare DAC Return Test point TP17 15 V Test point TP18 15 V Test point TP19 24 V Test point TP20 5 V Test point TP21 Ground DC return Test point TP22 12 V Test point TP23 Spare 2 DAC command Test point TP24 Spare 2 DAC return Test point TP25 External laser trigger Test point TP26 No laser trigger Test point TP27 3 3 V Test point TP28 Mirror DAC monitor DE DE Pro only Test point 2 54 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Inter
88. 5 male P1 03 5 V dc Not used DB15 male P1 06 TTL gate pulse in 50 ohm DB15 male P1 07 Pulse in return ground DB15 male P1 12 24 V dc return ground DB15 male P1 14 HV enable TTL Hi DB15 male P1 15 24 V dc power in DB15 male J1 0 to 1000 V 100 1 divider Test point J2 Ground return Test point J6 O to 1000 V 100 1 divider Test point J5 Ground return Test point J3 0 to 1000 V Coax output J4 0 to 1000 V Coax output See Section 5 5 Flight Tube and Mirror Chamber for how to adjust the TIS voltage 2 30 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Common in Most Voyager DE STR Instruments 2 2 7 TTL Output Opto Trigger Board V750065 Overview The TTL Output Opto Trigger board has two parts a laser pulse detection circuit and an At Limit feedback circuit Theory The primary function of the Opto Trigger PCA is to detect when the laser fires This feedback is required because a variable delay exists between when the laser is triggered electronically and when the laser actually fires The detected laser pulse is then synchronized with the 100 MHz clock All time based measurements are then based on this time The secondary function of the Opto Trigger PCA is to feed back the At Limit Home position of the stepper motor driven neutral density attenuator to the Autosampler Control PCA The
89. 5DDD 0101 1101 1101 1101 24029 12 3 994 6666 0110 0110 0110 0110 26214 13 4 329 6EEE 0110 1110 1110 1110 28398 14 4 662 7777 0111 0111 0111 0111 30583 15 4 995 7FFF 0111 1111 1111 1111 32767 16 5 328 8888 1000 1000 1000 1000 34952 17 5 661 9110 1001 0001 0001 0000 37136 18 5 994 9999 1001 1001 1001 1001 39321 19 6 327 A221 1010 0010 0010 0001 41505 20 6 66 AAAA 1010 1010 1010 1010 43690 21 6 993 B332 1011 0011 0011 0010 45874 22 7 326 BBBB 1011 1011 1011 1011 48059 23 7 659 C443 1100 0100 0100 0011 50243 24 7 992 CCCC 1100 1100 1100 1100 52428 25 8 325 D554 1101 0101 0101 0100 54612 26 8 658 DDDD 1101 1101 1101 1101 56797 27 8 991 E665 1110 0110 0110 0101 58981 28 9 324 EEEE 1110 1110 1110 1110 61166 29 9 657 F776 1111 0111 0111 0110 63350 30 10 FFFF 1111 1111 1111 1111 65535 D 6 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Setting the Low Mass Gate Delay Time Setting the Low Mass Gate Delay Time To set the low mass gate delay time you write a delay time You then have the optional to write to the Control register to specify whether the value is the start or end delay time To set delay times 1 2 This Document Contains CONFIDENTIAL Material of Applied Biosystems From the Address pulldown menu select 5 LMG delay Enter an 8 bit value in the Data Value text field for the start delay time Values range from 0 to 255 decimal and represent 8
90. 7 64 inch T handle allen wrench loosen the four 6 32 inch screws Figure 5 11 that mount the pedestal to the XY table CAUTION When servicing the pedestal avoid contacting the grid The grid is delicate and may be damaged Source pedestal Insulator board Figure 5 11 Sample Stage X Y Table 2 Onthe Linear 1 actuator use the extend orifice valve the bleed screw closest to the source housing to slow the extension of the grabber Figure 5 12 on page 4 25 The Linear actuators shown in Figure 5 12 on page 4 25 are the newer rectangular shaped actuators Linear actuators in older systems are cylindrical 3 Stop the magnetic grabber just 1 mm short of contacting the plate 5 24 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Main Source Chamber To source A sample stage Extend orifice PB100864 Figure 5 12 Linear Actuator 1 Extend and Retract Valves Rotate the pedestal so that the edge of the plate is the same distance from both poles of the grabber Retighten the mounting screws while verifying the source and the grabber assembly remain properly aligned Source pedestal FE PB100866 Grabber U Figure 5 13 Aligning the Source with the Grabber Reset the X and Y load coordinates as necessary See Resetting the Sample Stage Load Posit
91. 844 press 2 then press 4 1 650 638 5981 ABI PRISM 3100 Genetic Analyzer 1 800 831 6844 press 2 then press 62 1 650 638 5981 Peptide Synthesis 433 and 43x Systems 1 800 831 6844 press 3 then press 12 1 650 638 5981 Protein Sequencing Procise Protein Sequencing Systems 1 800 831 6844 press 3 then press 28 1 650 638 5981 PCR and Sequence Detection 1 800 762 4001 then press 1 for PCR2 2 for TaqMan applications and Sequence Detection Systems including ABI Prism 7700 7900 and 57008 6 for the 6700 Automated Sample Prep System or 1 800 831 6844 then press 52 1 240 453 4613 Voyager MALDI TOF Biospectrometry Workstations e Mariner ESI TOF Mass Spectrometry Workstations MassGenotyping Solution 17M MGS1 System 1 800 899 5858 press 1 then press 3 1 508 383 7855 Biochromatography BioCAD SPRINT VISION and INTEGRAL Workstations and POROS Perfusion Chromatography Products 1 800 899 5858 press 1 then press 42 1 508 383 7855 Expedite Nucleic Acid Synthesis Systems 1 800 899 5858 press 1 then press 52 1 508 383 7855 Peptide Synthesis Pioneer and 9050 Plus Peptide Synthesizers 1 800 899 5858 press 1 then press 5b 1 508 383 7855 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted
92. 9 251 24 243 France Paris 33 0 1 69 59 85 85 33 0 1 69 59 85 00 A 7 Appendix A A 6 Region Telephone Fax Germany Weiterstadt 49 0 6150 101 0 49 0 6150 101 101 Italy Milano 39 0 39 83891 39 0 39 838 9492 Norway Oslo 47 23 12 06 05 47 23 12 05 75 Portugal Lisboa 351 0 22 605 33 14 351 0 22 605 33 15 Spain Tres Cantos 34 0 91 806 1210 34 0 91 806 12 06 Sweden Stockholm 46 0 8 619 4400 46 0 8 619 4401 Switzerland Rotkreuz 41 0 41 799 7777 41 0 41 790 0676 The Netherlands Nieuwerkerk a d IJssel 31 0 180 392400 31 0 180 392409 or 31 0 180 392499 United Kingdom Warrington Cheshire 44 0 1925 825650 44 0 1925 282502 European Managed Territories EMT Africa English speaking Johannesburg South Africa 27 11 478 0411 27 11 478 0349 Africa French speaking Paris France 33169 59 85 11 33 1 69 59 85 00 India New Delhi 91 11 653 3743 91 11 653 3744 91 11 653 3138 Poland Lithuania Latvia and Estonia Warszawa 48 22 866 4010 48 22 866 4020 For all other EMT countries not listed Central and southeast Europe CIS Middle East and West Asia 44 1925 282481 44 1925 282509 Japan Japan Hacchobori ChuoKu Tokyo 81 3 5566 6230 81 3 5566 6507 Latin America Caribbean countries Mexico a
93. Altera firmware to line driver U6 and out SMA connector J6 TP26 If an external laser is present and selected the corresponding laser trigger line driver is U5 TP25 CPLD based digital divider trigger generator Available with 5 bit addressing and can be programmed to an optimal setting by the software To generate a trigger two programmable down counters are preloaded via the Voyager bus When the laser trigger is enabled by software 1 The first counter is enabled driven by a 63 kHz clock The first counter counts down from the preloaded value to zero 2 3 When the first counter reaches zero an output is generated triggering the second counter 4 The first counter reloads and starts again 5 The second counter generates the laser trigger leading edge and starts counting down from the preloaded value p When the second counter counts down to zero it generates the laser trigger trailing edge 7 The second counter then reloads 2 49 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics The first counter generates a laser trigger frequency calculated by the following equation F 63kHz N X Where N preloaded 16 bit number X overhead clock ticks 1 For example if Nis 63 k then F equals approximately 1 Hz As in the legacy trigger generator output from this circuit runs through the Altera
94. BL Assembly DVD LMG internal to box assembly N A Theory WARNING ELECTRICAL SHOCK HAZARD Potentials in the order of 3000 V dc are present on these boards Safe operating procedures and proper use of equipment are the responsibility of the authorized and qualified service person Precautions must be taken to protect against possible serious and or fatal bodily injury Low Mass Gate Switches The Voyager Low Mass Gate options convert a TTL input pulse into a floating high voltage pulse The Positive Pulse and Negative Pulse block diagrams illustrate how the TTL input logic is isolated from the floating high voltage output circuits by the optical signal coupler and the DC DC isolation converter A common mode inductor chokes transient ground currents resulting from rapid high voltage switching The output switch is a 1 KV MOSFET The HV voltage divider resistors are configured for positive or negative operation by jumpers on the PCB There are two identical inputs e Pin 2 Receives the TTL pulse The LMG enables the detector for the duration of the pulse Pin 3 Enables or disables the LMG function If high it enables the MOSFET switch continuously and the detector generates signal during the entire spectrum NOTE For the detector to function properly you must have input to either Pin 2 or Pin 3 Failure to provide this input prevents the detector from generating a signal 2 23 This Documen
95. Click on the Start Button to Begin the Test X LS Ji Figure 5 21 DE Switch Box Control Page NOTE Of the seven tests listed in the Test drop down menu you can run only the Check Control Wiring test at the field site The remaining six tests are performed only at the factory Checking the Control Wiring This test checks the operative states of the three high voltage kilovac relays by looking at resistance between J2 and J4 and the admittance between J3 and J2 Gnd Before you begin assemble your voltmeter and meter probes and access the DE switch box Next in the diagnostics software DE Switch Box control page select the type of DE switch box that the system contains V725059 Three connector high voltage switch box in Voyager DE STR workstation with serial numbers 4147 and earlier V725115 Four connector high voltage switch box in systems with serial numbers 4148 through 4160 V725125 Four connector fast DE switch box in systems with serial numbers 4161 and later 5 36 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Main Source Chamber Before running the Check Control Wiring Test 1 Select Check Wiring Test from the Test dropdown menu 2 Make sure you have selected the correct DE switch box type To run the Check Control Wiring Test 1 As prompted Figure 5 22 disconnect all high voltage connecti
96. Connectors Test Points and LEDs on the DC Distribution PCA Board Item Nara Function in Function in Tyne Single Power Supply Three Power Supplies YP Connectors J1 Power input 5 V 15 V Power input 5 V 15 V 12 pin Mini Fit 5 2 V J2 Power input 24 V Power input 24 V 8 pin Mini Fit J3 Not used Power input 12 V 6 pin Mini Fit J4 DE Pulse Generator DE Pulse Generator board 10 pin Mini Fit board 5 V 15 V 5 V 15 V 5 2 V J5 Control board Spare 12 pin Mini Fit 5 V 15 V 24 V 5 V 5 2 V 15 V 24 V 12 V J6 Spare Spare 12 pin Mini Fit 5 V 15 V 24 V 5 V 5 2 V 15 V 24 V 12 V J7 Timed lon Selector board Timed lon Selector board 10 pin Mini Fit 5 V 15 V 5 V 15 V 5 2 V J8 Test points board Test points board 12 pin Mini Fit 5 V 15 V 24 V 5 V 5 2 V 15 V 24 V 12 V J9 Spare Spare 12 pin Mini Fit 5 V 15 V 24 V 5 V 5 2 V 15 V 24 V 12 V continued 2 12 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Common in Most Voyager DE STR Instruments Table 2 3 Connectors Test Points and LEDs on the DC Distribution PCA Board Continued Item Name Function in Function in Type Single Power Supply Three Power Supplies Connecto
97. Copying Permitted Appendix C Pin 1 Connector Locations Use Figure 5 to find the pin 1 positions for commonly used connectors Pin 1 Pin2 PB100857 Figure C 5 Pin 1 Connector Locations C 4 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Interconnect CA Joy Limit Sw Limit Sw Ca Limit Sw Joystick MachIIT V77S890 VTTSWS V775049 V775049 y V600010 A EXTERNAL 10 A CNTRL BD RIBBON 2 PJ0 e we QuickPhase MOTOR STEPPER Soro sr 7 PJ 23 PCA Control Board 12V Power from l Distribution Je IM 9 computer supply BA d CA Vacuum Cer Con Vac Com MuttiGage Ctir PJIS STEPPER MOTOR CONTROL Jit p Crrseee k J TC 32 v209601 oc WF FENN E JPe16 CA 26 Interlocic ntertock W778898 778698 CA Mirror TurboMains M ac DC Power Genwac vac 4809849 UM VALVE CONTROL CABLE Line Voltage 90 240 vac 50 60 HZ Video Monitor MIRROR TURBO i V vzs 4319068 v209016 TURBO CONTROL C TURBO V775694 y PJ27 DIS Assy Roughin C Ji ac Distribution CA SourceTurbo Moins c Distribution ve cote V77 A ELX CA LASER A T INTERLOCK CR ae J4 ac Distribution CA Compressor AC p s RD j P3L VITSTS LASER TR ec Distribution J15 PT V FLAP VALVE C XL
98. E STR Biospectrometry Workstation Figure 1 1 is a floor standing MALDI TOF mass spectrometer that includes a reflector analyzer Computer Video External digitizer monitor monitor Mass Control stick spectrometer E components j Computer Data system 1 j inside cabinet il Electronics inside cabinets PB100427 Figure 1 1 Voyager DE STR Biospectrometry Workstation Workstation Components Major components of the Voyager DE STR Biospectrometry Workstation include a Mass spectrometer A time of flight mass spectrometer described in Section 1 3 Voyager DE STR Workstation Components See the Voyager User Guide for more information TheVoyager workstation uses a 337 nm wavelength nitrogen laser Computer Data system A computer that operates the Voyager workstation control software and the Voyager processing software You control the mass spectrometer using the computer Digitizer An analog to digital converter that allows the signals from the mass spectrometer to be transferred to the computer Video monitor A monitor that displays a real time video image of the sample spot on the sample plate in the mass spectrometer Control stick A peripheral device that allows you to control the position of the sample plate in the mass spe
99. HPOS1 Positive and negative test points Test point HNEG 1 for digital voltmeter VPOS1 Positive and negative test points Test point VNEG1 for digital voltmeter 2 36 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments 2 3 2 DE Switch Box V725115 V725125 The DE switch box Figure 2 23 provides a very fast and stable high voltage pulse to accelerate the sample ions after they are desorbed by a laser pulse oe N box v PB100853 Figure 2 23 DE Switch Box Location The DE switch box operates in conjunction with two programmable HV high voltage power supplies When the laser pulse fires one supply is providing a fixed grid rest value so that the ions do not see a voltage gradient until the DE switch box fires The other supply is providing a higher source so when the switch box fires the ion group accelerates past the grid and down the flight tube Theory WARNING ELECTRICAL SHOCK HAZARD Potentials up to 30 000 V dc are present in this assembly Safe operating procedures and proper use of equipment are the responsibility of the authorized and qualified service person Precautions must be taken to protect against possible serious and or fatal bodily injury In excess of 4 joules of stored energy may be present inside the enclosure and
100. HV 0 to 3000 V dc PCB internal MHV external J2 PCB HB Pulse Output 2 3 HV to full HV PCB internal MHV external J3 1 PCB J1 1 external Ground PCB internal J3 2 PCB J1 2 external TTL Enable Input DB15 Male external J3 3 PCB J1 3 external TTL Signal Input J3 4 PCB J1 4 external Ground J3 5 PCB J1 5 external 12 V dc Power Input J4 PCB HV Bias Output HV 0 to 3000 V dc PCB internal MHV external 2 25 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics 2 2 6 Timed lon Selector TIS Assembly V700471 Overview The Timed lon Selector TIS assembly provides a differential voltage pulse of 950 V for the selection of ions within a specified mass range When the positive and negative voltages are present on gate elements in the flight drift tube all charged ions are deflected from the normal flight path During the time that the TIS voltages are switched to ground potential all ions pass unimpeded down the flight tube TIS assembly 7 Vs Sy V 4 4 N S Rp LS 3 y DAD D PB100854 Figure 2 17 TIS Assembly Location Voyager DE STR Center Rear View Theory WARNING ELECTRICAL SHOCK HAZARD Potentials in the order of 1000 V dc are present on this assembly Safe operating procedures and
101. IDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments Firmware Configuration MALDI Consolidated Control Board Table 2 13 Firmware Configuration Switch Box Schematic MALDI Consolidated Control Board Assembly Switch S1 Position 34 V725125 V750095 On 3 Hz to 100 Hz V725115 V750075 Off 3 Hz V725059 V725059 Off 3Hz AThe four positions are numbered 0 through 3 Therefore the fourth dipswitch position is named Position 3 LEDs LED indicators on the bottom of the DE box high voltage relays indicate relay actuation Table 2 14 illustrates the LED pattern for each Voyager workstation operation mode Note that the green PCB on the bottom of the V725125 box assembly also has an orange LED to indicate that the 24 V to 5 V dc dc converter is operating correctly Voyager workstation mode indication is also is provided on the V750082 MALDI Control Board at location D3 by LEDs labeled RLY1 RLY2 and RLY3 Table 2 14 DE Switch Box LED Displays V725115 Switch Voyager Workstation 5 V dc Relay 1 Relay 2 Relay 3 Assembly Mode Orange Yellow Green Red V725125 DE Positive On Off Off Off DE Negative On On On On Continuous Positive On On Off Off Continuous Negative On On Off On DE Positive N A Off Off Off DE Negative N A On On Off Continuous Positive N A On Off On Continuous Negative N A On O
102. Information Safety and Compliance Information This section includes Instrument safety Safety and EMC standards Laser safety Instrument Safety In This Section This section includes Notes Hints Cautions and Warnings Safety symbols Before operating this instrument Material Safety Data Sheets MSDSs General Warnings Notes Hints Cautions and Warnings Notes Hints Cautions and Warnings are used in this document as follows A Note provides important information to the operator and appears as NOTE If you are prompted to insert the boot diskette into the drive insert it and then press any key A Hint provides helpful suggestions not essential to the use of the system and appears as Hint To avoid complicated file naming use Save First to Pass or Save Best Only modes A Caution provides information to avoid damage to the system or loss of data and appears as CAUTION Do not touch the lamp This may damage the lamp A Warning provides specific information essential to the safety of the operator and appears as WARNING CHEMICAL HAZARD Wear appropriate personal protection and always observe safe laboratory practices when operating your system vii This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Safety and Compliance Information Remarques recommandations et avertissemen
103. Make sure the Flap Door 1 actuator works properly B Flap Door 1 is improperly sealing Align Flap Door 1 Replace damaged O ring C Samples on the plate are not completely dry Dry the samples completely before loading sample plate D Foreline Valve 2 is improperly sealing Replace Foreline Valve 2 assembly E Linear 1 actuator is leaking at its O ring seal The knurled nut may be slightly loose try tightening The O ring seal under the knurled nut may be binding and in need of lubrication The Linear actuator shaft may be scratched or nicked allowing an air burst to enter the Sample Loading Chamber when the actuator is being extended during the plate loading ejection process continued 6 13 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 6 Troubleshooting by Symptoms Table 6 5 Vacuum System Troubleshooting Continued ltem Symptom Possible Cause Action 3 BA1 or BA2 ion gauge A Source or reflector turbo is Check that when the source reading shows higher than not pumping properly turbo or reflector turbo is normal pressure running the normal status shut down with E09 on loud whining noise replace display but TC2 reading is the turbo normal B Source or reflector turbo Check the source or reflector shuts down turbo fuse
104. Product Product Area Telephone Fax PNA Custom and Synthesis 1 800 899 5858 press 1 then press 52 1 508 383 7855 e FMAT 8100 HTS System e CytoFluor 4000 Fluorescence Plate Reader 1 800 899 5858 press 1 then press 62 1 508 383 7855 Chemiluminescence Tropix 1 800 542 2369 U S only or 1 781 271 0045 1 781 275 8581 LC MS Applied Biosystems MDS Sciex 1 800 952 4716 1 508 383 7899 a 5 30 A M to 5 00 P M Pacific time b 8 00 A M to 6 00 P M Eastern time c 9 00 A M to 5 00 P M Eastern time Outside North America To contact Applied Biosystems Technical Support or Field Service outside North America use the telephone or fax numbers below Region Telephone Fax Eastern Asia China Oceania Australia Scoresby Victoria 61 3 9730 8600 61 3 9730 8799 China Beijing 86 10 64106608 or 86 10 64106617 86 800 8100497 Hong Kong 852 2756 6928 852 2756 6968 Korea Seoul 82 2 5936470 6471 82 2 5936472 Malaysia Petaling Jaya 60 3 79588268 603 79549043 Singapore 65 896 2168 65 896 2147 Taiwan Taipei Hsien 886 2 2358 2838 886 2 2358 2839 Thailand Bangkok 66 2 719 6405 662 319 9788 Europe Austria Wien 43 0 1 867 35 75 00 43 0 1 867 35 75 11 Belgium 32 0 2 532 4484 32 0 2 582 1886 Denmark Naerum 45 45 58 60 00 45 45 58 60 01 Finland Espoo 358 0 9 251 24 250 358 0
105. SUPPORT NSF Through the internet go to http 167 116 75 148 msgboards Voyager nsf all Open View Through the Applied Biosystems intranet go to https gene peintranet net login to the intranet is needed Select Departments Product Support Link to the MALDI Knowledge Database A 3 Appendix A Applied Biosystems Voyager MALDI K l D MALDI Support Web Site Voyager Knowledge Database How to add E mail a Voyager product engineer If you have access to Lotus Notes or the content specialist Applied Biosystems intranet you can add content directly to the knowledge database Otherwise you can email contributions to Voyager appliedbiosystems com A 4 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Contacting Technical Support Overview By E Mail By Telephone or Fax You can contact Applied Biosystems for technical support By e mail By telephone or fax Through the Applied Biosystems Technical Support web site Note For information on obtaining technical documents such as Applied Biosystems user documents MSDSs and certificates of analysis see Obtaining Technical Documents on page A 10 You can contact technical support by e mail for help in the product areas listed below Product Product Area E Mail Address Genetic Analysis DNA Sequencing gala
106. Signal Lines J5 e r Control Lines NA PB100839 Figure 2 18 TIS Module Block Diagram 2 27 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics R3 Pos Adi Zero to 950V Clkwise Increase U2 Positive 1000V Power Supply U1 Negative 1000V Power Supply R75 Neg Adi Zero to 950V Clkwise Increase PB100840 Figure 2 19 TIS PCA Assembly Diagram All the power requirements for this assembly are provided by the 24 V dc input Power for the TTL logic and other low voltage electronics is provided by DC DC converters The two high voltage power modules have 24 V inputs and zero to 1000 V outputs The output voltage for each of the two modules can be measured with a voltmeter VOM at the 100 1 test point J1 J2 or J5 J6 Adjustment of their output to 950 V is controlled by potentiometers R3 and R75 Dynamic operation can be observed using Tektronix P5100 2500 V oscilloscope probes When 24 V dc is applied to the power input and HV Enable Input is pulled high or allowed to float high 950 V dc and 950 V dc appear at outputs J3 and J4 respectively High voltage is enabled at the same time and as a result of the same conditions as all other Voyager workstation high voltage sources To completely disable the high voltage see Disabling High Voltage on page 5 42 The TTL gate contro
107. Software Direct Bus Access control page xvii This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted How to Use This Guide Related Documentation These related documents are shipped with each Voyager DE STR system Voyager DE Biospectrometry Workstation User Guide Refer to this guide for detailed procedures and reference information on using the Voyager DE Biospectrometry Workstation Voyager DE Biospectrometry Workstation Getting Started Guide Use this guide to learn the basics of operating the system It provides step by step information for running your first experiment Data Explorer Software User Guide Use this guide to learn how to use the Data Explorer software to process and analyze data GPMAW General Protein Mass Analyzer for Windows Use this booklet to learn how to use the GPMAW software Acqiris Digitizers User Manual lf the system includes an Acqiris digitizer use this document to learn about this digitizer s functions that are not described in this document or in the Voyager DE Biospectrometry Workstation User Guide LeCroy lf the system includes a LeCroy digitizer use this document to learn about functions that are not described in this document or in the Voyager DE Biospectrometry Workstation User Guide Tektronix TDS 520A 524A 540A and 544A Digitizing Oscilloscope User Manual lf your s
108. Table 5 7 Table 5 7 Settings for COM2 Field Value Baud rate 9600 Data Bits 8 Parity Odd Stop Bits 1 Flow Control None If necessary select 9600 from the drop down list Click OK To set the Vacuum monitor com port to COM2 in the registry settings 1 2 3 4 Open the registry as described Accessing the Voyager Computer Registry Keys on page 5 48 Select the following path in the left panel of the Registry Editor window HKEY_LOCAL_MACHINE SOFTWARE PerSeptiveBiosystems Maldi Server HiVolt Vacuum Monitor Vacuum Monitor COMM Port In the Registry Editor window right panel double click default If necessary in the string field type COM2 Click OK Verifying and Resetting Vacuum Monitor Parity Similarly you can verify the parity setting The Voyager registry key must be set to 1 The multigauge controller can be set to any value The default parity setting in the Voyager computer registry is 1 Parity codes are summarized in Table 5 8 5 50 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Vacuum System Table 5 8 Parity Codes System Parity Code Voyager computer Default is Odd 1 Voyager software Must be set to 1 Multigauge controller Can be different from the Voyager software setting Can be set to any of the following O odd E even none
109. V Clkwise Increase U2 Positive 1000V Power Supply J5 J6 U1 Negative 1000V Power Supply R75 Neg Adi Zero to 950V Clkwise Increase PE100840 Figure 5 27 TIS PCA Assembly Diagram Adjusting TIS voltage The following table shows how to adjust the TIS voltage 950 V dc is normal using two potentiometers Figure 5 27 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Computer and Video Systems Potentiometer Function R3 0 to 1000 V dc adjustable clockwise to increase R75 0 to 1000 V dc adjustable clockwise to increase 5 5 2 Flight Tube Drift tube Power Supply The DC offset adjustments requires two steps 1 With the system in positive ion mode and with a digital voltmeter on the output the RP9 offset potentiometer for the OpAmp with a gain of 10 is adjusted for zero volts 2 With the system in negative ion mode the RP8 offset potentiometer for the OpAmp with a gain of one is adjusted for zero volts Diagnostics Software Voltages Delays Control Page Use the Voltages Delays control page Voltage Delays Control Page on page 33 to set Mode of operation Linear Reflector See Section 5 3 6 High Voltage On Off See Turning the High Voltages On and Off on page 34 Mirror voltage Desired observe Actual See Setting the Voltages on page 34 Timing delays Low Mass
110. V adjusting 6 Source or grid DAC voltage A High voltage arc Reload DAC by changing a output incorrect scrambled DAC and DAC value or loading a different output method 5 V reference is less than or greater than 5 V B 15 V fuse or power Check fuse or power supply supply is faulty Replace C DAC output is too low Replace DAC PCB D DAC output is incorrect Check 5 V reference test point 9 voltage on consolidated control board If necessary adjust to 5 00 V E 48 bit I O board is faulty Replace 48 bit I O board 6 10 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted 6 1 5 Vacuum System Troubleshooting Tables Multigauge Controller Common Error Codes on page 16 lists the error codes displayed by the Multigauge controller possible causes and actions Table 6 5 Vacuum System Troubleshooting Item Symptom Possible Cause Action TC2 reading shows higher than normal pressure i e TC2 reading shows atmospheric pressure It takes a long time to pump down after plate loading A Vent valve is stuck open after loading or ejecting the sample plate Close the vent valve Check that 24 V is present to operate the vent valve Clean or replace the vent valve if it is malfunctioning B Flap Door 2 is not closing properly Check that Flap Door 2 actuator is operating properly Close Flap D
111. VIQW 5c ierit etse de dan anaes 4 2 4 2 Voyager Software Compatibility 4 2 4 3 Accessing the Diagnostics Software 4 3 4 4 Diagnostics Software Features 4 5 4 4 1 Control Pages sesseee 4 5 4 4 2 Status Bar sse 4 11 4 1 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 4 Voyager Diagnostics Software 4 1 Overview The Voyager 32 Bit Diagnostics software for NT platform interface Figure 4 3 allows you to Troubleshoot or isolate electrical mechanical and vacuum problems Test the system after repairing or replacing parts Control the hardware components when the Instrument Hardware Controller IHC and Instrument Control Panel ICP are shut down You can run the diagnostics software whether the instrument is operating under vacuum or at atmosphere ATM 4 2 Voyager Software Compatibility 4 2 Table 4 1 shows the compatibility between the various Diagnostics and Voyager Software versions and platforms Table 4 1 Diagnostics and Voyager Software Version Compatibility Diagnostic Software Platform Compatible Voyager Software Voyager 32 bit NT Voyager Version 5 1 and later Voyager 16 bit NT Voyager Version 4 51 through Version 5 01 Voyager 16 bit Windows Voyager Version 4 04 and earlier This Doc
112. Voyager DE STR Biospectrometry Workstation Version 5 Series Software Service Reference and Troubleshooting Guide This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Applied Biosystems This is the back side of the front cover Applied Biosystems Voyager DE STR Biospectrometry Workstation Version 5 Series Software Service Reference and Troubleshooting Guide This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted ARE DR ns Copyright 2001 Applied Biosystems All rights reserved For Research Use Only Not for use in diagnostic procedures Information in this document is subject to change without notice Applied Biosystems assumes no responsibility for any errors that may appear in this document This document is believed to be complete and accurate at the time of publication In no event shall Applied Biosystems be liable for incidental special multiple or consequential damages in connection with or arising from the use of this document ABI PRISM and its Design Applied Biosystems Aquapore AmpliCover Anitron Biobytes Brownlee Delayed Extraction FastPhoramidite GeneScan Genotyper HLP INHERIT MicroAmp MicroCoat MPLC NEWGUARD ONESTEP OPC PCR MATE Phosphalink POLYPORE Precipitette PerSeptive Biosystems and the fractal icon ProBlott PROCISE ProFocus ProSo
113. Voyager Diagnostics Sur Voyager NT Diagnostics fh Voyager Sequence Control x Figure 4 2 Start Programs Voyager Options 4 3 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 4 Voyager Diagnostics Software 4 4 2 Use the View menu or click individual tabs to access the component control pages Diagram window 2 display only PIE Ld TE Pum Tabs Control pages Camera Mechanical Laser Volages Delays XY Table DE Switch Box Direct Bus Access Camera Status bar High Voltage Interlock MK 16114 Y 8058 XY Status LOAD Laser OFF Src Pres 0 0e 000 T Mir Pres 0 0e 000 T Smp Pres 0 0e 000 T vA Figure 4 3 Voyager 32 Bit Diagnostics Software for NT Platform Window 3 To restart the IHC you can do one of the following Manually restart through the Services dialog box Reboot the computer system Launch the Instrument Control Panel This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Diagnostics Software Features 4 4 Diagnostics Software Features 4 4 1 Control Pages Control pages Figure 4 3 provide control over the instrument components Using control pages for specific tasks is detailed in various sections in Chapter 5 Troubleshooting by Components and in Appen
114. Y Stage From Load Position 3 Start a single or multiple iteration load eject cycle The diagnostics software performs the usual sequence of steps for the specified operation but without moving the sample stage 5 13 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components Initiating Load Eject Cycles To start a single load cycle click mere To start a single eject cycle click rise EJECT Cycle To set up multiple load eject cycles set the number of load eject cycles you want to run in Total Number of Complete Load Eject Cycles to Run then click mm Table 5 3 lists the order of operations in load and eject cycles Table 5 3 Order of Operations in Single Load and Eject Cycles Eject Cycle Load Cycle Step Operation Step Operation 1 Open Flap Door 1 1 Retract Linear 2 actuator 2 Extend Linear 1 actuator 2 Close Flap Door 2 3 Turn grabber on 3 Close foreline valve 2 4 Retract Linear 1 actuator 4 Close vent valve 5 Turn grabber off 5 Open foreline valve 1 6 Close Flap Door 1 6 Wait 10 15 seconds 7 Close foreline valve 1 7 Check sample loading chamber pressure TC2 reads 8 x 107 torr 8 Open vent valve 8 After verifying TC2 reads 8 x 107 torr open foreline valve 2 9 Wait 5 seconds 9 Open Flap Door 1 10 Check sample loading chamber 10
115. YAG laser Class IV A class IV laser poses hazards to the eye and skin not only from the direct beam but in some cases also from diffuse reflection These lasers can be considered fire hazards which also may produce laser generated air contaminants and hazardous plasma radiation See the Safety and Compliance Information section in the front of this manual for safety precautions to be taken by the customer before performing service on the YAG Laser For more safety information see the Safety and Compliance Information section in the front of this manual and the documentation provided by the laser manufacturer WARNING ELECTRICAL SHOCK AND LASER HAZARD When instrument covers are removed high voltage contacts are exposed and the laser emits ultraviolet radiation Wear laser safety goggles and post a laser warning sign at the entrance to the laboratory when you remove covers for service WARNING LASER HAZARD Exposure to direct or reflected laser light can burn the retina and leave permanent blind spots Never look directly into the laser beam Remove jewelry and other items that can reflect the beam into your eyes Wear laser safety goggles during laser alignment Protect others from exposure to the beam Post a laser warning sign while performing the alignment This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter1 System
116. accuracy include e Contaminants Composition of gas used Outgassing of residual gases in the glass and metal parts X ray limit Degassing the Bayard Alpert Gauges If the vacuum does not come down contaminants may be trapped within the gauge The Degas function cleans the vacuum gauges of residual contaminants Degassing occurs through a controlled high temperature baking of the gauge Degas the gauge periodically and whenever the system has been open Before degassing can begin the Emission of the gauge must be on Pressure must be less than or equal to 1 x 107 torr To begin degassing press the multigauge controller Degas key Observe the pressure readings The pressure peaks asymmetrically and then drops to a lower equilibrium pressure NOTE If the Voyager system is On and the pressure rises above the vacuum setting Voyager software displays an error Reset the Voyager software after the pressure normalizes to below the vacuum setting 5 54 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Vacuum System You can shut off degassing manually When the equilibrium pressure stabilizes press the Degas key to end degassing If you do not manually shut off degassing degassing shuts off automatically after a preset time For information see the Varian Multigauge Controller Manual Multigauge Controller Error Codes When an error
117. ace the feedthrough if necessary Adjusting the Microswitches The stepper motor feedthroughs Figure 5 17 on page 4 29 have two switches Home triggering the Home Position switch occurs when the linear actuators are fully extended Due to its mounting configuration the Home switch has very little wear and rarely needs replacement However if you replace a Home switch the respective X or Y load coordinate will need to be adjusted Resetting the Sample Stage Load Position on page 5 20 e Load Triggering the Load Position switch retracts the linear actuator Check the Load Position switch as part of the preventative maintenance schedule and replace if necessary 5 28 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Main Source Chamber Load position microswitches Home position microswitches Figure 5 17 Stepper Motor Feedthrough Load and Home Position Switches Occasionally an error message is displayed during plate loading or ejection indicating that the source is not in the load position even though the compressor is energized Both the 5 V logic for the load position sensing and the 24 V for the compressor relay use the same load position microswitches on the sides of the linear feedthroughs If the switches are not adjusted to provide sufficient press
118. aintains positive pressure in the closed extended position maintaining integrity of the seal when the compressor is off Flap Door 2 separates the external atmosphere and the sample loading chamber Pneumatic System An on board air compressor provides up to 60 PSI 4 13 bar to the pneumatic system that controls the sample handling actuators and flap door valves For the actuators to operate correctly a minimum of 15 PSI 1 03 bar is needed The integrated compressor is activated only during plate ejection and loading 1 7 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter1 System Overview 1 3 2 Main Source Chamber 1 The main source chamber houses the ion source a high voltage region for ionizing desorbing and accelerating ions Figure 1 4 shows the main source chamber for systems with serial numbers 4154 and later Variable voltage grid Ground Sample grid plate Beam steering plate loading chamber Collision cell option Figure 1 4 Voyager DE STR Workstation Main Source Chamber Top View Figure 1 5 shows typical voltages applied for main source chamber components of Voyager DE STR instruments with serial numbers of 4154 and later o A Einzel lens 50 of source voltage Variable voltage grid Typically 60 95 of source Sample plate source max 25 000 kV To detector
119. al Use Only No Unauthorized Copying Permitted Chapter 4 Voyager Diagnostics Software Table 4 3 Summary of Diagnostics Software Control Pages Continued Fields and Actions Status Indicators Comment Direct Bus Access Control Page Writes data directly to the various DACs pulse generators and ion source pulsar control register For information see Appendix D Isolating Components Using Direct Bus Access You cannot enable high voltage or the Low Mass Gate using direct bus access With direct bus access you can only set the output voltage at the DACs and the Low Mass Gate value Before you write data to any component make sure you have appropriately connected or disconnected the high voltage lines and connected meter probes or voltmeters to the appropriate DACs WARNING ELECTRICAL SHOCK HAZARD Safe operating procedures and proper use of equipment are the responsibility of the authorized and qualified service person Precautions must be taken to protect against possible serious and or fatal bodily injury Write address NA Set value as decimal hexadecimal or binary directly to the data bus for the Source DAC Mirror DAC Grid DAC Beam guide DAC Control register 4 LMG delay DE delay TIS delay 4 10 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Diagnostics Software Features 4 4 2 Status Bar Us
120. ameter elock Start Delay End Delay cycle DE 10 ns How long accelerating voltage is NA withheld after the laser fires Values range from 10 to 32 768 ns LMG 222 ns How long the detector is NA steps deactivated reducing its sensitivity to low mass ions Values range from 8 000 to 65 000 ns TIS 10 ns Determines when the TIS is Determines when the TIS is deactivated voltage turned off to reactivated voltage applied pass the ions of interest to deflect unwanted ions Values range from 10 to 327 670 ns Resetting All Voltages and Delay Times To disable all high voltages reset all DAC voltage values to 0 0 V and disable all delay timing options Click Reset All Figure 5 1 9 5 35 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components 5 3 10 DE Switch Box Control Use the DE Switch Box control page Figure 5 21 to test the high voltages supplied to the source grid mirror and guide wire through the DE switch box DE Switch Box r DE Switch Box Type HV Switch Box V725059 Test HV Switch Box 4725115 Check Control Wiring Hi Pot Non DE Positive lon 4 Hi Pot Non DE Negative lon Fast DE Switch Box V725125 Hi Pot DE Positive lon Hi Pot DE Negative lon Check C Pulse DE Positive lon eck Ol Pulse DE Negative lon as VEI
121. and side panels are installed there should be no detectable radiation present If front or side panels are removed when the laser is operational you may be exposed to laser emissions in excess of Class 1 rating Do not remove labels or disable safety interlocks Additional Safety Information Refer to the user manual provided with the laser for additional information on government and industry safety regulations Required Customer Provided YAG Laser Safety Measures Before servicing a system using the YAG laser the customer is required to provide safety precautions The YAG accessory supplied with the Voyager DE STR is a class laser which is considered not capable of producing damaging radiation levels during operation When maintenance requires an Applied Biosystems field service engineer to defeat the interlocks protection system for the instrument the YAG laser is classified as a class IV laser A class IV laser poses hazards to the eye and skin not only from the direct beam but in some cases also from the diffuse reflection These lasers can be considered a fire hazard and may also produce laser generated air contaminants and hazardous plasma radiation Therefore before you can perform maintenance or service on the YAG Laser while at the customer facility the customer must Provide the appropriate Laser Warning Signs These signs shall be conspicuously displayed in a location where they will best serve to warn any and all onlooke
122. ars in the Home check box under Limit Switch NOTE Home position is marked on the attenuator wheel by a piece of reflective tape The attenuator assembly has an opto couple device that senses the reflective tape If the system does not detect Home position properly check the condition of the reflective tape 5 41 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components 5 5 Flight Tube and Mirror Chamber 5 5 1 Timed lon Selector The flight tube contains a timed ion selector TIS The TIS is a Bradbury Nielson gate When the TIS is turned on voltage 950 V is applied to the selector to deflect unwanted ions At the time that corresponds to the ions of interest voltage is turned off Start Delay and the ions of interest pass to the detector Figure 1 11 on page 1 16 After the ions pass through the selector voltage is turned on again End Delay to deflect ions of non interest Disabling High Voltage High voltage for the TIS is enabled at the same time and as a result of the same conditions as all other Voyager workstation high voltage sources To completely disable the high voltage 1 Turn off the High Voltage in the Voyager Instrument Control Panel see the Voyager User Guide 2 Remove the DB15 type input connector at P1 3 Remove the two output cables at J3 and J4 R3 Pos Adj Zero to 950
123. ass Gate Delay Timer Board V750069 V750073 2 15 2 2 5 Low Mass Gate Driver Boxes V700635 V700643 and Detector Filter Bias V750032 SPP TENA 2 20 2 2 6 Timed lon Selector TIS Assembly VZD TA nete td ensis omes af Ead 2 26 2 2 7 TTL Output Opto Trigger Board V750065 2 31 2 3 Electronics Only in Newer Model Instruments 2 33 2 3 1 Beam Steering Board V750091 2 33 2 3 2 DE Switch Box V725115 V725125 2 37 2 3 3 Einzel Lens Electronics Voltage Divider Box 4317251 2 44 2 3 4 48 Bit I O Board with Game Port 2500983 Rare tide etuer 2 45 2 3 5 MALDI Control Board V750082 and V750102 001 V750102 002 VY5027003 iiu cc ti terea 2 47 2 4 Electronics Only in Earlier Instruments 2 59 2 4 1 Flight Tube Drift Tube Power Supply V750061 2 60 2 4 2 Pulse Generator Board V750063 2 63 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics 2 1 Electronics Theory Overview Electronics Most of the electronics for the Voyager DE STR are in the two cabinets below the mass spectrometer components Figure 2 1 and Figure 2 2 MALDI control DC distribution AC distribution Grid HVPS Source HVPS
124. asses goggles must be rated for a YAG laser with a wavelength of 355 nm Provide and document laser safety training to their employees on the hazards associated with a YAG laser Remove all employees from the area where maintenance to the YAG laser is being performed In addition all customers must be in compliance with the ANSI standard Z136 1 1993 American National Standard for the Safe Use of Lasers XV This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Safety and Compliance Information Xvi This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted How to Use This Guide How to Use This Guide Purpose of This Guide The Applied Biosystems Voyager DE Biospectrometry Workstation Service Reference and Troubleshooting Guide provides the following Reference information such as theory and circuit board functionality Troubleshooting procedures and tables Contact information Audience This guide is intended for novice and experienced Voyager workstation field service engineers technical support and technical trainers Structure of This Guide The Applied Biosystems Voyager DE Biospectrometry Workstation Service Reference and Troubleshooting Guide is divided into chapters and appendices Each chapter page is marked with a tab and a header to help you locate
125. auge Controller Common Error Codes 6 16 6 3 LED Indicators 6 18 6 1 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 6 Troubleshooting by Symptoms 6 1 Troubleshooting Tables This section includes symptoms possible causes and actions to troubleshoot the Spectral problems Sample Loading and Main Source Chamber Computer and software Power supply Vacuum system For additional information see the Voyager User Guide 6 1 1 Spectral Problems Table 6 1 Spectral Troubleshooting Item Symptom Possible Cause Action Continuous Mode 1 In linear mode flat signal on A Defective fuse or DAC Check fuse Replace if oscilloscope or Monitor board defective window for matrix and sample Check that source and grid region when in positive ion DAC output is correct mode Same result when Replace if defective switched to reflector mode B Einzel lens is wrong Check einzel lens polarity polarity or is shorted to Check for shorts ground C High voltage connection to Adjust or replace connection the sample plate is broken or disconnected D High voltage power supply Replace high voltage power is defective supply E Laser beam is not striking Check the attenuator the sample with adequate functioning See Adjusting intensity the Attenuator Position o
126. b appliedbiosystems com Sequence Detection Systems and PCR pcrlab appliedbiosystems com Protein Sequencing Peptide and DNA corelab appliedbiosystems com Synthesis e Biochromatography tsupport appliedbiosystems com e PerSeptive DNA PNA and Peptide Synthesis systems FMAT 8100 HTS System e CytoFluor 4000 Fluorescence Plate Reader Mariner Mass Spectrometers MassGenotyping Solution 1 MGS1 System Voyager Mass Spectrometers LC MS support sciex com Applied Biosystems MDS Sciex Chemiluminescence Tropix tropix appliedbiosystems com In North America To contact Applied Biosystems Technical Support in North America use the telephone or fax numbers in the table below Note To schedule a service call for other support needs or in case of an emergency dial 1 800 831 6844 then press 1 Product Product Area Telephone Fax ABI PRISM 3700 DNA Analyzer 1 800 831 6844 then press 8 1 650 638 5981 DNA Synthesis 1 800 831 6844 press 2 then 1 650 638 5981 press 12 A 5 Appendix A Product Product Area Telephone Fax Fluorescent DNA Sequencing 1 800 831 6844 press 2 then press 22 1 650 638 5981 Fluorescent Fragment Analysis including GeneScan applications 1 800 831 6844 press 2 then press 34 1 650 638 5981 Integrated Thermal Cyclers ABI PRISM 877 and Catalyst 800 instruments 1 800 831 6
127. ble MALDI control board PB100858 48 bit I O SCSI cable Figure 5 15 Feedthrough Interconnects 5 27 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components Lubricating the X and Y Feedthroughs Useful Materials Silicon or PTFE based spray lubricant Lubricant extension tube with a 90 bend The bend allows perpendicular access to the feedthrough worm gear A grinding noise or erratic binding when the bobbin is moving indicates the feedthroughs need lubrication To lubricate the X and Y feedthroughs 1 Expose the worm gear drive screw by moving both feedthroughs to their Home positions fully extended See Homing the Sample Stage on page 5 19 2 With the lubricant sprayer extension tube inserted into the feedthrough worm gear slot lubricate the worm gear along its entire length Lubricate worm gear drive screw PB100863 Figure 5 16 Lubricating the Feedthrough Worm Gear 3 Repeatedly move the source between sample plate spot position 91 and position 10 until the grinding noise or erratic binding subsides Also cycle repeatedly from Home to Load Position 4 Ifthe grinding noise or erratic binding continues repeat lubrication or repl
128. bo 2 Lift up the lever attached to the turbo vent Loosen the vent screw slowly valve to open the valve CAUTION DO NOT loosen the vent screw completely The small knob may become lost and the vent screw O ring may become detached 3 When the sound of flowing air has stopped When the sound of flowing air has stopped completely close the turbo vent valve lever completely re tighten the knurled vent screw by hand CAUTION When tightening the knurled vent screw DO NOT over tighten it When the system is vented the ion detector is exposed to the atmosphere If the detector is exposed for more than 24 hours the following problems may occur A film of water and other molecules may form on the surface of the detector The film can cause arcs across the surface of the detector when full voltages are applied The detector may absorb moisture and may swell and crack For systems that will be at atmosphere for more than 24 hours purge the system to No Purging to No protects detector integrity as well as minimizes pump down time Pump down time is the time needed to return the system to vacuum after venting The length of time the system was at atmosphere determines the pump down time To estimate pump down time multiply the time the system was at atmosphere by three 3 2 3 Purging the System with N To purge newer systems with No gas 1 NOR ON Connect the No gas tank to the filter on the source turbo venting valve Connect one e
129. ce Grid and Mirror Test high voltages DE Switch Box Voltages Section 5 3 10 DE Switch Box Control Guide wire Set values Voltages Delays NA voltage Test high voltages DE Switch Box High voltages Observe status Section 5 3 4 Diagnostics Software Window Section 5 3 5 Status bar High Voltage Section 5 3 7 Enable Voltages Delays eee Test DE Switch Box section 5 4 10 m Section 5 5 1 Section 6 1 1 Section 6 1 4 Home position Home sample stage X Y Table see X and Y feedthroughs Laser Observe status Section 5 4 Diagnostics Software Window Section 6 1 1 Status bar Laser Section 6 1 3 Fire set repetition rate attenuation and laser type Laser Limit switches Observe status Mechanical Section 5 2 4 microswitches Section 5 3 Section 5 3 3 Section 6 1 2 Section 6 1 3 Linear actuators Retract extend Mechanical Section 5 2 Section 5 2 4 Section 5 3 Section 5 3 2 Section 6 1 2 Section 6 1 5 Linear mode Set mode Voltages Delays Section 5 3 7 Section 5 3 8 Section 6 1 1 54 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Troubleshooting Overview Table 5 1 Matching Components with Control Page and Troubleshooting Information Component or Parameter Task Control Page Troubleshooting Section Load position Set coordinates move sample stage X Y Table see X and Y feedthroughs
130. cesses and controls Game Port functions 48 bit I O board PB100867 Figure 2 28 48 bit I O Board in the Computer Rear view Theory The I O board has three 8255 parallel interface adapter PIA chips Each chip has an 8 bit data bus 2 bit addressing a chip select and a read write line all of which are connected to the computer data bus In addition each chip has three 8 bit I O ports Only two of the three chips are used U38 is a spare All inputs and outputs to the 8255 chips are optically isolated through an HCPL 2630 chip The isolators prevent noise on the computer bus and offer protection from high voltage arcs in the system NOTE 5 V 5 B on older schematics was supplied from the Voyager workstation system DC Distribution PCA in older systems In newer systems this 5 V cable is not connected to the card nor required and the buffered 5 V and grounds are jumped to obtain power from the computer Adding jumpers JP2 2 4 6 8 and JP3 2 4 and 6 8 enables this Connectors Table 2 15 Connectors on the 48 Bit I O Board Connector Function Type JO Enable address and 1 0 26 pin ribbon J1 Data and I O 26 pin ribbon J3 5 V 5 B on older schematics power Plug 2 46 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments Table 2 15 Connectors on the 48 Bit
131. corresponding to the Low Mass Gate value Outputs a pulse of fixed width The circuit has 222 ns resolution and an 8 bit maximum delay with an 8 us offset which corresponds to a delay range of 8 to 65 us Theory The low mass gate delay timer circuit can be divided into the following blocks Figure 2 10 18 MHz clock Trigger buffer and sync Latches Counters used as delays Address decoder Integrator Regulators Drivers 2 15 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted penunueg Buikdo2 pazisoyineun ow AJUO esr jeusajuy 404 suiejsAsoig parjddy jo JeW TVLLN3GIJNOO Sulejuog jueunoog SIUL 9L c weibeig 20 g pseog sau Aejag 9129 sseyy Mo OL 2 ainbl4 Clock 18 Mhz Clock 3 9 Divide by 4 DE 8us Delay Tri Trigger Buffer e Synch 6 bit Down rigger Counter reset T data bus 8 bits Start Counter 8 bit Start Buffer Temporary Latch 8 bit Down Register Counter 5 bits reset address bus Valid Buffer Adoress Digital Integrator Load Decoder Load Clock ft 45v 5 volt regulator 069 and 073 SS SS 12v 12 volt regulator 073 only latch Drivers
132. ctrometer and to start and stop acquisition The control stick allows you to Align a sample plate in the path of the laser Start and stop acquisition Save data This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager DE STR Biospectrometry Workstation Overview Accessories and Options Customers can purchase the following Voyager workstation options from Applied Biosystems CID Collision induced dissociation capability to enhance fragmentation in Post Source Decay PSD analysis For more information see the Voyager User Guide Enhancing Fragmentation with CID The hardware needed for the CID option is factory installed However the workstations are plumbed for CID only when the customer orders this option Nd YAG An integrated external 355 nm wavelength neodymium yttrium aluminum garnet laser The Nd YAG Laser Option is compatible with any Voyager DE STR workstation with a serial number of 4154 or later GPMAW General Protein Mass Analysis for Windows A factory installed software package useful for protein specific applications theoretical digest and post source decay PSD fragmentation CD ROM Reader Recorder A device for storing or backing up data on CD ROM media Test standards kits Useful for Voyager workstation optimization and applications Kits available include Sequazyme Peptide Mass Standards Kit
133. d Biosystems Technical Support web site To order documents by telephone 1 From the U S or Canada dial 1 800 487 6809 or from outside the U S and Canada dial 1 858 712 0317 2 Follow the voice instructions to order documents for delivery by fax Note There is a limit of five documents per fax request To view download or order documents through the Applied Biosystems Technical Support web site 1 Access the Applied Biosystems Technical Support web site at www appliedbiosystems com techsupp 2 Under the Resource Libraries heading select the type of technical document you want 3 In the search form enter or select search criteria then click Search 4 Inthe results screen do any of the following Click t3 to view a PDF version of the document Right click pn then select Save Target As to download a copy of the PDF file Select the Fax check box then click Deliver Selected Documents Now to have the document faxed to you Select the Email check box then click Deliver Selected Documents Now to have the document PDF format e mailed to you Note There is a limit of five documents per fax request but no limit on the number of documents per e mail request This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Obtaining Customer Training Information The Applied Biosystems Training web site at www
134. dental collisions This configuration also ensures that the paths of incoming and reflected ions do not overlap The reflector detector Measures the abundance of reflected ions over time sadual microchannel plate optimized for response time Hasa grounded shield to protect the ions from stray electromagnetic fields Is positioned perpendicular to the ion beam for improved performance This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager DE STR Workstation Components 1 3 6 Digitizer The digitizer converts the analog signal from a detector to a digital signal that can be transmitted to the computer Currently Voyager DE STR requires a 2 GHz digitizer minimum for optimal performance Supported digitizers are listed below LeCroy 2 GHz Provides real time display of spectra Requires a dedicated Ethernet board and Voyager 5 0 or later software Tektronix 2 GHz and 4 GHz Requires a GPIB Card and IEEE cable Works with Voyager 4 51 software and Voyager 5 0 and later software Acqiris 2 GHz Provides real time display of spectra Requires Voyager 5 1 or later software Installs in the computer PCI slot See the Voyager User Guide for information on connecting the digitizer 1 3 7 Computer and Video Systems Computer System The Voyager DE STR Biospectrometry Workstation serial numbers 4154 and later includes the
135. dix A Isolating Components Using Direct Bus Access Where to find information about each control page is summarized in Table 4 2 Table 4 2 Matching Control Page with Figure and Specific Task Information Control Page Figure Section Describing Tasks Camera Figure 5 28 Section 5 6 Computer and Video Systems Mechanical Figure 5 3 Section 5 2 4 Grabber Linear Actuators and Valves Laser Figure 5 25 Section 5 4 1 Laser Firing Repetition Rate and Reinitialization Voltages Delays Figure 5 19 Section 5 3 8 Source Grid and Mirror Voltages X Y Table Figure 5 7 Section 5 3 Main Source Chamber DE Switch Box Figure 5 21 Section 5 3 10 DE Switch Box Control Direct Bus Access Figure D 1 Appendix D Isolating Components Using Direct Bus Access This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 4 Voyager Diagnostics Software Table 4 3 summarizes the functions of each control page To find the control page and troubleshooting sections applicable to a specific workstation component refer to Table 5 1 Matching Components with Control Page and Troubleshooting Information Table 4 3 Summary of Diagnostics Software Control Pages Fields and Actions Status Indicators Comment Camera Control Page Powers on and powers off the camera Camera Off On None By default the Camera contr
136. down takes too long 6 11 6 12 troubleshooting 6 11 6 12 Purging to nitrogen 3 5 R Ratings laser 1 11 Reflection mode function 1 17 Reflector description 1 17 detector description 1 1 disk potentials 1 18 how it works 1 18 tilt 1 18 Reflector detector 1 18 description 1 18 function 1 16 1 18 5 31 position 1 18 within mirror chamber 1 16 5 31 Reflector mode compared to linear mode 5 31 description 1 17 ion beam path in 1 17 superior resolution and mass accuracy 1 17 whento use 1 17 1 fo Registry Editor path to vacuum monitor baud rate setting 5 48 Index path to vacuum monitor Comm port setting 5 50 path to vacuum monitor parity setting 5 51 Related documents xviii Remote interlock connector nitrogen laser 1 12 Repetition rate laser adjusting components required for maximum value of 20 Hz 5 40 setting 5 39 5 40 Resources accessing A 2 Rough pump see fore pump S Safety information laser xiv 1 4 3 2 Safety standards see Warnings safety xiii Sample loading chamber description 1 7 5 39 diagram of 1 7 5 7 5 24 5 25 B 8 flap valves 1 7 linear actuators 1 7 overview 1 7 5 7 troubleshooting 5 7 troubleshooting symptoms 6 4 Sample loading diagnosing using Mec control page 5 11 Sample plate description 1 9 falling of the grabber 6 4 grabber fails to contact 6 8 not loading onto the stage 6 5 hanical stays on sample stage during ejection 6 6 testi
137. e ion mode to negative ion mode The deflection voltages are also automatically enabled and disabled along with the other system high voltages The Beam Steering DAC address is at the same address as the Source Power Supply DAC address address 7 3 bit mode address 31 5 bit mode Therefore changing the source power voltage makes the same change to the beam steering board voltage In earlier instruments containing a guide wire when the source voltage changed the guide wire voltage tracked the source voltage based ona percentage Before shipment the system is optimized for performance During final test the optimum polarity is selected by actuating the slide switches and the optimum voltage scaling for each axis is determined by adjusting the potentiometers while running a prescribed sequence of test samples The values are documented on a label adhered to the right drawer base next to the beam steering board The values are based on an acceleration source voltage of 25 kV Specifications Power Power to the five relays is supplied by 24 V dc at approximately 30 mA Power to the two 12 V to 500 V programmable DC DC converters is suppled by 12 V dc at approximately 40 mA from the DVDT PCA The converters specify a no load to full 2 mA load current requirement of 16 mA to 150 mA The deflector plates are essentially no load devices Input Input impedance load presented to the DAC is 3 6 K resistive An input divider scales the DAC outp
138. e Only No Unauthorized Copying Permitted lt xmMmo2 Index N NdYAG laser 355 nm wavelength 1 11 Voyager serial numbers compatible with 1 11 Negative drive assembly 2 20 Nitrogen laser 337 1 nm wavelength 1 11 attenuation of beam 1 14 5 40 beam path 1 14 beam path through Voyager DE STR 1 14 beam splitter 1 14 component functions 1 12 components of 5 38 control panel diagram 1 12 controls 1 12 energy striking the sample 1 1 external trigger connection 1 13 external trigger setting 1 4 1 11 1 13 3 2 5 38 fan 1 13 high voltage power supplies 1 1 Interlocks Defeated LED 1 12 Internal External Trigger Adjustment 1 13 Key Control 1 12 low voltage power supplies 1 12 manual pulse repetition rate adjustment 1 13 plasma cartridge 1 12 plasma cartridge replacement 1 12 5 38 power receptacle 1 12 pulse width 1 11 rear panel 1 12 remote interlock connector 1 1 repetition rate adjustment 5 39 replacement of 1 12 5 38 Trigger input 1 13 trigger transformer board 1 12 Nitrogen laser attenuator adjusting laser intensity 1 14 5 40 step controls 5 40 Nitrogen laser beam path description 1 14 5 40 focusing ring 1 14 prism 1 14 Nitrogen laser connectors 1 1 Nitrogen plasma cartridge alignment needed in laser unit 1 12 5 38 replacement of laser unit 1 12 5 38 Noises in source area 6 4 NT Registry load home positions in microns 5 20 overwriting load position using diagnostics
139. e full voltage to the detector is delayed ions strike the detector but only a weak signal is generated There are two versions of the LMG Figure 2 10 and Figure 2 11 show the locations of the circuit appropriate boards The two versions are Positive Pulse PCA Mounted in a box that has two MHV Medium High Voltage connectors Eigure 2 13 This PCA controls a single plate MCP microchannel plate detector associated with the High Current Detector Negative Pulse PCA Mounted in a box that has three MHV Medium High Voltage connectors Figure 2 14 This PCA controls a dual MCP chevron detector and is associated with the Detector Filter Bias DFB PCA Low mass gate negative and positive Low mass gate delay timer board PB100851 TIS assembly ls lt 2 D PEL CL Figure 2 12 Detector Filter Bias 2 20 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted penuneg Buikdo2 pazisoyineun on Ajuo esr jeusajuy 404 suiejsAsoig perjddy jo j amp i49 8JJ TVLLN3GIJNOO Surejuo jueuinoog SIUL lecce es nd 8AHISOd 8129 SSeN MO7 ay jo wesbeig yIo0 g 1 z enDi4 Input Transistors e J1 15 Jmpr for ON 9 J1 14
140. e linear detector power supply and the Mirror HVPS bit enables the mirror HVPS and the mirror detector power supply 2 51 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Connectors Resistors and Test Points Table 2 17 MALDI Control Board Connectors Resistors and Test Points Item Name Function Type Connectors JO J1 Workstation 48 bit I O 26 position ribbon cable J2 Power ground 1 4 quick disconnect J3 From opto trigger board detected pulse SMA female J4 Output from YAG Q switch firing pulse SMA female J5 External laser trigger SMA female J6 Internal laser trigger SMA female J7 DE switchbox control 24V relay 8 position Mini Fit J8 DE Switchbox trigger SMA female J9 Digitizer trigger SMA female J10 DVDT trigger SMA female J11 TIS trigger SMA female J12 TIS control 4 position Mini Fit J14 DAC control monitors HVPS enables DB25 Receptacle J15 Vacuum gauge serial connection to DB9 plug multigauge controller J17 Voyager bus to right hand drawer DB37 plug electronics mirror beam steering low mass gate J18 Voyager bus expansion 34 position ribbon cable J22 Camera grabber vent solenoid foreline 12 position Mini Fit solenoid control J23 Linear and flap actuator solenoid control 8 position Mini Fit J25 Detector 24 V switc
141. e mirror turbo controller J13 Observe the turbo status indicator lights on the Voyager workstation top panel LED display or the D12 LEDs on the MALDI control board Both of the status indicator lights on the turbos should display the following sequence of colors Yellow for about 1 minute Indicating initial startup Yellow and green briefly Indicating turbo reached 80 of full speed e Green only Indicating the turbo is at normal operating condition 56 krom Red indicates a fault Wait an additional 10 to 30 minutes After the turbo has stabilized 1 Using the multigauge controller turn on the BA1 and BA2 gauges For information see Section 5 7 2 Multigauge Controller Both vacuum readings should be below 8 x 10 torr or you should see indications that the system is pumping down to a lower level Allow the system to pump down further to reach system operational pressures Normally BA1 should be below 9 x 10 torr BA2 the mirror is typically 10 times lower 9 x 10 torr NOTE To achieve a pressure below 9 x 1 07 torr may take the system a day or more When the system pressure readings are 9 x 10 torr or less reboot the computer and launch the Voyager control panel This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted 4 Voyager Diagnostics Software This chapter contains the following sections 4 QUVOI
142. e permanent blind spots Never look directly into the laser beam Remove jewelry and other items that can reflect the beam into your eyes Wear laser safety goggles during laser alignment Protect others from exposure to the beam Post a laser warning sign while performing the alignment WARNING ELECTRICAL SHOCK AND LASER HAZARD When instrument panels are removed high voltage contacts are exposed and the laser emits ultraviolet radiation Wear laser safety goggles when you remove panels for service 5 21 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components Review safety warnings on page 21 and in Safety and Compliance Information To be provided see Table D 2 Voltage Values on page D 8 for DAC output voltage Figure 5 9 Source Troubleshooting Flowchart 5 22 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Main Source Chamber Useful Materials e Small flat file Small flat blade screwdriver Long T handle Allen wrench MicroFinish cloth Teflon based spray lubricant with a sprayer extension tube 40 kV high voltage probe Multimeter Feeler gauge High voltage Y adapter to be available in the future Safety interlock tag jumper 5 3 1 So
143. e the Diagnostics Software window status bar expanded drawing shown in Figure 4 4 to check the items described in Table 4 4 High Voltage Interlock X 4186 Y 13216 KY Status NONE laser OFF Src Pres 5 0e 008 T Mir Pres 976 0097 Smp Pres 25e002T Figure 4 4 System Status Bar Shown in Two Parts for Clarity Table 4 4 Diagnostics Software Status Bar Indicators Component Status High Voltage Indicates whether the high voltage is ON or OFF Interlock Indicates if the Voyager workstation covers top front side and rear panels are locked in place When the covers are securely in place the interlock LED remains lit If the interlocks are breached during normal operation the system automatically disables the lasers and high voltage supplies For example if the panels are off or ajar the lasers high voltages and the interlock and high voltage LEDs remain off until the panels are secured To operate the system with the panels removed during servicing you can bypass the interlocks X Displays the current X coordinate position of the sample stage Y Displays the current Y coordinate position of the sample stage XY Status Indicates whether the sample stage is currently in the load home or other None position Laser Indicates whether the laser is ON or OFF Src Pres BA1 Displays the current pressure in torr in the main source chamber Mir Pres BA2 Display
144. e valve being parallel to the face of the Sample Loading Chamber when closed If it is not parallel adjust the Flap Valve hinge bar G Leaking from the knurled nut on Linear 1 actuator Finger tighten the nut Do not over tighten it H Leaking from the knurled nut on Linear 2 actuator Finger tighten the nut Do not over tighten it Leaking from the knurled nut on Flap Door 1 Finger tighten the nut Do not over tighten it J Samples on the plate are not completely dry Dry the samples completely before loading sample plate WARNING CHEMICAL HAZARD Ethanol is a flammable liquid and vapor It may cause eye skin and upper respiratory tract irritation Prolonged or repeated contact may dry skin Exposure may cause central nervous system depression and liver damage Please read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves 6 12 continued This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Troubleshooting Tables Table 6 5 Vacuum System Troubleshooting Continued Item Symptom Possible Cause Action BA1 ion gauge shut down with E09 displayed on Multigauge controller display after plate loading ejecting A Flap Door 1 is improperly closing Check that the sample plate is not stuck at Flap Door 1
145. eb site and the Voyager MALDI Knowledge Database 24 hours day 7 days a week Each database is a repository of information that is fully text searchable and is individually replicated on Notes The following table describes the information available and how to access each database Applied Biosystems Voyager MALDI Support Web Site Voyager MALDI Knowledge Database Purpose To provide released documents To provide communication tool for FSE to from Houston share facts questions and new technical information Categories Installation documents Electronics Parts list General Service bulletins service manual Installation and operation service notes Mechanical Shareware software and soft Service bulletins and notes ware installation documents Software Support contact information Spare parts Guides and related manuals Utility programs Primary Through the internet go to Through Lotus Notes desktop go to access mode http usfosdws03 intranet pbiosupportweb nsf docs 4LFFAJRMIR opendocument File Database Open Server USFOSDWSO3 FOS PEC Database MSGBOARDS Folder VOYAGER Additional access modes Through the Applied Biosystems intranet go to https gene peintranet net login to the intranet is needed Select Departments Product Sup port Voyager Support Through Lotus Notes desktop go to File Database Open Server USFOSDWS03 FOS PEC Database INTRANET Folder PBIO
146. ectriques Le tableau suivant donne la signification des symboles d alertes de s curit non lectriques qui figurent sur les appareils AVERTISSEMENT Danger associ la pr sence d un appareil de chauffage Proc der avec pr caution pour viter de se br ler au contact de pi ces ou d l ments chauds Indique que l appareil renferme un laser D gt Before Operating This Instrument Ensure that anyone involved with the operation of the instrument is instructed in both general safety practices for laboratories and specific safety practices for the instrument Make sure you have read and understood all related Material Safety Data Sheets Material Safety Data Sheets MSDSs Some of the chemicals that may be used with your system are listed as hazardous by their manufacturer When hazards exist they are prominently displayed on the labels of all chemicals In addition MSDSs supplied by the chemical manufacturer provide information about Physical characteristics Safety precautions Health hazards First aid Spill clean up Disposal procedures This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Safety and Compliance Information WARNING CHEMICAL HAZARD Familiarize yourself with the MSDSs before using reagents or solvents AVERTISSEMENT RISQUE CHIMIQUE II convient de se familiariser avec
147. ed Writing Data Directly Over the Data Bus Writing Data Directly Over the Data Bus Before you write data to any component make sure you have appropriately connected or disconnected the high voltage lines and connected meter probes or voltmeters to the appropriate DACs WARNING ELECTRICAL SHOCK HAZARD Safe operating procedures and proper use of equipment are the responsibility of the authorized and qualified service person Precautions must be taken to protect against possible serious and or fatal bodily injury To write data directly to a component 1 Select the component you want to write to from the Address dropdown menu Figure D 2 Address MEE 3 Beam Guide DAC a 4 Control Register 5 LMG Delay 6 DE Delay 7 TIS Dela m Figure D 2 Direct Bus Access Address Menu 2 Select the format of the data Figure D 3 by clicking the appropriate button under Format gi Data Value oo C Binay C Decimal Figure D 3 Direct Bus Access Format Menu Note When writing to the Control Register it s often easier to enter a decimal or hexadecimal value initially then switch to binary format to set or clear specific bits This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Appendix D Isolating Components Using Direct Bus Access D 4 3 Enter a 16 bit data value in the Data Value field The value you e
148. ed Copying Permitted For newer Voyager DE STR workstations the Dell computer is shipped from the factory with Voyager DE STR Workstation Supporting Systems Microsoft Windows NT 4 0 Voyager software includes Voyager version 5 0 and later Instrument Control Panel and Sequence Control Panel and Data Explorer version 3 4 and later software Microsoft Office 2000 Small Office Suite NT Service Pack 5 Internet Explorer Software Features Voyager version 5 0 and later software includes Voyager Instrument Control Panel Controls the mass spectrometer for calibration and data acquisition Voyager Sequence Control Panel Works with the Instrument Control Panel and Data Explorer Allows you to acquire and process data automatically You can acquire multiple samples using the same or different instrument settings BIC files Data Explorer Software Allows post processing analysis of mass spectral data Replaces the GRAMS software Instrument Hardware Controller IHC For instruments running Voyager software versions 5 0 and later runs in the background to record errors in the NT event log Interfaces with instrument control and data acquisition software In manual mode you start the computer then manually launch the IHC from the Windows NT control panel In automatic mode the IHC launches when you start the computer Voyager Diagnostics Software Provides diagnostic system status and manual operation of Voyage
149. ed as a Class laser Under certain conditions during servicing when interlocks have been circumvented the lasers fall into the following categories and can cause permanent eye damage Nitrogen Class IIIb Nd YAG Class IV The Voyager DE Biospectrometry Workstation complies with Title 21 U S Government DHEW BRH Performance Standards Chapter 1 Subchapter J Section 1040 as applicable Laser Safety Features The following safety features are included on the Voyager DE Biospectrometry Workstation Cabinet is designed to prevent access to collateral laser radiation exceeding the accessible emission limits in Performance Standards for Laser Products 21 CFR 1040 10 Top front back and side panels have interlock switches that disable the laser when panels are opened or removed Safety labels for Class standards are affixed to the unit Laser Safety Requirements To ensure safe laser operation note the following The system must be installed and maintained by an Applied Biosystems Technical Representative Top front back and side panels must be installed during instrument operation When front and side panels are installed there should be no detectable radiation present If front or side panels are removed when the laser is operational you may be exposed to laser emissions in excess of Class 1 rating Do not remove labels or disable safety interlocks Additional Safety Information Refer to the user manua
150. eet fee ber e pct ene aaa eataa 5 24 5 3 3 Stepper Motor Feedthroughs sessssssssseeneee eene nenne 5 26 5 3 4 Sample Plate and Grid Voltage cceceeeeeeeeeeeceeeeeaeeeaeeeeeeeeeeeeeeeeeaeeaeaaaes 5 30 5 3 5 Internal High Voltage Cable o eccecceeececeeee cee ceca eeeeeteeeeeeeeeeeeeeeseeaeaaaaaaaeees 5 30 5 3 6 Operation Mode ss 5 31 5 9 7 Delayed Extraction lon Source ssssssssseeeeeneen enne 5 32 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Table of Contents 5 3 8 Source Grid and Mirror Voltages cceceececcccceseeececeeaeeeeeeeeeaaeeeeeeeaaaaaeeees 5 33 5 3 9 Delayed Extraction Low Mass Gate and Timed lon Selector Delay Times 5 35 5 3 10 DE Switch Box Control sien 21 2 tre eint rte pene a iege e haee 5 36 5 4 jLaser System oscura che ve A ted ene Pr Dos ecu e addo rv e vds 5 38 5 4 1 Laser Firing Repetition Rate and Re initialization sssesessss 5 38 5 4 2 Laser Atte nuatlom eat ERE GENUINE 5 40 5 5 Flight Tube and Mirror Chamber ssssssssssseeneneemenmenenenn nn nnn nnne tenens 5 42 5 5 1 Timed lon Selector uie nie etn ea Re onere Prodi ter hare reda o eque 5 42 5 5 2 Flight Tube Drift tube Power Supply eeeesesemm 5 43 5 6 Computer and Video Systems 5 43 57 Vac UM Systemes uie ptt na he a e E teo HERO reb tee et oet ea
151. eject cycle the diagnostics software Turns off the ion vacuum gauges Stops the operation Displays a message describing the fault and asks whether you want to restart the gauges if they are off Pauses waiting for the timeout period specified in the Registry to expire Depending on your input the software either aborts or completes the operation A vacuum fault occurs when the sensors detect pressure greater than the pressure specified for operation e Over pressure Pressures gt 8 x 107 sample loading chamber gt 9 x 1075 main source chamber Persistent Over pressure Over pressure that persists longer than a Registry specified timeout period typically 120 seconds Shuts down the ion gauges e Stability fault Over pressure that far exceeds the limit Shuts down the ion gauges 5 15 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 5 Troubleshooting by Components COMM fault Failure by the diagnostics software to communicate with the ion gauges Generates a warning you can override Init fault Failure by the diagnostics software to initialize the ion gauges Generates a warning you can override Faulty valves and gauges and leaky seals and pumps are potential sources of vacuum faults When the instrument is operating at atmosphere you can force the diagnostics software to ignore all vacuum gauge faul
152. enable signal to the two 15 bit counters Registers There are three registers in the circuit Start pulse register Loaded off the data bus with a 15 bit value that determines the start of the delayed output pulse Along with the end pulse register this register determines the pulse delay and the pulse width End pulse register Loaded off the data bus with a 15 bit value that determines the end of the delayed output pulse Along with the start pulse register this register determines the pulse delay and the pulse width Configuration register Loaded off the data bus with a 16 bit value whose bits control logic functions and relays such as Timed lon Selector high voltage enable and control DE box relays and pulse generator enables Counters There are two 15 bit down counters loaded from the start and end count registers These counters are pre loaded at the same time the start and end count registers are loaded When an enable signal is received from the Trigger buffer the counters start counting down from their preset values When the start and end counters reach zero the following occurs Start counter A latch is set high as the start of the delayed pulse End counter tThe latch is reset low as the end of the delayed pulse The rest of the circuit is also reset and waits for the next input trigger Address Decoder The address decoder decodes the address lines and the load control line then loads the correct
153. er Motor Feedthroughs Section 6 1 2 Sample Loading and Main Source Chamber Flap Doors 1 and 2 Close open observe status Mechanical Section 5 1 Troubleshooting Overview Section 5 7 1 Vacuum Gauges and Pumps Section 6 1 2 Sample Loading and Main Source Chamber Section 6 1 5 Vacuum System Foreline Valve 1 and 2 Close open Mechanical Section 5 2 2 Internal Interlocks Operation Section 5 2 5 Load Eject Cycles Section 5 2 7 Mechanical Control Page Errors and Warnings Section 6 1 5 Vacuum System Grabber Turn grabber off on Mechanical Section 5 2 2 Internal Interlocks Operation Section 5 2 4 Grabber Linear Actuators and Valves Section 5 2 5 Load Eject Cycles Section 5 3 2 Source Pedestal Section 5 3 5 Internal High Voltage Cable Section 6 1 2 Sample Loading and Main Source Chamber 5 3 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components Table 5 1 Matching Components with Control Page and Troubleshooting Information Component or Task Control Page Troubleshooting Section Parameter Grid DAC Set output voltage Section 5 3 8 Source Grid and Mirror Direct Bus Access Voltages Section 5 3 10 DE Switch Box Control Grid Voltage Set values Voltages Delays Section 5 3 8 Sour
154. esired Position spin controls to set the x y coordinates of the new Load position 4 Click MovetoDesied to move the sample stage to the new Load position specified in Desired Position The value in Current Position changes to match the value in Desired Position 5 Repeat step 3 and step 4 until moving the sample stage to Desired Position trips the microswitches and turns on the air compressor If you are unable to set a Load position that trips the microswitches you may need to adjust and reset the microswitches For details see Adjusting the Microswitches on page 28 6 Click SET Load Position to reset the Load position of the sample stage to the location specified in Current Position The new values display in the Load Position field Viewing the Troubleshooting Flowchart The flowchart in Figure 5 9 on page 5 22 outlines a preliminary troubleshooting routine to use if you do not see peaks when acquiring a standard sample Review the following warnings before performing troubleshooting WARNING ELECTRICAL SHOCK HAZARD Potentials in the order of 30 000 V dc are present Safe operating procedures and proper use of equipment are the responsibility of the authorized and qualified service person Precautions must be taken to protect against possible serious and or fatal bodily injury WARNING ELECTRICAL SHOCK AND LASER HAZARD Exposure to direct or reflected laser light can burn the retina and leav
155. essure Vacuum Pump Sample loading chamber Lower than atmospheric pressure 3 x 10 torr TC2 Fore pump Main source chamber High vacuum lt 5 x 1077 torr BA1 Turbo pump 1 Mirror chamber analyzer High vacuum lt 5 x 1078 torr BA2 Turbo pump 2 The fore pump or roughing pump creates a lower than atmospheric pressure condition before the turbo pumps start and provides backing pressure to the turbo pumps The fore pump can reduce pressures down to the 10 torr range Valves and Flap Doors Vacuum is maintained in the main source chamber and sample loading chamber by valves and flap doors that isolate the chambers Vacuum differential between the main source and mirror chambers is maintained by a differential pumping baffle Gauges Two types of gauges monitor vacuum pressures one thermocouple TC2 gauge and two ion gauges Bayard Alpert gauges BA1 and BA2 To monitor these gauges you use a multigauge controller See Section 5 7 2 Multigauge Controller The following table summarizes the gauges and corresponding measurement ranges This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Vacuum System Gauge Type Gauge Range Gauge Name Comment Thermocouple Gauge Atmospheric pressure TC2 On initial pumpdown 7 6 x 10 torr to the turbo pumps start 1 x 107 torr 2 minu
156. f Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 5 Troubleshooting by Components The Voyager baud rate is factory set and is displayed on the multigauge controller as 9 6 kBaud Verifying and Resetting the Baud Rate Occasionally the Voyager software displays a Vacuum Gauge Communication Failure error message upon initialization This error can occur if the baud rate is set correctly in the multigauge controller but is set incorrectly in the Voyager external computer registry Verify that the baud rate setting on the multigauge controller is 9 6 kBaud If the multigauge controller baud rate is correct verify the Voyager computer registry baud rate To verify the baud rate on the multigauge controller press Function kBaud A blinking number is displayed If necessary you can change the number to 9 6 by pressing the arrow keys To enter and apply the number press the Function key Press the Function key again to return to the pressure display Accessing the Voyager Computer Hegistry Keys You can verify and reset baud rate and other Voyager registry keys To access the registry keys Onthe Voyager computer desktop select Start then Run Inthe run dialog box type regedt32 or select regedt32 from the drop down list Click OK The Registry Editor is displayed Verifying and Resetting Baud Rate in the Voyager Registry Verify the Voyager computer registry baud rate as follows 1 Acces
157. ff On V725059 DE Positive N A Off Off Off DE Negative N A On On Off Continuous Positive N A On Off On Continuous Negative N A On Off On This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics 2 3 3 Einzel Lens Electronics Voltage Divider Box 4317251 Overview This assembly is a resistive tap off the source power supply that provides 50 of the source voltage to the einzel lens The Voltage Divider box is mounted on the side of the DE switch box enclosure Figure 2 26 Voltage divider box DE not visible along di side the DE switch box PB100853 Figure 2 26 Voltage Divider Box Location Voyager DE STR Left Cabinet Rear View Theory The Voltage Divider box consists of an epoxy potted plastic or metal box with two series 500 Mohm resistors The one end top of the resistors is connected to two HVPS high voltage power supply type Alden connectors The other end bottom of the resistors is tied to the Voltage Divider Box ground lug The Voltage Divider Box ground is tied to the instrument frame ground through a braided cable WARNING ELECTRICAL SHOCK HAZARD Severe electrical shock can occur if the Voltage Divider box ground lug is not grounded to the instrument frame The ground lug carries high voltage unless grounded Failure to proper
158. firmware to line driver U6 and out SMA connector J6 TP26 DE and Timed lon pulse generators The 15 bit pulse generators are firmware based and are functionally identical to the stand alone pulse generator described in Section 2 4 4 Pulse Generator PCA V750063 The DE pulse generator provides triggers to the DE switch box Digitizer Low Mass Gate delay timer Timed lon selector Pulse generator The Timed lon pulse generator provides a trigger to the Timed lon Selector TIS Assembly V700471 Discrete 1 0 Input Input for the consolidated control board from the instrument consists of 8 bits that reflect the state of the linear actuators flap valves and load position of the sample stage Inputs specify the following conditions Linear 1 actuator extended Linear 1 actuator retracted Linear 2 actuator retracted Flap Door 1 open Flap Door 1 closed Flap Door 2 closed Load Position Interlock Status You can view the state of these signals using the MALDI consolidated control board LEDs D6 and D11 2 50 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments Output Discrete outputs from the computer via the MALDI consolidated control board are interlocked through the firmware buffered and then sent to drivers that drive the relays and solenoids Output are to the F
159. he grabber during the grabber switches sample plate loading properly From a low 5 V logic state when the grabber is off to a high 5 V logic state when energized If the voltage is not switching properly check for continuity through grabber coils B The Y load coordinate is With the source open adjust misaligned the alignment of the Y coordinate by varying the Y load coordinate value in the diagnostics software Use a mirror and a small light to verify distance from edge of sample plate to inside edges of source not to source clips 6 4 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Troubleshooting Tables Table 6 2 Source and Sample Loading Chamber Troubleshooting Continued Item Symptom Possible Cause Action Sample plate either occasionally or consistently falls off the grabber during sample plate loading continued C Source pedestal is not rotationally aligned with the grabber Place a known good plate in the source When extending the grabber check that both poles of the grabber touch the sample plate simultaneously If not adjust alignment For information see Aligning the Source Pedestal on page 5 24 D Source side clips have damaged leading ends or Sample plate s have damaged edges Check the clip edges for denting dimpling and other damage Smooth the edges with a s
160. hed 24 V polarity DB25 Receptacle switching LMG enable vacuum gauge to workstation right hand drawer electronic controls J26 Linear flap load position sensors 16 position Mini Fit J27 Turbo controllers DB15 Receptacle 2 52 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments Table 2 17 MALDI Control Board Connectors Resistors and Test Points Continued Item Name Function Type Connectors J28 Laser control from stepper motor PCBA 8 position Mini Fit continued J29 To I O Internal laser attenuator 8 position Mini Fit J30 To external laser attenuator 12 position Mini Fit J31 Internal laser interlock 2 position Mini Fit J32 Interlock switches 2 position Mini Fit J34 Power in 5 24 415 15 V 12 position Mini Fit JU1 Analog Digital ground normally open 2 position 0 1 inch header JU2 Legacy trigger frequency normally 2 position 0 1 inch header jumped JUS Auto Manual laser type select normally 3 position Mini Fit 1 2 JU4 Stepper PCB 5 V select normally 1 2 3 position Mini Fit JU5 Stepper PCB ground select normally 1 2 3 position Mini Fit JU6 3 3 5 0 V select U46 normally 2 3 3 position Mini Fit JU7 10 Open not used 2 position Mini Fit Pots R24 DAC 5 V reference monitor at TP9 Potentiometer R
161. his First conditions in Table 5 2 Internal Interlock Hazard Control on page 3 9 Extending and Retracting Linear Actuators To extend or retract a linear actuator click the Retract or Extend radio button of the particular actuator Observe the perquisites listed in Table 5 2 Internal Interlock Hazard Control on page 5 9 The check boxes under Limit Switches indicate when the linear actuators have fully retracted or extended Powering the Grabber On and Off To turn the magnetic grabber Figure 5 4 on or off click the ON or OFF radio button Remember that The magnetic grabber is connected to the end of the Linear 1 actuator The grabber attaches to the handle end of the sample plate to transport it into and out of the main source chamber If the sample plate is inserted backward the grabber has no suitable surface to magnetize and cannot eject the plate Under normal operating conditions the grabber powers on just before the Linear 1 actuator starts to extend or retract if ejecting and it powers off just after the Linear 1 actuator has fully retracted fthe Linear 1 actuator is extended the grabber remains powered on and the sample stage is in any position other than Load 5 12 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Sample Loading Chamber Grabber o voltage 4 0 5 0 V Sample stage
162. iagram of TIS Function The TIS is controlled by the same type of high frequency counter as the delayed extraction DE function Switches and jumpers on the Pulse Generator board determine the mode of operation DE or TIS For information see Section 2 4 2 Pulse Generator Board V750063 1 3 5 Mirror Chamber Overview The Voyager DE STR workstation offers two flight path modes of operation Linear and Reflector The mirror chamber houses the linear detector reflector and reflector detector The detectors measure ion abundance over time and send an analog signal to the digitizer for conversion to mass spectra see Section 1 3 6 Digitizer The detector may consist of a single multichannel plate or dual multichannel plates Low Mass Gate Function The low mass gate function screens out low mass ions Low mass ions from the matrix are not of interest yet they can be produced in quantities large enough to overload the detector The Low Mass Gate delays application of full high voltage to the detector microchannel plate until after the matrix ions pass The microchannel plates have an inherent gain recovery time and the delay of full high voltage preserves the gain until a region of interest When the full high voltage to the detector is delayed ions strike the detector but generate only a weak signal Linear Mode In Linear mode the ion beam travels approximately 2 meters down the flight tube directly to the linear detector The shorter
163. igh current 1 17 within mirror chamber 1 16 5 31 Linear mode allowing high voltage supply to discharge 5 34 beam path 1 16 compared to reflector mode 5 31 delay when changing from reflector mode 5 34 detector 1 17 length of beam path 1 16 mirror voltage and Timed lon Selector delay time invalid 5 31 sensitivity relative to other modes 1 16 when to use 1 16 Linear 1 actuator and grabber 5 12 Load and eject cycles 5 13 aborting 5 15 backtracking toa safe state 5 15 conditions to avoid 5 15 continuing despite gauge errors and high pressures 5 15 determining current operation 5 14 diagnosing using Mechanical control page 5 11 ending before cycle completes 5 15 initiating 5 14 initiating multiple 5 14 monitoring 5 14 multiple iterations 5 11 order of operations 5 14 overriding vacuum faults 5 15 running using Mechanical control page 5 11 single iteration 5 11 status display 5 14 stop prematurely 5 15 dui P Load and Latch signals 2 9 Load position see Microswitch see Sample stage not reached although compressor energized 5 29 Low Mass Gate delay time clock cycle 5 35 enabling using diagnostics software 5 33 function 1 16 setting delay time D 9 setting start delay time 5 33 timing signal 1 14 Low Mass Gate Delay Timer board connectors 2 18 diodes 2 19 Drivers 2 17 drivers 2 17 functions 2 15 headers 2 18 input output signals 2 18 jumpers 2 18 location 2 15 overview 2 15 regulators
164. information within the chapter The table below describes the material covered in each chapter and appendix Chapter Contents Chapter 1 System Overview Describes the parts of the system and software Chapter 2 Voyager DE STR Describes the function theory and specifications for each Workstation Electronics Theory Voyager workstation circuit board Also includes tables of connectors switches and test points Chapter 3 Before Servicing the Provides laser safety information procedures for venting and Workstation powering up after venting Chapter 4 Voyager Diagnostics Introduces the Voyager 32 Bit Diagnostic Software for Software Windows NT platform Chapter 5 Troubleshooting by Includes step by step procedures for troubleshooting and Components using the Diagnostics software for selected components Chapter 6 Troubleshooting by Provides symptoms error codes possible causes and Symptoms corrective actions Appendix A Technical Support and Describes how to contact Technical Support Also includes Training how to obtain technical documents and customer training Appendix B Assembly Drawings Shows the locations of many components Provides detailed drawings of some components Appendix C Electronic Drawings Electronic interconnect diagrams and circuit board drawings Appendix D Isolating Components Describes how to write data directly to the bus through the Using Direct Bus Access Diagnostics
165. ing Direct Bus Access This appendix contains the following Diagnostics Software Direct Bus Access Control Page D 2 Writing Data Directly Over the Data Bus D 3 Data Values for Direct Access D 5 Setting the Low Mass Gate Delay Time D 9 Setting and Disabling Delayed Extraction D 10 Setting the Timed Ion Selector D 1 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Appendix D Isolating Components Using Direct Bus Access Diagnostics Software Direct Bus Access Control Page Use the Direct Bus Access control page Figure D 1 to write data directly to selected components over the data bus Use this method if you do not want to use the individual component control page Laser Voltages and Delays and DE Switch Box Camera Mechanical Laser Voltages Delays xY Table DE Switch Bo m Multiplex Data Bus Control Data Value Joooo Address TETE Binary C Decimal Write Figure D 1 Direct Bus Access Control Page You cannot enable high voltage or the Low Mass Gate using direct bus access With direct bus access you can only set the output voltage at the DACs and the Low Mass Gate value m This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitt
166. ion on page 20 Reset the Extend Orifice valve to allow for the proper extension speed of the grabber The usual adjustment range is 11 2 to 217 turns counterclockwise from fully closed fully clockwise position 5 25 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 5 Troubleshooting by Components 5 3 3 Stepper Motor Feedthroughs The stepper motor feedthroughs provide detection of the Home and load positions Figure 5 14 Figure 5 15 on page 4 27 shows the feedthrough interconnects PB100862 Load Position Home Position Figure 5 14 Stepper Motor Feedthroughs in Load and Home Positions 5 26 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted AC distribution board Compressor Y feedthrough X feedthrough XY Laser Main Source Chamber Compressor Stepper 48 Bit Computer relay motor board I O card rear view 95 2928 Be aoa microswitch p stepper motor control ca
167. ke effect To do so click APPLY ALL Ramp Voltages Set Delays If you leave the Voltage and Delays control page without applying the changes you will lose the changes The values revert to the last applied settings If you set and apply voltage for the source grid mirror or guide wire without enabling high voltage the diagnostics software programs only the corresponding DACs You can verify these output voltages with a voltmeter DAC voltages are shown in Table D 2 Voltage Values on page D 8 To detect output voltages at the test points of the corresponding components you must also enable and apply high voltage By pressing APPLY ALL Ramp Voltages Set Delays you set the delays specified for Delayed Extraction Low Mass Gate and Timed lon Selector only when you have also enabled them It does not affect delays associated with ramping component voltages The status field Figure 5 20 tracks the state of the voltages Status Finished Ramping And Resetting Delays Figure 5 20 Voltages Status Display 5 33 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components Setting the Voltages The voltage options provide complete control of the high voltage components You can Enable disable high voltage for all components the DACs control Set the voltage polarity Ramp each DAC to a specified vo
168. l provided with the laser for additional information on government and industry safety regulations xiv This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Safety and Compliance Information Required Customer Provided YAG Laser Safety Measures Before servicing a system using the YAG laser the customer is required to provide safety precautions The YAG accessory supplied with the Voyager DE STR is a class laser which is considered not capable of producing damaging radiation levels during operation When maintenance requires an Applied Biosystems field service engineer to defeat the interlocks protection system for the instrument the YAG laser is classified as a class IV laser A class IV laser poses hazards to the eye and skin not only from the direct beam but in some cases also from the diffuse reflection These lasers can be considered a fire hazard and may also produce laser generated air contaminants and hazardous plasma radiation Therefore before you can perform maintenance or service on the YAG Laser while at the customer facility the customer must Provide the appropriate Laser Warning Signs These signs shall be conspicuously displayed in a location where they will best serve to warn any and all onlookers Provide the appropriate safety glasses goggles to their employees if they are in the area while the laser is being serviced The safety gl
169. l signal input has an on board 50 ohm termination When the TTL input gate signal is high the positive and negative 950 V outputs are both switched to ground zero volts The gate input logic is coupled by a torroidal transformer to totem pole FET output switches Each polarity has AFET for rapid pull down to ground AFET for rapid pull up to voltage Series termination resistors that serve as convenient points for attaching an oscilloscope probe to observe dynamic operation 2 28 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Common in Most Voyager DE STR Instruments Specifications Specifications are summarized in the following table Item Comment Input power 24 V dc at approximately 200 mA Gate Pulse TTL gate pulse input impedance 50 ohms resistive Output J3 0 to 1000 V dc J4 0 to 1000 V dc Normal operation is at 950 V dc The TIS gates draw no current other than the instantaneous current required to switch a capacitive load Output short circuit protection is provided on the PCA 2 29 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Connectors Table 2 6 Connectors on the TIS Board Name Function Type P1 02 5 V de return ground DB1
170. l to the source pulse level The rise time of the HV pulse is typically 50 ns A Tektronix P6015A HV probe connected to a special HV Y adapter cable is required to view these waveforms 2 41 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Specifications Power Table 2 10 Low Voltage Power Requirements Switch Assembly 5 V dc Requirements 24 V dc Requirements V725125 None 100 mA to 700 mA V725115 400 mA 0 mA to 600 mA V725059 400 mA 0 mA to 600 mA Table 2 11 High Voltage Power Requirements Supply Voltage Current Source power supply 0 to 30 kV or 0 to 30 kV 0 to 400 pA Grid power supply 0 to 30 kV or 0 to 30 kV O to 400 pA Input Input impedance expects TTL level pulse generator capable of driving a 50 ohms load Output Maximum source pulse level of 30 kV Grid rest level must be at least 67 of source level Connectors Table 2 12 Connectors on the V750074 Board Within the DE Switch Box Name Function Type J1 Low voltage power input relay control Amphenol 206486 1 input and TTL pulse input J2 Source HV power supply input Alden B102 J3 Grid feedthrough Grid HV potential Alden B102 J4 Source feedthrough Source HV pulse Alden B102 output J6 Grid HV power supply input Alden B102 This Document Contains CONF
171. l trigger 1 13 high voltage testing 5 30 5 31 Calculating DAC board grid expected output voltage 5 32 calculating DAC board source expected output voltage 5 32 Calibrating load position thermocouple TC2 gauge 5 52 Camera control page 5 11 5 43 see also Diagnostics software 4 6 function 4 6 Certificates of analysis obtaining A 10 CHAN 5 45 CHAN multigauge controller key 5 46 calibrating TC2 using 5 52 Check Control Wiring Test see DE switch box control page CID 1 3 Circuit board connectors 48 bit I O 2 46 beam steering 2 35 DAC 2 10 DC distribution 2 12 flight tube 2 62 Pulse Generator PCA 2 65 Timed lon Selector 2 30 TTL Output Opto trigger 2 31 voltage divider box einzel lens 2 45 Circuit boards 2 2 48 bit I O 2 46 AC Distribution 2 5 5 beam steering 2 33 47 ND C1 Control board 2 47 DAC 2 9 DC Distribution board 2 11 flight tube power supply 2 61 in earlier Voyagers 2 59 in most Voyagers 2 4 in newer Voyagers 2 33 Low Mass Gate Delay Timer 2 15 MALDI control 2 47 pulse generator 2 63 Timed lon Selector 2 26 continued Circuit boards continued TTL output opto trigger 2 31 voltage divider box einzel lens 2 45 Collision cell description 1 9 Com Port 2 settings parity 5 50 5 51 resetting 5 50 verifying 5 48 5 50 COMM fault 5 16 Communication failure diagnostics software and ion gauge 5 16 overriding COMM fault 5 16 Compressor relay and diodes 2 6 Computer system 1
172. la MSDS feuille de donn es concernant la s curit des mat riaux avant d utiliser des r actifs ou des solvants General Warnings WARNING FIRE HAZARD Using a fuse of the wrong type or rating can cause a fire Replace fuses with those of the same type and rating AVERTISSEMENT DANGER D INCENDIE L usage d un fusible de type ou de valeur nominale diff rents risque de provoquer un incendie Il convient donc de remplacer les fusibles usag s par des fusibles du m me type et de la m me valeur nominale WARNING LASER HAZARD The laser emits ultraviolet radiation Lasers can burn the retina and leave permanent blind spots Do not remove instrument front or side panels or look directly into the laser beam or allow a reflection of the beam to enter your eyes Wear proper eye protection if front or side panels are removed for service AVERTISSEMENT DANGER LASER Le laser met des radiations ultraviolettes Les lasers peuvent br ler la r tine et laisser des points aveugles permanents ll convient de ne pas retirer le panneau avant ou les panneaux lat raux de l appareil et de ne pas regarder directement dans le faisceau laser ou laisser une r flexion du faisceau entrer dans les yeux Portez des protections ad quates pour les yeux si le panneau avant ou les panneaux lat raux ont t retir s afin d effectuer l entretien Xi This Document Contains CONFIDENTIAL Material
173. le signal Data and address lines from the Voyager bus 24Vor 12 V The output signals from the pulse generator consist of A delayed pulse to the low mass gate packs Power connections to the low mass gate packs Power connection to the flight tube drift tube power supply Connectors Headers Jumpers Test Points and Switches Table 2 5 Connectors Headers Jumpers Test Points and Switches on the Low Mass Gate Timer PCA V750073 later models only Item Name Function Type Connectors J1 Voyager bus 34 position dual row header J2 DE pulse in pwr out not normally used 3 position 0 1 inch header J3 12 V power in 4 position 0 1 inch header V750069 earlier models only J4 DE pulse in not normally used 3 position 0 1 inch header J5 Delayed pulse to Linear Low Mass Gate 5 position 0 1 inch header PCA J6 Delayed pulse to Reflector Low Mass Gate 5 position 0 1 inch header PCA J7 Enable in from control board 4 position 0 1 inch header J8 DE pulse in BNC J9 Flight tube drift tube power out 2 position Mini Fit J10 24 V power in 4 position Mini Fit J11 Programming header 10 position dual row header 2 18 continued This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Common in Most Voyager DE STR Instruments Table 2 5 Connectors Headers Jumpers Tes
174. led in various sections in Chapter 5 Troubleshooting by Components The procedures in Chapter 5 Troubleshooting by Components The tables in Chapter 6 Troubleshooting by Symptoms These methods are complimentary For example you may view the Diagnostic software control pages to determine which component is experiencing a problem then turn to the appropriate section in Chapter 5 Troubleshooting by Components In other cases you may look up a symptom in Chapter 6 Troubleshooting by Symptoms and use the diagnostics software to verify or correct the problem referring to Chapter 5 Troubleshooting by Components for information on the appropriate control pages for servicing a specific component To find the control page and troubleshooting sections applicable to a specific workstation component refer to Table 5 1 Table 5 1 Matching Components with Control Page and Troubleshooting Information Component or p Task Control Page Troubleshooting Section Parameter BA1 BA2 TC2 Observe status Section 5 2 6 Vacuum Faults Diagnostics Software Window Section 5 7 1 Vacuum Gauges and Status bar Pumps BA1 Srce Pres Section 5 7 2 Multigauge Controller BA2 Mir Pres Section 6 1 5 Vacuum System TC2 Smp Pr Section 6 2 Multigauge Controller PAMP ie Common Error Codes Beam Set laser attenuation Laser Section 5 4 1 Laser Firing Repetition attenuation Rate and Reinitialization Section 5
175. lied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics 2 32 This page intentionally left blank This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments 2 3 Electronics Only in Newer Model Instruments Instruments with serial numbers 4154 and later have the following electronics Beam steering V750091 DE switch box V725115 3 Hz V725125 15 Hz Einzel lens voltage divider box 4317251 e 48 bit I O board V750033 e MALDI control board V750082 and V750102 001 STR V750102 002 DE PRO V750102 003 Voyager DE Figure 2 20 shows the housing of these electronics DE switch box Beam steering Computer 48 bit I O Einzel lens MALDI control board PB100427 Left cabinet Right cabinet Figure 2 20 Housing of Electronics Only in Earlier Model Instruments 2 3 1 Beam Steering Board V750091 Overview Instruments with serial numbers 4154 and later have beam steering plates and an einzel lens to focus and direct the beam of ions There are two horizontal and two vertical beam steering plates This combination of X Y deflection plates and an adjustable 500 V power supply allows fine tuning of the ion trajectory Earlier instr
176. ltage Enable and set specific delays for voltages applied to Delayed Extraction the Low Mass Gate and the Timed lon Selector Turning the High Voltages On and Off To power the high voltages on or off click the Off or On radio button next to HV Enable and click apply If you set DAC voltages without enabling HV only the corresponding DACs output voltages are detectable with a voltmeter DAC voltages are shown in Table D 2 Voltage Values on page D 8 Enabling disabling HV turns high voltage on and off for all HV components source grid mirror and guide wire Setting the Voltage Polarity To set the voltage polarity click the Positive or Negative radio button next to Polarity and click apply Positive polarity is the instrument default setting The polarity setting determines which ions or are repelled from the sample plate and accelerated down the flight tube Ramping the DAC Voltages To set DAC voltages under Desired increase or decrease the appropriate spin button or enter a value in the appropriate field Source 0 to 20 kV range For the STR usually set to 20 000 0 V The source voltage defaults to 20000 0 when the Voltage and Delays control page opens Changing this voltage automatically changes the voltage of the beam steering plates and the Einzel lens which receives approximately 5096 of the source voltage You must set and apply the source and grid voltages at the same time Grid
177. ly ground the ground lug can also damage the einzel lens The middle 5096 of the resistors is brought out to another HVPS type Alden connector The two connectors at the top of the Voltage Divider Box Figure 2 27 on page 2 45 allow you to connect the source HVPS to the Voltage Divider Box and also to the DE switch box The connector on the bottom of the box provides a connection to the einzel lens 2 44 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments Connectors From source HVPS To DE switch box source Ground lug 500 Mohm 500 Mohm 1 ee To einzel lens Connector Figure 2 27 Voltage Divider Box Connectors Connectors Function Type Source HVPS Alden HV 40 kV DE switchbox source PS Alden HV 40 kV Einzel lens Alden HV 40 kV Ground lug 10 32 and hardware 2 45 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics 2 3 4 48 Bit I O Board with Game Port V750033 Overview This I O board has a dual function tinterfaces the input and output control signals between the computer and the other system components e tinterfaces pro
178. mall flat file and MicroFinish cloth Replace if necessary If no clip replacements are available reverse the clips For information see Source Clips on page 5 23 Also check the sample plates Smooth the edges with a small file and MicroFinish cloth or replace them as appropriate Sample plate cannot be pushed fully onto the stage A Rear source clip is damaged Check the rear source clip for dimples or dents Smooth the edges with a small file and MicroFinish cloth If necessary replace the clip For information see Source Clips on page 5 23 Also check the sample plates Smooth the edges with a small file and MicroFinish cloth or replace them as appropriate continued This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 6 Troubleshooting by Symptoms Table 6 2 Source and Sample Loading Chamber Troubleshooting Continued Item Symptom Possible Cause Action During sample plate ejection the sample plate either occasionally or consistently cannot be pulled off the stage by the grabber A Grabber is not being energized With the grabber attached to circuit check that voltage to the grabber switches properly From a low 5 V logic state when the grabber is off to a high 5 V logic state when energized If the voltage is not switching properly check
179. me position at 0 0 Load Indicates the sample stage has reached the load region approximately 16000 counts for the X position 8000 counts for the Y position plus or minus 300 to 500 counts 5 19 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components microswitch Y feedthrough X feedthrough sample stage Load position sample stage X Y table Figure 5 8 Sample Stage and Feedthroughs You use the sample stage X and Y coordinate fields to adjust and reset the load position of the sample stage Current Indicates the current location in x y coordinates of the sample stage Load Indicates the current location in x y coordinates of load position Desired Specifies the desired location in x y coordinates to which to move the sample plate Units Although the stepper motors operate in step units Voyager software Version 5 0 and later use micron um units One step equals 3 175 um You can use either unit and switch back and forth between them The diagnostics software performs the necessary conversions automatically The micron unit of measure is used in the NT Registry editor NOTE The SET Load Position button on the X Y Table control page initiates a data write to the Registry file The next time it is accessed the Voyager Instrument Control Panel reads the new X Y coordi
180. mes 5 33 applying values 5 31 5 33 disabling delay time options 5 34 5 35 disabling high voltage 5 34 5 35 function 4 8 options for controlling voltage 5 34 ramp stage status 5 33 resetting DAC voltages 5 34 5 35 reverting to last applied settings 5 31 2 33 saving values 5 31 5 33 setting Linear or Reflector mode 5 31 values lost 5 31 5 33 verifying output values set 5 33 when to enable high voltages 5 33 Index 14 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager Diagnostics software see Diagnostics software Voyager electronics circuit board locations in earlier Voyagers 2 59 inmost Voyagers 2 4 in newer Voyagers 2 33 overview 2 2 see also circuit boards 2 1 Voyager Instrument Control Panel 1 21 Voyager registry path to vacuum monitor baud rate setting 5 48 path to vacuum monitor Com Port 2 setting registry key 5 50 path to vacuum monitor parity setting 5 51 resetting parity in 5 51 Voyager Sequence Control Panel 1 21 Voyager software compatible Diagnostics software versions 4 2 features 1 21 function 1 2 1 20 parity setting 5 50 platform 1 20 troubleshooting tables 6 9 Voyager DE STR Biospectrometry Workstation accessories 1 3 CID option 1 3 components overview 1 6 computer system 1 19 description 1 2 diagram 1 2 B 3 diagram of mass spectrometer components 1 6 5 18 GPMAW option 1 3 lase
181. n page 5 41 For the Nitrogen laser verify laser output is gt 200 uJ F Linear detector is Troubleshoot the linear defective detector This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Troubleshooting Tables Table 6 1 Spectral Troubleshooting Continued Item Symptom Possible Cause Action In linear mode flat signal on oscilloscope or Monitor window for matrix and sample region when in positive ion mode Same result when switched to reflector mode continued G Reflector detector is defective H Digitizer or one of its channels is deflective Troubleshoot the reflector detector Troubleshoot the digitizer Delayed Extraction Mode 2 Flat signal on oscilloscope or monitor window for matrix and sample region when in linear or reflective mode Peaks display when switched to continuous mode A Delayed extraction switch box is defective B Delayed extraction timer pulse generator board is defective Verify source voltage output is rising when the laser is firing Verify all DE switch box LEDs are unlit Check the 5 at connector on DE switch box Adjust Check control wiring Replace DE switch box Warning Before servicing the DE switch box disable high voltages Check for 5 2 V Replace DE timer pulse generator board Note In one version of
182. n C3 Devices Hivolt C3 Delayed Extraction Installed High Voltage Auto Shutdown Delay min High Voltage Auto Shutdown Enable High Voltage Polarity Switch Delay sec MALDI Instrument Type Max Source High Voltage Volts Timed lon Selector Delay Timed lon Selector Flight Length Timed lon Selector Gate Width Vacuum Monitor Mirror Chamber Vacuum Limit Tor Sample Chamber Load Cycle Vacuum Limit Tor Sample Chamber Nominal Vacuum Limit Torr C3 Sample Chamber Pump Down Time sec Source Chamber Pump Down Time sec Source Chamber Vacuum Limit Torr Vacuum Monitor Baud Rate Vacuum Monitor COMM Port Vacuum Monitor Parity Figure 5 32 Path to the Vacuum Monitor Baud Registry Setting 5 49 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 5 Troubleshooting by Components Verifying and Resetting Com Port Settings The multigauge controller communicates via the computer communications port 2 A Vacuum Gauge Communication Failure error occurs if the Voyager computer Com Port settings are incorrect Verify the Voyager software Com Port settings by selecting the following on the Voyager computer desktop 1 On the Voyager computer desktop select Start Settings Control Panel 2 Double click Ports then Com2 3 Check that the settings displayed match those in
183. n Eder eia tg 5 44 5 7 1 Vacuum Gauges and Pumps iii 5 44 5 7 2 Multigauge Controller sesssssssssssssseeene eene enne nenne 5 45 5 7 8 Multigauge Controller Computer and Workstation Interaction 5 47 Chapter 6 Troubleshooting by Symptoms 6 1 Troubleshooting lables rss ss EE te Eee e oe ES dee ELE Ee eua 6 2 6 1 1 Spectral Problems 5 25 hr dte Ad nee Me eee 6 2 6 1 2 Sample Loading and Main Source Chamber sss 6 4 6 1 3 Computer System and Software ssssssssssssssseeee 6 9 6 1 4 Power Supplies and Circuit Boards sessssssssseeeeneneee 6 10 6 1 5 Vacuum System iioc hte eh e E D a tte es 6 11 6 2 Multigauge Controller Common Error Codes 6 16 0 3 LED IndiCatorS occ ee ed Hee Et een AE E ke DN ERES 6 18 Appendix A Technical Support and Training A 1 Appendix B Assembly Drawings eee eeeeeeeee B 1 Appendix C Electronic Drawings eeeeeeeess C 1 Appendix D Isolating Components Using Direct Bus Access D 1 Index This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Table of Contents vi This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Safety and Compliance
184. n the DC Distribution PCA Board Continued ltem Name Function in Function in Type Single Power Supply Three Power Supplies LEDs LED1 15 V indicator 15 V indicator LED1 LED2 Not used 5 2 V indicator LED2 LED3 5 V indicator 5 V indicator LED3 LED4 15 V indicator 15 V indicator LED4 LED5 24 V indicator 24 V indicator LED5 LED6 Not used 12 V indicator LED6 2 14 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Common in Most Voyager DE STR Instruments 2 2 4 Low Mass Gate Delay Timer Board V750069 V750073 Overview The Low Mass Gate Delay Timer Detector Voltage Delay Timer DVDT PCA is used to delay application of full high voltage to the detector MCP microchannel plate until the matrix ions pass The microchannel plates have an inherent gain recovery time and the delay of full high voltage preserves the gain until a region of interest Low mass gate driver boxes negative positive Low mass gate delay timer board PB100851 Figure 2 9 Low Mass Gate Driver Boxes and Delay Timer Board Locations During instrument operation the board e Captures an input trigger Counts off a fixed delay then counts off a a pre programmed delay
185. na and leave permanent blind spots Never look directly into the laser beam Remove jewelry and other items that can reflect the beam into your eyes Wear laser safety goggles during laser alignment Protect others from exposure to the beam Post a laser warning sign while performing service 5 38 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Laser System Camera Mechanical CLaser Voltages Delays X Y Table DE Switch Box Direct Bus Access m Laser Control Laser Type Internal LOI Fire Laser Desired Repetition Rate 3 0 ie External 2 Re Initialize Attenuator Desired Current Limit Switch Position 50 0 joo Home Iv Apply Figure 5 25 Laser Control Page Firing the Laser To fire the laser 1 Select Laser Type by clicking the appropriate radio button 2 If you switched lasers in step 1 click Redni alze for details see Re initializing the Laser on page 40 3 Click software to set the attenuator at minimum intensity 096 and initialize the diagnostics 4 Setthe laser repetition rate and attenuator 96 as needed for details see Adjusting the Attenuator Position on page 41 You can adjust the laser repetition rate only if the system contains laser optimization components for details see Setting the Lase
186. nal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments MALDI Consolidated Control Board LEDs and Switches Table 2 18 MALDI Consolidated Control Board LEDs and Switches LED Switch Name Position Function LED D3 1 Laser opto trigger In 2 Timed lon Selector enable 3 TIS pulse Out 4 DE pulse Out 5 DE switch box Relay 1 On 6 DE switch box Relay 2 On 7 DE switch box Relay 3 On 8 DE switch box Relay 4 not used 9 Linear detector On 10 Internal N2 laser selected LED D6 1 12 V 2 24 V 3 15 V 4 15 V 5 5 V 6 Cover removed interlock open 7 Computer enabled 8 Negative ion mode 9 Mirror On 10 Low mass gate enable 2 55 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Table 2 18 MALDI Consolidated Control Board LEDs and Switches Continued LED Switch Name Position Function LED D11 1 Linear 1 actuator extended 2 Linear 1 actuator retracted 3 Linear 2 actuator retracted 4 Flap Door 1 open 5 Flap Door 1 closed 6 Flap Door 2 open 7 Flap Door 2 closed 8 Sample stage at load position 9 3 3 V 10 Mirror detector On LED D18 1 Linear 1 solenoid On 2 Linear 2 solenoid On 3 Flap Door 1 solenoid On 4 Flap Door 2 s
187. nates from the Registry file to determine the sample stage load position Resetting the Sample Stage Load Position You may need to reset the load position to Properly align the sample stage with the linear actuators When the sample stage is misaligned with the linear actuator in the load position the sample plate misses the sample stage during loading The sample plate may jam or fall inside the main source chamber To verify proper positioning of the sample stage vent the system to atmosphere and open the main source chamber For details see Section 3 2 Venting the Voyager DE STR Workstation Ensure that the sensor bobbins trip the Load position microswitches to turn on the air compressor Failure to trip these microswitches deprives the linear actuators and flap doors of adequate operating pressure 15 psi NOTE Record the old coordinates in case you need to revert to them When you click SET LoadPosition the diagnostics software overwrites the coordinates of the Load position in the system Registry file 5 20 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Main Source Chamber To reset the Load position 1 Click i to move the sample stage to the Home position at 0 0 and initialize the diagnosucs sortware 2 Click Movetoload to move the sample stage to the current Load position 3 Usethe scroll bars or the D
188. nd Central America 52 55 35 3610 52 55 66 2308 Brazil 0 800 704 9004 or 55 11 5070 9694 95 55 11 5070 9654 Argentina 800 666 0096 55 11 5070 9694 95 Chile 1230 020 9102 55 11 5070 9694 95 Uruguay 0004 055 654 55 11 5070 9694 95 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Through the Technical Support Web Site To contact Technical Support through the Applied Biosystems web site 1 Access the Applied Biosystems Technical Support web site at www appliedbiosystems com techsupp Under the Troubleshooting heading click Support Request Forms then select the support region for the product area of interest In the Personal Assistance form enter the requested information and your question then click Ask Us RIGHT NOW In the Customer Information form enter the requested information then click Ask Us RIGHT NOW Within 24 to 48 hours you will receive an e mail reply to your question from an Applied Biosystems technical expert Appendix A Obtaining Technical Documents Overview Ordering Documents by Telephone Obtaining Documents Through the Web Site A 10 You can obtain technical documents such as Applied Biosystems user documents MSDSs certificates of analysis and other related documents for free 24 hours a day You can obtain documents By telephone Through the Applie
189. nd later 4 Control Register high frequency counter and ion source pulser TIS frequency select DE and TIS counter enable TIS high voltage enable Power level NA DE mode enable Bits 0 2 Value is 000 10 ns 100 MHz Bit 3 Values are 0 disabled 1 enabled Bit 4 Values are 0 disabled 1 enabled Bit 5 Ignored for Voyager DE STR workstation Values for other models are 0 low 1 normal Bit 6 Not used Set to 0 Bit 7 Values are 0 disabled 1 enabled This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted D 5 Appendix D Isolating Components Using Direct Bus Access Table D 1 Direct Access Data Values continued Component Parameter Bit values 4 Control DE mode select Bits 8 10 Register Each bit represents a relay bit 8 relay 1 bit 9 relay 2 continued and bit 10 relay 3 Bit combinations set the DE switch box mode Values are 110 DE negative ion mode 101 Non DE mode positive and negative ion 000 DE positive ion mode NA Bits 11 14 Not used Set to 0 Low Mass Gate timer Bit 15 Determines whether the value is the timer start start end or end time 0 start 1 end 5 LMG delay Low Mass Gate delay Bits 0 7 represent 8 000 to 65 000 ns Values entered time represent the target delay time ns 8 ns 222 ns Values are Dec 0 to 255 Hex 00 to FF
190. nd of the regulator to the vent filter using a 3 8 O D clear PVC tubing and connect the other end of the regulator to the nitrogen drop line Preset pressure on the regulator to 5 psig Open the valve on the No gas tank Lift up the lever attached to the turbo vent valve allowing N to flow into the chamber slowly Close the turbo vent valve when the sound of flowing N has stopped completely Close the gas valve on the Np tank Disconnect the clear PVC tubing from the filter on the turbo venting valve This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 3 Before Servicing the Workstation 3 3 Powering Up After Venting Before powering up the Voyager workstation after venting 1 2 3 Close all open vent valves Reconnect and secure all vacuum connections Switch on the Voyager workstation main power Once the valves are closed vacuum connectors are secure and the Voyager workstation main power is on 1 5 On the AC distribution board connect plug in the fore pump to the J1 connector Figure 3 1 on page 3 4 Monitor the TC2 vacuum reading on the multigauge controller For information see Section 5 7 2 Multigauge Controller When the reading reaches below 3 x 107 torr reconnect the following cables to the AC distribution board Figure 3 1 on page 3 4 The source turbo controller J14 Th
191. ng Tables 6 1 3 Computer System and Software Table 6 3 Computer System and Software Troubleshooting Item Symptom Possible Cause Action Error message displays Waiting for laser trigger 4 5 Software A Laser is not firing Verify proper operation of laser See laser warnings below B Opto trigger board is faulty Replace trigger PCB C Digitizer trigger channel is defective Replace digitizer Acquisition Error Version 5 0 software A Laser is not firing Verify proper operation of laser See laser warnings below B Opto trigger board is faulty Replace opto trigger PCB C Digitizer trigger channel is defective Replace digitizer An error message appears during plate loading or ejection indicating that the source is not in the load position even though the compressor is energized A load position microswitch needs adjusting or replacing Adjust the load switch bracket closer to the feedthrough post Caution Moving the switch too close to the post will cause premature failure of the switch Replace the switch if necessary WARNING LASER HAZARD When instrument panels are removed high voltage contacts are exposed and the laser emits ultraviolet radiation Wear laser safety goggles when you remove panels for service WARNING LASER HAZARD Exposure to direct or reflected laser light can burn the retina and
192. ng alignment 5 13 troubleshooting E09 error when ejecting 6 13 troubleshooting E09 error when loading 6 13 voltage measuring 5 30 Sample plate holder 5 18 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Index 11 dui P Index Sample stage and air compressor 5 20 description 1 9 homing to initialize diagnostics software X Y table 4 9 5 19 keeping stationary when testing pneumatics 5 13 load position microswitch nottripping 5 21 load position recalibration 5 19 load position linear actuator and flap door interaction 5 20 not moving 5 13 sample plate misses during loading 5 20 selecting units steps microns 5 20 typical voltage applied 1 9 when to reset load position 5 20 writing load position to the NT Registry 5 20 X coordinate display 4 11 X coordinate scroll bar 5 19 Y coordinate display 4 11 Y coordinate scroll bar 5 19 Scintillator in linear detector 1 1 Sequencing kit 1 3 Source cannot reach position set 6 4 component grid 5 18 components of 5 18 DE switch box 5 18 Delayed Extraction 5 32 description 1 9 5 18 enabling voltage using diagnostics software 5 34 error message when loading or ejecting 6 9 grids in 5 30 power supply 5 18 sample plate holder 5 18 setting voltage using diagnostics software 5 33 troubleshooting 5 18 troubleshooting Delayed Extraction 5 32 troubleshooting flowchart
193. ns The following describes the applications for negative and positive pulse Detector Filter Bias Board Negative Pulse The Detector Filter Bias board provides a method of tapping off 1 11 of the full negative voltage to make the Anode slightly positive relative to the dual microchannel plate detector When the ions strike the microchannel plate electrons are liberated and attracted to the Anode by the positive bias The resulting signal is applied to the digitizer input High Current Detector Positive Pulse The positive version of the LMG is used to polarize a single microchannel plate that converts ion collisions to free electrons The electrons are attracted to a scintillator by a 15 kV bias voltage The scintillator converts electron collisions to light photons The photons strike a photomultiplier unit that converts the information back to an electrical signal that is applied to the digitizer input Specifications Power Power is 12 V dc at approximately 37 mA idle and 45 mA switching Input The TTL gate pulse input impedance is 10 Mohm resistive Output The external programmable power supplies provide either zero to 3 kV or zero to 3 kV When the input signal is low two thirds of the programmed voltage appears on the J2 pulse output When the input is high the full programmed voltage appears on the J2 output Connectors The following table describes the connectors Name Function Connector Type J1 PCB HV Input
194. nter depends on the component you are programming For details see Table D 1 on page D 5 When you write directly to the Control Register you must write the entire sixteen data bits even if you want to change only some of the register bit values Only the corresponding DACs output voltages are detectable with a voltmeter when you set their voltages without enabling high voltage DAC voltages are shown in Table D 2 on page D 8 4 Click Write to transmit the data over the data bus This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Data Values for Direct Access Data Values for Direct Access Table D 1 lists each of the components that you can write to directly and describes their corresponding sixteen data bits Table D 1 Direct Access Data Values Component Parameter Bit values 0 Source DAC Voltages from 0 to 30 kV Values written correspond to voltages 0 to 10 V at the DAC For details see Table D 2 on page D 8 1 Mirror DAC Voltages from 0 to 30 kV Values written correspond to voltages 0 to 10 V at the DAC For details see Table D 2 on page D 8 2 Grid DAC Voltages from 0 to 30 kV Values written correspond to voltages 0 to 10 V at the DAC For details see Table D 2 on page D 8 3 Beam Guide DAC Voltages from 0 to 30 kV Ignored for Voyager DE STR workstation with serial number 4154 a
195. ntrol 4 position 0 1 inch header J6 Control I O Control I O Control I O Control I O J7 Pulse out DE Pulse TIS pulse 7 position Control lines 0 1 inch header J8 Trigger in Laser opto Laser opto BNC J9 Pulse out DE Pulse TIS pulse BNC J10 Control lines DE box control TIS control 8 position Mini Fit power J11 JP1 Pulse out Digitizer trigger Not used BNC J12 JP2 Pulse out Spare Spare BNC spare J13 24 V out can Not used Not used 2 position Mini Fit supply the fan J14 Not populated Not populated Not populated Not populated J15 24 V in 24 V in 24 V in 4 position Mini Fit J16 Power in 5 V Powerin 5 V Power in 5 V 10 position Mini Fit continued 2 65 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Table 2 20 Functions of Pulse Generator Connectors Headers Jumpers Test Points and DIP Switches Continued Item Name Generic DE Function TIS Function Type Function Connectors J17 Programming Not used Not used 10 position ribbon continued header JU1 Addressing Jumped 5 6 Jumped 5 6 3x2 options 0 1 inch header JU2 Board function Shorted Open 2x1 DE TIS 0 1 inch header Switches SW1 Begin pulse bO off b0 1 2 3on 4 position address b1 2 3 on DIP switch SW2 End pulse b0 3 off b0 1
196. oading source Linear 1 actuator chamber Flap door 1 chamber lt 5 x 1077 torr 3 x 107 torr BA1 TC2 5 8 Foreline pump PB100876 Figure 5 2 Sample Loading System and Typical Vacuum Pressures This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted 5 2 2 Internal Interlocks Operation Sample Loading Chamber Under normal operating conditions procedures that require you to open and close any of the various valves move the actuators or power off the grabber can compromise the system s internal interlocks and damage the instrument unless prerequisites specific to the operation are first met Before performing such operations know their prerequisites and the possible consequences of noncompliance Table 5 2 Internal Interlock Hazard Control on page 3 9 lists these operations and their prerequisites When using the diagnostics software to control the component failure to meet the prerequisites generates an error or a warning An error is the result of a severe hazard and forces the operation to abort A warning allows the option of continuing the operation with risk of damaging the instrument Table 5 2 Internal Interlock Hazard Control Close Flap Door 2 Close the vent valve To perform this operation Do this first Otherwise this occurs Flap Door 1 Open Flap D
197. occurs the multigauge controller software displays an error code Error messages may be displayed in the Voyager Instrument Control Panel Figure 5 36 Wording of error messages may vary depending on the version of Voyager Software Instrument Fault e High Pressure Shutdown on lon Gauge BA2 Press Reset to restart gauge Press OK to dismiss notification Shutdown OK Figure 5 36 Voyager Software Error Message Corresponding to the Multigauge Controller E3 Error Code Some of the most common error codes and corresponding troubleshooting hints are presented in Section 6 2 Multigauge Controller Common Error Codes See the Varian Multigauge Controller Manual for the complete list of codes 5 55 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components 5 56 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted 6 Troubleshooting by Symptoms This chapter contains the following sections 6 1 Troubleshooting Tables 6 2 6 1 1 Spectral Problems 6 2 6 1 2 Sample Loading and Main Source Chamber s same 6 4 6 1 3 Computer System and Software 6 9 6 1 4 Power Supplies and Circuit Boards 6 10 6 1 5 Vacuum System sse 6 11 6 2 Multig
198. of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Safety and Compliance Information Xii WARNING ELECTRICAL SHOCK HAZARD Severe electrical shock can result by operating the instrument without the front or side panels Do not remove instrument front or side panels High voltage contacts are exposed with front or side panels removed AVERTISSEMENT RISQUE DE D CHARGE LECTRIQUE Des d charges lectriques s rieuses peuvent r sulter du fonctionnement de l appareil lorsque le panneau avant et les panneaux lat raux sont retir s Ne pas retirer le panneau avant ou les panneaux lat raux Des contacts haute tension sont expos s lorsque les panneaux sont WARNING CHEMICAL HAZARD To prevent eye injury always wear eye protection when working with solvents AVERTISSEMENT RISQUE CHIMIQUE Pour viter les blessures aux yeux porter toujours des protections pour les yeux lorsque vous manipulez des solvants WARNING PHYSICAL INJURY HAZARD Use the Voyager DE Biospectrometry Workstation only as specified in this document Using this system in a manner not specified may result in injury or damage to the system AVERTISSEMENT DANGER DE BLESSURES CORPORELLES Veuillez suivre avec attention les indications figurant dans ce document lorsque vous utilisez la Station de Travail de Biosptectrom trie Voyager Un usage diff rent de la station
199. ol page appears and powers on the camera and video lamps when you start the Voyager diagnostics software for NT platform Mechanical Control Page Opens and closes the valves extends and retracts the linear actuators turns the grabber on and off runs single or multiple load eject cycles and restarts faulted vacuum gauges Valves Close Open Flap Door 1 Allows you to manually open and close the doors Flap Door 1 2 Closed Open and valves to remove a stuck sample plate Foreline Valve 1 2 Flap Door 2 Open Note You can activate the flap doors and linear Vent valve actuators only when the air compressor is running The air compressor runs only when the sample Actuators Retract stage is in the load region Extend Linear 1 Linear 1 Retracted Extended Linear 2 Linear 2 Retracted Grabber Off On Under normal operating conditions the grabber powers on just before the Linear 1 actuator starts to extend or retract if ejecting and it powers off just after the Linear 1 actuator has fully retracted continued 4 6 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Diagnostics Software Features Table 4 3 Summary of Diagnostics Software Control Pages Continued Fields and Actions Status Indicators Comment Mechanical Control Page continued Load Eject Cycle Load Eject Cycle You can abor
200. olenoid On 5 Foreline 1 solenoid On 6 Foreline 2 solenoid On 7 Vent solenoid 8 Camera power On 9 Grabber solenoid On 10 5 V stepper 2 56 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Newer Model Instruments Table 2 18 MALDI Consolidated Control Board LEDs and Switches Continued LED Switch Name Position Function Switch 1 1 Source turbo On normally On 2 Mirror turbo On normally On 3 Not used spare turbo 4 old 3 Hz DE box Off new On 5 not used 6 Laser trigger select old new 7 3 5 bit addressing 3 bit 5 bit 8 Internal External laser manual select normally IntLas 2 57 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics J25 J17 v too00000000008 00000000000000000000 ID000000000000OE k 610000000000000000000k oocooocoa R51 J22 J18 JO QNO H3MOd 34 o ol 5 oooooooo 000000 1 LD00O0000000000 amp Bel J26 s go ll O000000000000 Be Joa H T R40 D060000660006 sz JU4 0000 al oo JU3 JU5 J15 J1 o oj o of g OO D18 oo oo o of 8 c g ero S2 Reset a on Ho omo go O D11 oue peo b c o ola lO ol o a 00 a o P p ope alo off RE JA E mk OJ O ol o Pin
201. ond to values from 10 to 32767 are Dec 0 to 32767 Hex 0000 to 7FFF Bin 0000 0000 0000 0000 to 0111 1111 1111 xxxx Where 0 10 ns and 32767 327670 ns at the DAC You must interpolate all values between the min max Valid end times correspond to values ranging from 10 to 32768 are Dec 32768 to 65535 Hex 8000 to FFFF Bin 1000 0000 0000 0000 to 1111 1111 1111 xxxx Where 32768 10 ns and 65535 327680 ns at the DAC You must interpolate all values between the Not all values in the range are valid do not write all 1s to the low four bits of the data value This Document Contains CONFIDENTIAL Material of Applied Biosystems Table D 2 lists the voltages and the data bits that program them For Internal Use Only No Unauthorized Copying Permitted Appendix D Isolating Components Using Direct Bus Access Table D 2 Voltage Values Component Voltage Output kV DAC Output Voltage Hex Binary Decimal 1 0 3333 0888 0000 1000 1000 1000 2184 2 0 6666 1111 0001 0001 0001 0001 4369 3 0 9999 1999 0001 1001 1001 1001 6553 4 1 332 2222 0010 0010 0010 0010 8738 5 1 665 2AAA 0010 1010 1010 1010 10922 6 1 998 3333 0011 0011 0011 0011 13107 7 2 331 3BBB 0011 1011 1011 1011 15291 8 2 664 4444 0100 0100 0100 0100 17476 9 2 997 4CCC 0100 1100 1100 1100 19660 10 3 33 5555 0101 0101 0101 0101 21845 11 3 663
202. ons input and output from the DE switch box r Check Control Wiring Step 1 E3 Remove all high voltage connections from the DE Box Figure 5 22 Check Wiring Test Step 1 Status Message 2 Click Start 3 As prompted Figure 5 23 check the diagnostics software test status area for instructions regarding connections or expected results Check Control Wiring Step 2 The Resistance between J2 and J4 should be infinite with all LEDs OFF Figure 5 23 Check Wiring Test Step 2 Status Message 4 Connect your meter probes to the appropriate connectors Figure 5 24 Both V725115 and V725125 have four connectors Only V725125 has the 5 V pull up control board Source PS source in Ground stud source out Grid PS Grid Grid out not used as a test point in the Check Control Wiring test Figure 5 24 DE Switch Box Connections You can click at any time to cancel the test or start over 5 37 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components 5 Click Net when you are ready to continue Continue to check the test status area for expected voltage readings and instructions each time you click Next 7 Ifthe test results in mismatched values run the test again 5 4 Laser System The nitrogen laser is replaced as a unit You cannot replace
203. ontroller key functions are CHAN Toggles through readings as described in the following table Table 5 6 Multigauge Controller CHAN Key Function Gauge Measures Expected Pressure torr BA1 Pressure in main Less than 5 x 1077 source chamber BA2 Pressure in mirror Less than 5 x 10 8 chamber TC2 Pressure in sample Less than 5 x 107 during operation Higher loading chamber when loading or ejecting a sample plate TC1 TC3 TC4 Not used displays E03 indicating gauge not connected EMIS Turns Bayard Alpert gauges BA1 and BA2 on or off F EMIS Pressing F then EMIS turns BA1 and BA2 on Pressing EMIS turns the gauge off DEGAS Turns degassing of BA1 and BA2 on and off When activated the red DEGAS legend lights up VAC Allows calibration of the thermocouple gauge TC2 vacuum reading ATM Displays TC2 atmosphere E KBAUD Pressing F then KBAUD displays and allows programming of the RS232 baud rate and parity This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Vacuum System Up arrow Increments digits when you enter parameters Down arrow Decrements digits when you enter parameters F The F key has several functions Accesses the second function of a subsequently pressed key when pressed Advances from one flashing digit to another when pressed when entering
204. oor 1 When under vacuum Warning Close Flap Door 2 Close the vent valve Close Flap Door 1 Retract Linear 1 actuator Error Flap Door 2 Open Flap Door 2 When under vacuum Warning Close Flap Door 1 Close Foreline valve 1 Open the vent valve Close Flap Door 2 Retract Linear 2 actuator Error Foreline 1 Open Foreline 1 When under vacuum Error 5 9 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components Table 5 2 Internal Interlock Hazard Control Continued To perform this operation Do this first Otherwise this occurs Foreline 2 Open Foreline 2 When under vacuum close Warning Foreline valve 1 OR 1 Close the vent value and Flap Door 2 2 Open Foreline valve 1 3 Wait until TC2 reads less than 8 x 10 torr Foreline valve 1 Wait to open Foreline valve 2 until TC2 reads less than 8 x 10 torr If you open Foreline valve 2 before the foreline pump has reestablished a vacuum in the sample loading chamber you create a pressure burst that impacts the back of the turbo pumps The burst may shut down the ion gauges BA1 and BA2 You can restart the ion gauges after approximately 10 seconds However the vacuum system takes some time to stabilize CAUTION After you vent the sample loading chamber close the vent valve Open Vent valve
205. oor 2 Check Flap Door 2 O ring for any cracks or damages If it is damaged replace the O ring C Asample plate that was improperly loaded in the transporter and has jammed is interfering with Flap Door 2 closure If possible eject the transporter out Reseat the plate properly D The fore pump is not pumping efficiently Check the pump oil level and color Refill oil or replace the oil if the oil color is dark ice tea color Replace pump if it is malfunctioning E Gas flows at vacuum hose connections Check the gasket on the clamps Replace the gasket if it is damaged Tighten the clamps continued 6 11 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 6 Troubleshooting by Symptoms Table 6 5 Vacuum System Troubleshooting Continued Item Symptom Possible Cause Action TC2 reading shows higher than normal pressure i e TC2 reading shows atmospheric pressure It takes a long time to pump down after plate loading continued F Flap Door 2 is not sealed properly Check that the Flap Door and the O ring are free of dust and fibers If necessary clean up any dust or fibers using a laboratory wipe moistened with ethanol 100 Replace the O ring if it is damaged Check that the Flap Valve presses evenly on the O ring with the face of th
206. or Voltage out is 0 to 10 V analog Connectors Table 2 2 describes the connectors Table 2 2 Connectors on the DAC PCA Board Item Name Function Type Connectors Ji Bus connection 34 pin ribbon J2 DAC Vout 4 pin MTA J3 Power 5V 15 V 15 V 5 pin MTA J4 Power 5 V 15 V 15 V 6 pin Mini Fit J5 DAC Vout 2 pin Mini Fit 2 10 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Common in Most Voyager DE STR Instruments 2 2 3 DC Distribution Board V750034 Overview The DC Distribution board distributes the following DC voltages from the power supplies to individual circuit boards 5 V 5 2 12 V 15 V and 24 V DC distribution board Figure 2 8 DC Distribution Board Location Theory Older versions of the Voyager DE STR have three power supplies connected to this board e Quad supply 5 V 5 2 V 15 V 12V supply 12 V 24V supply 24 V More recent versions have a single power supply that provides 5 V 15 V and 24 V 2 11 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Connectors Test Points and LEDs Table 2 3
207. oreline Solenoids 1 and 2 Vent Solenoid Linear Actuators Polarity and High Voltage Enable Linear Detector Enable Mirror HVPS Enable Turbo Pump Delay Enable Camera and Camera lamp Timed lon Selector control from Voyager bus DE Switch Box Control from Voyager bus Laser Interlock Linear Actuators and Flap Doors The linear actuators and flap door switches are magnetic reed switches that complete the 5 V interlock circuit Interlock Status System Interlock The system interlock consists of a series chain of panel switches The panel switches when made provide a ground to relay K9 When K9 is activated 24 V switched is available for HVPS and the laser interlock relay and a signal is sent to the computer via U13 18 Load Position The Load Position consists of two limit switches one on the X axis and one on the Y axis The switches are wired in series to ground and when made present this ground to the computer via U13 3 to signify the sample stage is in the load position Turbo 2 Minute Delay IC U40 provides a 2 minute inhibit signal to the turbo controllers This delay allows time to generate a rough vacuum Polarity High Voltage Enable Linear Detector Enable Mirror HVPS Enable The Polarity bit is applied to the source grid and mirror HVPSs The High Voltage Enable bit is applied to the source and grid power supplies but not the mirror power supply The Linear Detector Enable bit enables th
208. ough 10 DE mode select to 101 for non DE mode positive or negative polarity Remember you must write the entire sixteen bits of the control register so enter a value that sets all components the control register configures including TIS and LMG parameters appropriately Click Write This Document Contains CONFIDENTIAL Material of Applied Biosystems D H For Internal Use Only No Unauthorized Copying Permitted Appendix D Isolating Components Using Direct Bus Access Setting the Timed Ion Selector To set up and invoke the Timed lon Selector you Set the start and end times for the delay Write to the Control register to set the TIS frequency Enable TIS high voltage For non STR systems you also set the TIS power level Enable the TIS counter To set the TIS counter 1 2 From the Address pulldown menu select 7 TIS delay Enter a 16 bit value in the Data Value text field for the start delay time Values range from 0 to 32 767 decimal and represent 0 to 327 670 ns at the DAC However because of a limitation of the pulse generator you cannot write all 1s to the low four bits of the data value Click Wiite Enter a 16 bit value in the Data Value text field for the end delay time Values range from 32 768 to 65 535 decimal and represent 0 to 327 670 ns at the DAC Although values range from 32 768 to 65 535 a limitation of the pulse generator prevents you from writing all 1s to the low fo
209. parameters Fast forwards to the end of the procedure when pressed and held The multigauge controller requires Two fuses AC distribution board fuses F11A and F11B The fuse OK indicator is DS11 Figure 5 31 110 V power From the AC distribution board connection J11 If the power does not turn on check that the main power switch on the back of the multigauge controller is in the On position F11B F11A Left cabinet drawer Side view onoooonon ooooooooocogood 0 PB100852 J11 Figure 5 31 Multigauge Controller AC Distribution Board Connection and Fuses See the Varian Multigauge Controller Manual shipped with each Voyager DE STR system for detailed information about the functioning of this unit 5 7 3 Multigauge Controller Computer and Workstation Interaction Baud Rate The multigauge controller to Voyager connection uses RS232 technology The Voyager workstation computer serial ports and the multigauge controller communicate bidirectionally at 9600 baud decimal The baud rate sets the number of bits per second that can be transmitted to the computer system If the baud rate is set incorrectly the multigauge controller can not communicate with the Voyager software and the Voyager software will not initialize the vacuum system 5 47 This Document Contains CONFIDENTIAL Material o
210. pened or removed Safety labels for Class standards are affixed to the unit WARNING ELECTRICAL SHOCK AND LASER HAZARD In External Trigger mode the nitrogen laser energy storage capacitors are charged and the laser is ready to fire at any time When you perform service on the laser in External Trigger mode remove jewelry and other items that can reflect the beam into your eyes or the eyes of others Wear laser safety goggles and protect others from exposure to the beam Post a laser warning sign WARNING ELECTRICAL SHOCK AND LASER HAZARD When instrument covers are removed high voltage contacts are exposed and the laser emits ultraviolet radiation Wear laser safety goggles and post a laser warning sign at the entrance to the laboratory when you remove covers for service WARNING LASER HAZARD Exposure to direct or reflected laser light can burn the retina and leave permanent blind spots Never look directly into the laser beam Remove jewelry and other items that can reflect the beam into your eyes Wear laser safety goggles during laser alignment Protect others from exposure to the beam Post a laser warning sign while performing service This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager Laser Safety Laser Safety Requirements To ensure safe laser operation note the following The system m
211. plied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Table 2 9 describes the characteristics of each DE switch box model Table 2 9 Characteristics of the Three DE Switch Box Models Feature Condition V725059 V725115 V725125 Serialnumbers of NA STR STR Voyager on which 4142 4160 4161 and later installed DE Pro DE Pro 6056 6130 6131 and later Voyager DE Voyager DE 1143 1170 1171 and later Laser pulse rate 3Hz 3Hz 3 to 100 Hz with grid voltage to source voltage ratio of 6796 or greater Source pulse voltage 401 Mohm 401 Mohm Diode isolation from the grid resistor network resistor network rest voltage HV terminals 3 4 4 Damping resistors in the grid cables This resistance is required This resistance is included in the 3 Mohm and 1 Mohm resistors This resistance is included in the 3 Mohm and 1 Mohm resistors Small wire harness Bottom of the box Bottom of the box Replaced by green V750074 printed circuit relay control board Power required 24Vand5V 24Vand5V 24 V dc only instruments S N 4154 through 4160 may have been upgraded from V725115 to V725125 This circuit board also includes a 24 V to 5 V dc dc converter to supply the 5 V dc required by the Behlke switch The new model V725125 can be used only on newer Voyager workstations that contain a MALDI Consolidated Control Board This board provides
212. ponent e Task Control Page Troubleshooting Section Parameter Vent valve Close open Mechanical Section 5 2 2 Section 5 2 4 X and Y Set load position X Y Table Section 5 3 feedthroughs Section 5 3 3 Home and Load Section 6 1 2 positions Section 6 1 3 The multigauge controller in the Voyager system monitors the vacuum system thermocouple TC2 and Bayard Alpert gauges BA1 and BA2 Additional Resources In addition to this manual and the Voyager Diagnostics Software you can access information in two databases The Voyager MALDI Product Support web site Provides standard information such as Service Bulletins Service Notes and support contact information The Voyager MALDI knowledge database Allows an exchange information with other service engineers You can review the web site and the knowledge database 24 hours day 7 days a week Each database is fully text searchable and is individually replicated on Lotus Notes You can also call on the Regional Specialist the Field Service Technical Specialist and the Product Support Specialist For information see Appendix A Technical Support and Training This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Sample Loading Chamber 5 2 Sample Loading Chamber When loading a sample plate the sample plate is transported from the outside holder into the sample loading chamber
213. pourrait causer un accident ou endommager le syst me This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Safety and Compliance Information WARNING CHEMICAL HAZARD Before handling any chemicals refer to the Material Safety Data Sheet provided by the manufacturer and observe all relevant precautions AVERTISSEMENT RISQUE CHIMIQUE Avant de manipuler des produits chimiques veuillez consulter la fiche de s curit du mat riel fournie par le fabricant et observer les mesures de pr caution qui s imposent Safety and EMC Electromagnetic Compliance Standards US Safety Standards Safety This instrument has been tested to and complies with standard ANSI UL 3101 1 Electrical Equipment for Laboratory Use Part 1 General Requirements 1st Edition It is an ETL Testing Laboratories listed product WARNING Changes or modifications to this unit not expressly approved by the party responsible for compliance could void the user s authority to operate the equipment Canadian Safety and EMC Standards Safety This instrument has been tested to and complies with standard CSA 1010 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements It is an ETL Testing Laboratories listed product S curit Cet instrument a t v rifi avec la
214. proper line voltage Accommodated line voltages are 100V e 120V e 220V 240V Fusing F1A B Through F15A B Both sides of the power line neutral and hot are fused LEDs For every output connector an LED is provided to indicate that the fuses are intact The LED is unlit when one or both fuses are blown This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Compressor Relay and Diodes J15 the output connector for the compressor is gated through a relay This relay allows only J15 power when the autosampler is in the Load Position both the x load and y load microswitches are closed The diodes are necessary so the ground that is present in the Load Position is seen by both the compressor relay and control board logic Output Connectors All fifteen output connectors except J15 the compressor power are identically powered Label A label on the board provides the current revision of the board fuse values and the destination of each output connector 2 6 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Auto connections transformer _____ Strip J16 From load position switches Load position to control board Voltage selection Terminal J17 Compressor
215. proper use of equipment are the responsibility of the authorized and qualified service person Precautions must be taken to protect against possible serious and or fatal bodily injury More than 0 02 joules of stored energy are present at outputs J3 and J4 The TIS assembly V700471 TIS ASSY is a replaceable unit that contains an OEM original equipment manufacturer PCA V109032 HV Pulse Module 1000 V The block diagram Figure 2 18 on page 2 27 provides an overview of the theory of operation The PCA Assembly diagram Figure 2 19 on page 2 28 illustrates the location of the I O connectors and other important components 2 26 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Common in Most Voyager DE STR Instruments HV DC Volt Mon 100 1 24VDC In P1 15 P1 12 1000V Power 24V 5V Suppl Positive 24V 15V 75V Power Pull Up Convert Supply Positive Output To TIS Gate Electrode Pulse Positive Gate Invert on off Pull Down Pulse Generation Primary Drive Transformer P1 6 Over Current Inhibit P1 7 Negative Pull Down Over Current Output Current Negative To TIS Sense Sense Output o J4 Electrode HV Enable Negative P1 14 Pull Up P1 2 e VW 1000V Power Supply HV DC Volt Mon 100 1 Legend J e
216. pying Permitted Chapter5 Troubleshooting by Components WARNING ELECTRICAL SHOCK HAZARD High voltage contacts are exposed with front or side panels removed Because the DE switch box uses 30 kV disable the high voltages before servicing the DE switch box Servicing the DE switch box when the high voltages on severe electrical shock can result Wear proper eye protection Set the system to Continuous Linear Mode and acquire a standard sample If you still do not see peaks when acquiring a standard sample check the following Source DAC output Source DAC output voltage is at expected value Calculate the expected value by dividing the accelerating voltage by 3 000 For example a 15 000 V accelerating voltage equals a 5 V expected reading A 20 000 V accelerating voltage equals a 6 66 V expected reading Grid DAC output Grid voltage for Continuous Extraction is at expected value 75 of DAC output For example for a 20 000 V accelerating voltage 75 of the 6 66 V DAC outputs equals a trim pot 5 0 V reading 30 kV High Voltage power supply Current I trumpet is set at 3 turns counterclockwise or counterclockwise from the x stop point Check that the polarity is correct If the current I pot and polarity are set correctly and no voltage is present replace the power supply High voltage cable Connection to source pedestal is secure Laser Llaser is delivering adequate power and is positioned cor
217. r Address Decoder and Digital Integrator The address decoder decodes the address lines and the load control line The decoded load latches the data on the address bus to a temporary latch The width of the decoded load is then measured with a digital integrator and the appropriate action is taken as indicated in Table 2 4 Table 2 4 Address Decoding Criteria and Actions If Decoded Load Is The Signal Is Action Taken Longer than 1 1 us Data The data is latched through to the start register and the delay counter Shorter than 1 1 us Noise The load is ignored Drivers The line drivers take the delayed pulse from the programmable logic circuit and provide enough current to drive the cabling to devices 2 17 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Regulators The original release of the V750069 DVDT board is powered by 12 V provided by the system An onboard regulator supplies 5 V for the board The next release board V750073 is powered by 24 V Two regulators are present on the board one to provide 5 V and one to provide 12 V for the low mass gate and flight tube drift tube power supply circuits Types of Signals The input signals to the DVDT board consist of A trigger event on newer systems a DE pulse on older systems a laser trigger Acomputer generated enab
218. r DE STR hardware Allows you to troubleshoot or isolate electrical mechanical and vacuum problems or to test the system after repairing or replacing parts See Chapter 4 Voyager Diagnostics Software for an overview of the diagnostics software Using each control page during troubleshooting is detailed in various sections in Chapter 5 Troubleshooting by Components and in Appendix D Isolating Components Using Direct Bus Access The Voyager Diagnostics software for NT platform enables you to control the hardware components when the Instrument Hardware Controller IHC and Instrument Control Panel ICP are shut down You can run the diagnostics software whether the instrument is operating under vacuum or at atmosphere ATM 1 21 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 1 System Overview 1 22 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted 2 Voyager DE STR Workstation Electronics Theory This chapter contains the following sections 2 1 Electronics Theory Overview 2 2 2 2 Electronics Common in Most Voyager DE STR Instruments 2 4 2 2 1 AC Distribution Board V750053 2 5 2 2 2 DAC Digital to Analog Converter Board V750025 2 9 2 2 3 DC Distribution Board V750034 2 11 2 2 4 Low M
219. r Repetition Rate on page 39 5 Click Fire Laser The laser pulses continuously 6 To stop the laser pulsing click FieLaser again s Setting the Laser Repetition Rate You can adjust the laser repetition rate only if the system contains these optimization components Voyager Version 5 1 and later software Consolidated control board V750082 and V750102 001 V750102 002 V750102 003 with firmware V960005rD and D V960006rD installed Fast DE switch box V725125 e 48 bit I O control board V750033 configured for 5 bit addressing 5 39 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 5 Troubleshooting by Components To set the laser repetition rate 1 If necessary select the laser and re initialize it For details see Re initializing the Laser 2 Set the repetition rate by increasing or decreasing the value in Desired Repetition Rate NOTE Currently regardless of the laser optimization components the Voyager laser does not support repetition rates greater than 20 Hz Setting the repetition rate to a value gt 20 Hz causes the laser to cease firing after it emits the first pulse Re initializing the Laser After switching lasers you need to re initialize the newly selected laser before use This procedure resets the transmission path for control signaling to the newly selected laser Reinitializa
220. r option 1 3 nitrogen laser beam 1 14 options 1 3 overview 1 2 1 7 5 7 powering up 3 6 test standard kits 1 3 W Warnings safety cooling fan 1 13 DE switch box high voltage 2 37 ethanol chemical hazard 6 12 high voltage xii 5 32 high voltages present 5 38 continued 2 Index Warnings safety continued laser always ready to fire in external mode 5 38 laser beam hazard 1 4 1 11 1 13 3 2 5 21 5 38 6 9 laser burn hazard 1 13 laser charged in external trigger mode 1 4 1 13 3 2 5 38 laser emission 1 11 laser emits radiation 5 38 laser potentially damaging the eyes 5 38 laser radiation hazard 1 4 1 11 3 2 5 21 5 38 6 9 nitrogen laser overheating 1 13 posting a laser warning sign 5 38 posting laser warning sign 5 38 remove reflective items before servicing 5 38 removing instrument covers xii 5 32 safety standards xiii storage capacitors charge when laser in external mode 5 38 symbols on system viii UV radiation from laser xi Web site MALDI product support 5 6 A 3 X X coordinate see Sample stage X feedthrough see Stepper motor feedthroughs XY Status display 4 11 X Y Table control page 5 19 see also Diagnostics software function 4 9 overview 4 9 5 18 setting load position 5 19 testing alignment 5 13 writing load position to the NT Registry 5 20 Y Y coordinate see Sample stage Y feedthrough see Stepper motor feedthroughs Index 15 This Documen
221. rectly Delayed Extraction switch box Switch Box is functioning properly in Delayed Extraction and Continuous Linear mode Delayed Extraction Timer circuit board Output for older systems with the ECL logic board is 5 2 V Newer systems with TTL boards and the MALDI consolidated control board do not use 5 2 V 5 32 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Main Source Chamber 5 3 8 Source Grid and Mirror Voltages Use the Diagnostics Software Voltages Delays control page Figure 5 19 to set system voltage parameters and timing delays Camera Mechanical Laser Voltages Delays Y Table DE Switch Box Direct Bus Access Linear Reflector Mode of Operation ol C Voltages r Delays Off On Positive Negative r Delayed Extraction DE HV Enable C Polarity LL Enable Start Delay 10 0 Zi ns Voltage Values Desired Actual Low Mass Gate LMG Source 20000 D 2j no Enable E Start Delay 8000 0 E ns Grid fi 5000 0 00 pis 2000 uo Timed lon Selector TIS Guide Wire 30 0 foo Enable I Start Delay 10 0 zi ns Status End Delay 20 0 APPLY ALL Ramp Voltages Set Delays Reset All Figure 5 19 Voltage Delays Control Page Applying the Settings After changing any of the settings on this control page you must apply them before they can ta
222. reflector mode Electronic connection Figure 1 2 Voyager DE STR Workstation This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager DE STR Workstation Components 1 3 1 Sample Loading Chamber Overview The sample loading chamber Figure 1 3 transports the sample plate between vacuum chambers at various pressures Flap Door 1 me Flap Door 2 actuator B Linear 1 actuator Linear 2 actuator Flap Door 1 not visible attached Flap Door 2 shown closed to source housing To main A EM atmosphere source chamber paiooess Figure 1 3 Voyager DE STR Workstation Sample Loading Chamber The sample loading chamber system consists of Linear actuators Two pneumatic actuators that control the load eject movement of the sample plate Linear 1 actuator with a magnetic grabber transports the sample plate between the sample loading chamber and the main source chamber It places the sample plate on and removes the sample plate from the sample stage Linear 2 actuator with its sample transporter transports the sample plate into and out of the sample loading chamber Flap door actuators Two pneumatic actuators that control the opening of the flap doors that maintain vacuum pressure Flap Door 1 separates the sample loading chamber and the main source chamber Flap Door 1 is spring loaded The spring m
223. rs Provide the appropriate safety glasses goggles to their employees if they are in the area while the laser is being serviced The safety glasses goggles must be rated for a YAG laser with a wavelength of 355 nm Provide and document laser safety training to their employees on the hazards associated with a YAG laser Remove all employees from the area where maintenance to the YAG laser is being performed In addition all customers must be in compliance with the ANSI standard Z136 1 1993 American National Standard for the Safe Use of Lasers This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 1 System Overview 1 3 Voyager DE STR 1 Workstation Components Components Overview The components of the Voyager DE STR Biospectrometry workstation shown in Figure 1 2 and described in the sections that follow are the Sample loading chamber Main source chamber Laser system Flight tube Mirror chamber Digitizer Computer system video system and Voyager software Computer data system and monitor Digitizer Laser attenuator Prism l Reflector MEN l m detector Laser TTT TTT Linear detector DE chamber LITT Video camera ube Mirror chamber Monitor ipw B Laser path gt lon path in
224. rs J10 DAC 5 V 15 V DAC 5 V 15 V 10 pin Mini Fit continued J11 DAC 5 V 15 V DAC 5 V 15 V 10 pin Mini Fit J12 DAC 5 V 15 V DAC 5 V 15 V 10 pin Mini Fit J13 DAC 5 V 15 V DAC 5 V 15 V 10 pin Mini Fit J14 Fan 24 V Fan 24 V 2 pin Mini Fit J15 Compressor relay 24 V Compressor relay 24 V 2 pin Mini Fit J16 Solenoid valves 24 V Solenoid valves 24 V 2 pin Mini Fit J17 48 Bit I O 5 V 24 V 48 Bit I O 5 V 24 V 6 pin Mini Fit J18 Timed lon Selector box Timed lon Selector box 6 pin Mini Fit 5 V 24 V 45 V 24 V J19 Not used DVDT 24 V 2 pin Mini Fit J20 Not used Opto trigger 12 V 2 pin Mini Fit J21 Not used Stepper motor 12 V 2 pin Mini Fit J22 Not used Flight drift tube PS 12 V 2 pin Mini Fit J23 Distribution board 24 V Distribution board 24 V 4 pin Mini Fit J24 Control board 24 V Control board 24 V 4 pin Mini Fit J25 Lift switch Lift switch 4 pin Mini Fit J26 High Voltage switch box High Voltage switch box 6 pin Mini Fit 45 V 24 V 45 V 24 V Test Points TP1 45V 5 V TP1 TP2 415V 15 V TP2 TP3 15V 15V TP3 TP4 Not used 5 2 V TP4 TP5 Not used 12 V TP5 TP6 24V 24V TP6 TP7 Ground Ground TP7 continued 2 13 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Table 2 3 Connectors Test Points and LEDs o
225. rt ProSpin SeqEd Sequence Navigator SPHERIS SPHERI10 StockMarks Stretch Synergy SynthAssist and VeloSep are registered trademarks of Applera Corporation or its subsidiaries in the U S and certain other countries Data Explorer AB Design ABI ABI Masterpiece Applera AutoAssembler BaseSprinter Biospectrometry CATALYST Data Explorer GeneAssist LV40 MatchMaker PDQ Primer Express ProSorb Sequazyme and Voyager DE are trademarks of Applera Corporation or its subsidiaries in the U S and certain other countries 3Com is a registered trademark of 3Com Corporation Acqiris is a registered trademark of Acqiris SA Acrobat and Adobe are registered trademarks of Adobe Systems Incorporated Altera is a registered trademark of Altera Corporation AmpErase AmpliTaq AmpliTaq Gold EnviroAmp GeneAmp and TaqMan are registered trademarks of Roche Molecular Systems Inc AppleScript and Macintosh are registered trademarks of Apple Inc IBM is a registered trademark of International Business Machines LeCroy is a registered trademark of LeCroy Corporation Lexan is a registered trademark of General Electric Co Corp Lotus is a registered trademark of Lotus Development Corporation Microsoft MS MS DOS Windows and Windows NT are registered trademarks of Microsoft Corporation Mini Fit and Mini Fit Jr are trademarks of Molex Incorporated MTA is a trademark of Amp Incorporated Pentium is a registered trademark of Intel Corpora
226. s adjusting 5 29 feedthrough limit switches 5 19 Home 5 29 Home 0 0 position 5 19 linear actuators 5 29 Load 5 29 load position nottripping 5 21 load position linear actuator and flap door interaction 5 20 Load region 5 19 continued Index Microswitches continued Load region typical counts 5 19 shorting to run the air compressor 5 19 troubleshooting 5 29 Mirror see reflector Mirror chamber components within 1 16 5 31 function 1 16 Mirror turbo controller J13 AC Distribution board 3 6 Mirror voltage and mode of operation 5 34 diagnostics software values 5 34 enabling using diagnostics software 5 34 setting using diagnostics software 5 33 5 34 testing high voltage 5 36 MSDSs obtaining A 10 Multigauge Controller description 5 45 Multigauge controller baud rate 5 48 5 50 baud rate required 5 47 Com Port 3 5 48 5 50 functions 5 45 fuse LED location 5 47 fuses 5 47 gauges monitored 5 45 key functions 5 45 keys accessing second functions with F key 5 45 location 5 45 overview 5 45 parity 5 48 5 50 parity setting 5 50 power source 5 47 requirements 5 47 RS232 connection to Voyager 5 48 5 50 uses 5 45 using to calibrate the thermocouple gauge 5 52 Multigauge controller error code E02 6 16 6 17 E03 6 16 E04 6 16 E05 6 E08 6 E09 6 E14 6 17 overview 5 55 table of common 5 55 Index 9 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Us
227. s 760 torr Vacuum 1 Expose TC2 to a known vacuum pressure 107 torr range 2 Press the VAC key The display shows the most recent vacuum setting with the most significant digit flashing 3 Set the display to the vacuum level desired TC2 is now calibrated lon Gauge The ion gauge Figure 5 34 on page 5 53 consists of a collector grid and filament Figure 5 35 on page 5 54 shows the location of BA1 within the Voyager DE STR Grid Filament Filament Grid Collector PB100877 Figure 5 34 Bayard Alpert BA1 BA2 lon Gauge 5 53 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components BA1 location GP BA1 is not visible in this drawing J QU the gauge is within a mesh bag ND PB100853 Figure 5 35 BA1 Location Voyager STR Workstation Rear View An ionization gauge calculates pressure by simultaneously measuring emission current and ion current The emission current results from the electrons emitted from the filament I The positive ions that impact the collector and pick up electrons from ground account for the positive ion current I Pressure is directly proportional to the ratio of ion current to emission current and indirectly proportional to the sensitivity of the gauge Factors affecting ion gauge
228. s CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted J Joy stick see Control stick K KBAUD multigauge controller key secondary function 5 46 Key control nitrogen laser 1 12 Knowledge database MALDI 5 6 A 3 L Label 2 6 Laser see alsoNdYAG 1 11 adjusting the attenuator 5 38 class rating 1 11 diagnosing using Laser control page 5 38 emission danger 1 11 external mode warning 5 38 firing 5 38 5 39 firing prevented 5 40 optional laser Voyager serial numbers compatible with 1 11 potential eye damage 5 38 re initializing 5 38 reinitializing process 5 40 safety information xiv 1 4 3 2 setting repetition rate 5 39 5 40 status bar display 4 11 stop firing 5 40 stops firing after first pulse 5 40 UV radiation warning xi warning 1 11 Laser see also Nitrogen laser 1 11 Laser attenuator adjusting 5 41 home position 5 41 home position improperly detected 5 41 home position reflective tape 5 41 homing 5 40 keyboard control 5 40 optical density 5 41 opto couple device 5 41 resetting to Registry file values 5 40 setting using diagnostics software 5 41 stepper motor 5 40 theory of operation 5 41 Index Laser beam path nitrogen 1 14 Laser control page 5 38 see also Diagnostics software Laser control page function 4 7 Laser emissions ratings 1 11 Laser hazard warning 1 4 1 11 3 2 5 21 5 38 6 9 cooling fan 1 13 laser charged in external trigger mode
229. s the Voyager computer registry Voyager vacuum monitor baud as described in Accessing the Voyager Computer Registry Keys above 2 Check the Voyager vacuum monitor baud rate setting in the registry by the selecting the following path in the left panel of the Registry Editor window Figure 5 32 on page 4 49 HKEY LOCAL MACHINE SOFTWARE PerSeptiveBiosystems Maldi Server HiVolt Vacuum Monitor Vacuum Monitor Baud Rate 3 Inthe Registry Editor window right panel double click default The DWORD Editor box is displayed 4 Inthe DWORD Editor box select Decimal 5 Ifthe baud rate registry setting is other than 9600 type 9600 in the Data field 6 Click OK 7 Close the Registry Editor window 5 48 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Vacuum System Hegistry Editor HKEY_LOCAL MACHINE on Local Machine B Reoisty Edt Tree View Security Options Window Help l 1814 E3 HKEY LOCAL MACHINE 2 HARDWARE max REG_DWORD 0x4b00 SAM min REG_DWORD 0x4b0 EI SECURITY SOFTWARE 3Com Applied Biosystems DWORD Editor Classes GJ Clients R Dell Computer Corporation Description Executive Software G INTEL KasperskyLab LeCroy McAfee Microsoft National Instruments Nico Mak Computing ODBC PerSeptiveBiosystems Maldi LE Server Acquisition CurrentSamplePlatelD C3 DefaultCalibratio
230. s the current pressure in torr in the reflector mirror chamber Smp Pres TC2 Displays the current pressure in torr in the sample loading chamber This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 4 4 12 Voyager Diagnostics Software This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted 5 Troubleshooting by Components This chapter contains the following sections 5 1 Troubleshooting Overview sesssese 5 2 5 2 Sample Loading Chamber ssessssseseeeeeeeeene 5 7 5 2 1 Vacuum System Interaction cceeeeeeeeeeeeeeeees 5 7 5 2 2 Internal Interlocks Operation ssssssse 5 9 5 2 9 Camera isi PS 5 11 5 2 4 Grabber Linear Actuators and Valves 5 11 5 2 5 Load Eject Cycles rrei ieena 5 13 5 2 6 Vacuum Faults rarei eee E aia 5 15 5 2 7 Mechanical Control Page Errors and Warnings 5 16 5 3 Main Source Chamber cccceeeeeeeeeeeeeeeeeeneeencaeeaeeeeeeeeeeees 5 18 5 3 1 Source Clips ocio tet eater phis 5 23 5 3 2 Source Pedestal ccccccscccceceeceeeeeeeeeeeeeeeeeeenees 5 24 5 8 3 Stepper Motor Feedthroughs 5 26 5 3 4 Sample Plate and Grid Voltage 5 30 5 3 5 Internal High Voltage
231. sists the problem is Control panel between the Voyager hardware and displays an multigauge controller error message Collector cable Replace or reconnect the cable indicating a connection is bad or high pressure dislodged shut down on the ion gauge E04 Filament BA gauge filament is Measure filament to grid with an ohm over current or meter If the reading is not open shorted Commonly replace the BA gauge filament is shorted to If reading is open move the BA the grid board to an open slot on the multigauge controller mother board If the board fails in the new slot replace the BA board continued 6 16 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Multigauge Controller Common Error Codes Table 6 6 Multigauge Controller Common Error Codes Continued Prior FoRS EITOE Possible Cause Action Code Source E05 Gauge does Power not plugged in Move the BA board to an open slot not ignite to the ion gauge on the multigauge controller mother Faulty BA Board board Faulty BA slot on the If the board fails in the new slot multigauge controller replace the BA board mother board On reflector systems On the back of the multigauge bad cable or controller disconnect the BA1 and connection BA2 cables Connect the BA2 cable to the BA1 gauge Check the BA2 display to verify the BA1 stat
232. software 5 20 writing load position to using diagnostics software 5 20 O O ring seals conditions damaging to 5 16 Oscilloscope see Digitizer Over pressure far exceeds limit 5 15 Over pressure vacuum fault 5 15 P Parity accepted values 5 50 codes 5 50 resetting 5 50 resetting in Voyager registry 5 51 verifying 5 48 5 50 verifying in Voyager registry 5 51 Peaks do not appear in spectrum 5 32 Photomultiplier in linear detector 1 17 Plasma cartridge Nitrogen plasma cartridge 1 1 see Nitrogen plasma cartridge Pneumatic actuators flap valve movement 1 7 for sample plate movement 1 7 linear 1 7 Pneumatic system compressor activation 1 7 pressure available 1 7 pressure needed for actuator control 1 7 Positive drive assembly 2 20 Posting a laser warning sign 5 38 Power receptacle nitrogen laser 1 12 Power supply Source 5 18 Index 10 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Powering up Vacuum system 3 6 Voyager DE STR Biospectrometry Workstation 3 6 Preface xvii Pressure ranges for vacuum gauges 5 46 Product support web site 5 6 A 3 Pulse Generator 2 63 Pulse generator triggered by DE pulse generator 2 Pulse Generator board drivers 2 64 Pulse generator board drivers 2 64 registers 2 64 theory 2 63 Pulse Generator PCA connectors 2 65 DIP switches 2 65 headers 2 65 jumpers 2 65 test points 2 65 Pump
233. source chamber Ground grid The ground surface for formation of the potential gradient to the variable voltage grid Charged ions stop accelerating at the ground grid but retain their initial velocity After the ground grid the ions enter the field free region of the analyzer e Collision cell A chamber available as the collision induced dissociation CID option for enhanced fragmentation in PSD analysis Einzel lens A three element Figure 1 6 cylindrical electrostatic lens Figure 1 7 designed to organize the stream of ions into a narrow straight beam Electrostatic lenses focus charged particles in the same way as optical lenses focus light lon flow V3 Vo V4 V4 V4 Typically Vo gt V4 Figure 1 6 Potentials Configuration of an Einzel Lens Cross Section This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 1 System Overview lon flow Einzel lens assembly CID cell Figure 1 7 Einzel Lens Assembly Expanded View The potentials of the first and third elements are the same As the ion stream passes through the einzel lens the ions are repelled toward the center of the cylinder forming a collimated beam at a focal distance farther down the flight path The focal length depends on the dimensions of and the potentials applied to the lens elements Beam
234. stomer must Provide the appropriate Laser Warning Signs These signs shall be conspicuously displayed in a location where they will best serve to warn any and all onlookers Provide the appropriate safety glasses goggles to their employees if they are in the area while the laser is being serviced The safety glasses goggles must be rated for a YAG laser with a wavelength of 355 nm Provide and document laser safety training to their employees on the hazards associated with a YAG laser Remove all employees from the area where maintenance to the YAG laser is being performed In addition all customers must be in compliance with the ANSI standard Z136 1 1993 American National Standard for the Safe Use of Lasers This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 3 Before Servicing the Workstation 3 2 Venting the Voyager DE STR Workstation 3 2 1 Preparing to Vent To prepare the Voyager workstation for venting 1 Close the Voyager software and other applications in the computer Newer Systems Older Systems Voyager Instrument Control Panel Voyager control window Voyager Data Explorer GRAMS Voyager software Version 4 51 and earlier Voyager Sequence Control Panel NA Instrument Hardware Controller access from NA Only available with Voyager software Windows Control Panel Services Version 5 0 and later
235. supply PB100850 Figure B 4 Right Cabinet Rear View This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted B 5 Appendix B Einzel lens assembly Einzel lens voltage connection Beam steering plates voltage connection PB100870 lon exit aperture Figure B 5 Einzel Lens Assembly with Variable Voltage and Ground Grids Removed Figure B 6 lon Exit Flange Showing the Einzel Lens Assembly B 6 Beam steering internal connections Einzel lens Variable grid This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted To detector lt lt Aperature Beam steering plates Einzel lens assembly CID cell Figure B 7 Einzel Lens Assembly This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Grids B 7 Appendix B microswitch X feedthrough microswitch home position sample stage 0 0 load position Y feedthrough sample stage X Y table PB100847 Figure B 8 Feedthroughs and Sample Stage Flap Door 1 actuator Flap Door 2 actuator Linear 2 actuator Linear 1 actuator Flap Door 1 not visible attached to source housing Flap Door 2 shown closed To main source chamber To atmosphere
236. t Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics The TP1 TP2 jumper is an optional disable input The PCA has a 12 V dc power input and draws 45 mA in normal operation Dynamic operation can be observed using Tektronix P5100 2500 V scope probes Figure 2 15 and Figure 2 16 illustrate operation in negative and positive modes and the negative and positive detector application circuits Low Mass Gate Pulse Diagrams Negative Pulse Positive Pulse Detector Filter Hi Current Bias Board Detector Dual MCP Chevron Programmable ions 0 to 3kV P S A HV Negative Gnd 1818V e 7 electrons 182v ae Ra 10 Pulse in m Single MCP Digitizer ions p Rb 1M C 0 1F Input t2kV Signal electrons dole photons E Photomultiplie Digitizer Input JL Signal Programmable gna 0 to 3kV P S Positive Gnd LT 2 24 Figure 2 15 Low Mass Gate Pulse Diagrams Negative Pulse gt im Time gt 1 33 V 2 3 V Eom 3 3 V 2 3 V 1 3 V Positive Pulse gt im A Time Figure 2 16 Low Mass Gate Wave Forms This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Common in Most Voyager DE STR Instruments Applicatio
237. t Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted lt xmo2 Index Index 16 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Headquarters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free In North America 1 800 345 5224 Fax 1 650 638 5884 Worldwide Sales and Support Applied Biosystems vast distribution and service network composed of highly trained support and applications personnel reaches into 150 countries on six continents For sales office locations and technical support please call our local office or refer to our web site at www appliedbiosystems com or to the Technical Support and Training appendix in this document www appliedbiosystems com BS ebbe NP Biosystems Applera Corporation is committed to providing the world s leading technology and information for life scientists Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses Printed in the USA 04 2001 Part Number Hardcopy 4319245 Rev A Part Number CD 4327166 Rev B an Applera business
238. t Points and Switches on the Low Mass Gate Timer PCA Continued Item Name Function Type Switches S1 Reset Push button S2 First 5 dips determine address 8 position DIP Sixth dip not connected Seventh dip selects XL Eighth dip ties enable to Oscillator enable 3 Bit Addressing Defaults S2 1 is on S2 2 is off S2 3 to 5 are on S2 6 to 8 are off 5 Bit Addressing Defaults S2 1 is on S2 2 is off S2 3 is on S2 4 to 5 are off S2 6 to 8 are off Test Points TP1 Pulse in NA TP2 Pulse out 1 NA TP3 Pulse out 2 NA TP4 12 V NA TP5 5 V NA TP6 Comparator out NA TP7 18 MHz clock NA Diodes D1 Pulse in NA D2 Pulse out NA D3 Low Mass Gate on NA D4 45V NA D5 12 V NA 2 19 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics 2 2 5 Low Mass Gate Driver Boxes V700635 V700643 and Detector Filter Bias V750032 Overview Low mass ions from the matrix usually are not of interest yet they can be produced in such large quantities that they may overload the detector The Low Mass Gate LMG is used to delay applying full high voltage to the detector microchannel plate until the matrix ions pass The microchannel plates have an inherent gain recovery time and the delay of full voltage preserves the gain until a region of interest During the period th
239. t load eject operations while they are Single iteration current operation executing but doing so could place the system in Multiple iterations an unsafe state You can return the system to a safe state by clicking the appropriate radio buttons to open or close the affected components flap doors foreline valves and linear actuators When the instrument is operating at atmosphere you can force the diagnostics software to ignore all vacuum gauge faults and finish load eject operations Ignore vacuum CAUTION Using this option to ignore and override faults vacuum gauge faults when the system is operating Restart faulted under vacuum could damage the ion gauges O vacuum gauges ring seals and vacuum pumps Laser Control Page Sets the laser repetition rate re initializes the internal and external if installed laser and adjusts the attenuator Fire laser You can adjust the laser repetition rate only if the Desirea repetition NA system contains these optimization components rate Voyager V5 1 and later software Consolidated control board V750082 and V750102 001 V750102 002 V750102 003 with firmware V960005rD and D V960006rD installed Fast DE switch box V725125 e 48 bit I O control board V750033 configured for 5 bit addressing NOTE Currently regardless of the laser optimization components the Voyager laser does not support repetition rates greater than 20 Hz Setting the repeti
240. t output voltages at the test points of the corresponding Ramp voltages Ramping status components you must also enable and apply high Reset all voltage Delays NA By pressing Delayed Extraction Enable Start delay APPLY ALL Ramp Voltages Set Delays time Low Mass Gate Enable Start delay time Timed lon Selector Enable Start delay time End delay time you set the delays specified for Delayed Extraction Low Mass Gate and Timed lon Selector only when you have also enabled them It does not affect delays associated with ramping component voltages Set delays Reset all continued 4 8 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Diagnostics Software Features Table 4 3 Summary of Diagnostics Software Control Pages Continued Fields and Actions Status Indicators Comment X Y Table Control Page Moves the sample stage resets home and load positions Before you can access the functions on this control page you must click the sample stage to its home position 0 0 This initializes the diagnostics software controls enabling the software to calculate all other positions including load position Sample stage Current position One step equals 3 175 um You can use either unit X Y position and switch back and forth between them The scroll bar diagnostics software performs the necessary
241. tal on page 5 24 D Linear 1 retract speed is too fast The retract speed control valve bleed screw on the end of Linear actuator 1 farthest away from the source housing may be set improperly The actuator may retract too quickly breaking the magnetic connection between the sample plate and grabber Adjust the retraction rate to a slower speed by turning the retract speed control valve clockwise See Figure 5 12 on page 5 25 E Detent balls on source are binding because sample contamination is getting into the holes where the balls are mounted If the detent balls provide too much resistance to compression the grabber may have insufficient force to pull the plate from the source To break the resistance press down on the balls with an Allen wrench or similar tool If necessary disassemble and clean or replace the source F Springs are too stiff Press down on the balls with an Allen wrench or similar tool continued This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 6 Troubleshooting by Symptoms Table 6 2 Source and Sample Loading Chamber Troubleshooting Continued Item Symptom Possible Cause Action 4 During sample plate ejection G Defects on plate edges not Check the edges of all the sample plate either allowing plate to release sample pla
242. terial of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components 5 3 Main Source Chamber The main source chamber Figure 5 6 has the Sample stage source pedestal and X Y table Variable voltage grid Delayed Extraction DE switch box Two 30 kV high voltage power supplies located in the left cabinet and associated high voltage cables Laser attenuator Sample stage and plate source J4 L ZEE Laser Variable voltage grid J2 J2 J4 Delayed extraction switch box and high voltage connections Figure 5 6 Voyager DE STR lon Source Components The source pedestal receives the sample plate from the sample loading chamber and is attached to the X Y table The X Y table moves the source pedestal to the desired spot location and between the Home and Load positions Microswitches on the X Y table feedthroughs provides the status of the source pedestal Home and Load position Sample Stage Load Position Use the X Y Table control page Figure 5 7 to recalibrate the load position of the sample stage and to move the sample stage to the load position before you open the Mechanical control page see Keeping the Sample Stage Stationary During Load Eject Cycles on page 13 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Main Source Chamber
243. ternal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Connectors and Trim Pots Table 2 19 Connectors Adjustments and Tests on the Flight Tube PCA Item Name Function Type Connectors J1 Power Output Horizontal BNC 0 to 100 V Positive lon mode and 0 to 100 V Negative lon mode J2 HV Enable Pos Neg lon Polarity 24 V 8 pin MTA locking relay power header 0 1 inch spacing J3 12 V power for dual DC DC converters 2 pin MTA locking and OpAmps header 0 1 inch spacing J4 Program input from DAC 4 pin MTA locking header 0 1 inch spacing Trim Pots RP9 Zero DC offset U2 gain 100 OpAmp Potentiometer measure with digital voltmeter on output RP8 Zero DC offset U1 gain 10 OpAmp Potentiometer measure with digital voltmeter on output Ripple Approximately 5 mV peak to peak BNC Output Connector switching noise measure with a coax cable directly connected to an oscilloscope 2 62 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Electronics Only in Earlier Instruments 2 4 2 Pulse Generator Board V750063 Overview The Pulse Generator PCA can be configured for Delayed Extraction timing Timed lon Selector timing See Table 2 20 for configurations In both functions the board Captures an input trigger Waits and counts off a pre programmed delay Ou
244. tes after AC power is supplied to the instrument lon Gauge Bayard 9 9 x 107 torr to BA1 BA2 You can enable high Alpert Gauge 1 0 x 1078 torr voltage power only when BA1 reads 9 0 x 1078 torr or less 5 7 2 Multigauge Controller The multigauge controller in the Voyager system monitors the vacuum system thermocouple TC2 and Bayard Alpert gauges BA1 and BA2 The multigauge controller is located in the left cabinet Figure 5 29 AULA Multigauge jg agod 188 controller PB100848 Figure 5 29 Location of the Multigauge Controller in Left Cabinet Front View Use the multigauge controller to Verify the status of the BA1 and BA2 gauges Verify the status of the TC2 gauge Degas the BA1 and Verify the baud rate BA2 gauges You access the multigauge controller functions and parameters through the front panel keyboard Figure 5 30 The readings prompts and error messages are displayed on the liquid crystal display LCD Pressing the F unction key before pressing another key accesses the second function of the next key you press 5 45 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components PB100878 Figure 5 30 Multigauge Controller Screen and Keyboard The multigauge c
245. tes in use for occasionally or consistently from detent balls or source damage Smooth the edges cannot be pulled off the stage edge clips with a small flat file and by the grabber MicroFinish cloth If continued necessary replace the sample plate H Contamination on sample Check the bottoms and edges plate of all sample plates in use for contamination Clean If necessary replace the sample plate 5 Grabber not contacting plate Insufficient X load Unscrew the grabber during loading or ejection adjustment available to approximately 3 32 roughly enable plate to be two turns back on actuator adequately contacted by shaft Leave enough threads the grabber during plate available on actuator shaft to loading or ejection securely attach the jam nut Linear 1 actuator shaft is cap back onto shaft To too short for system prevent the grabber and cap tolerances More often from loosening place a small seen with older Bimba amount of thread sealant style actuators such as LockTite on the actuator shaft threads 6 XorY load coordinates The X and Y home switch Tighten such that when the require continual adjustment brackets are loose linear feedthroughs are fully Or extended to the home The X or Y home switches posman YOU eee Np movement of the home are moving switches 6 8 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Troubleshooti
246. the Quad power supply the 5 2 V is not present on the pulse generator board This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 6 Troubleshooting by Symptoms 6 1 2 Sample Loading and Main Source Chamber Table 6 2 includes troubleshooting symptoms related to the sample load and eject mechanisms such as the following components Flap doors Linear actuators Magnetic grabber Sample plate Source pedestal and clips XY feedthroughs XY microswitches Error and warning messages displayed when using the Diagnostics Mechanical control page are explained in Section 5 2 7 Also because the linear and flap door actuators are pneumatically controlled the performance of the sample loading chamber may be affected by problems in the vacuum system Table 6 2 Source and Sample Loading Chamber Troubleshooting Item Symptom Possible Cause Action 1 When the system covers are A X and or Y feedthoughs Lubricate feedthroughs See removed and the source is in need lubrication Lubricating the X and Y motion a loud grinding or Feedthroughs on page 5 28 squeaking noise can be heard in the source area or the source sticks when trying to achieve desired location 2 Sample plate either A The magnetic grabber With the grabber attached to occasionally or consistently failed circuit check that voltage to falls off t
247. then into the main source chamber through vacuum chambers at various pressures The sample loading chamber Figure 5 1 transports the sample plate between these areas using linear actuators flap door actuators and stepper motors Flap Door 1 me Linear 2 actuator Flap Door 2 actuator Linear 1 actuator Flap Door 1 not visible attached to source housing To main A source chamber Flap Door 2 shown closed Ne To atmosphere PB100855 Flap valve block Figure 5 1 Voyager DE STR Workstation Sample Loading Chamber 5 2 1 Vacuum System Interaction The actuators operate with a minimum of 15 PSI 1 03 bar An integrated compressor supplies pneumatic energy to Open and close the flap doors Extend and retract the linear actuators NOTE You can activate the flap doors and linear actuators only when the air compressor is running The air compressor runs only when the sample stage is in the load region Because the linear and flap door actuators are pneumatically controlled the performance of the sample loading chamber may be affected by problems in the vacuum system Figure 5 2 on page 5 8 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components High vacuum area Mirror Mirror turbo pump chamber lt 5 x 1078 torr BA2 Linear 2 actuator Sample Main p l
248. tion Tektronix is a registered trademark of Tektronix Inc All other trademarks are the sole property of their respective owners Printed in the USA 04 2001 Part Number Hardcopy 4319245 Rev A Part Number CD 4327166 Rev B Table of Contents Table of Contents Safety and Compliance Information How to Use This Guide shirts ses Chapter 1 System Overview 1 1 Voyager DE STR Biospectrometry Workstation Overview 1 2 Voyager DE STR Laser Safety 1 8 Voyager DE STR Workstation Components sssssseseeeeeme 1 3 1 Sample Loading Chamber sss eene nnne 1 3 2 Main Source Chamber tete arto i tret ond Op e Ke EaR 1 3 3 Laser System seca etaed utei eh tee eA eset 1 3 4 Flight Tube Drift Tube seeeeeeeeeeeseeenneeneneeenmeneennn nnne nnns 1 3 5 Mirror Ghamber rs ia te an d er tec deve tty etes 1 3 6 DIQIIZE ait epe ER NE 1 3 7 Computer and Video Systems sss 1 4 Voyager DE STR Workstation Supporting Systems Chapter 2 Voyager DE STR Workstation Electronics Theory 2 1 Electronics Theory Overview sisi 2 2 Electronics Common in Most Voyager DE STR Instruments 2 2 1 AC Distribution Board V750053 sss 2 2 2 DAC Digital to Analog Converter Board V750025 sss 2 2 3 DC Distribution Board V750034
249. tion rate to a value gt 20 Hz causes the laser to cease firing after it emits the first pulse Laser type NA NA re initialize continued 4 7 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 4 Voyager Diagnostics Software Table 4 3 Summary of Diagnostics Software Control Pages Continued Fields and Actions Status Indicators Comment Laser Control Page continued Beam attenuation Current beam NA attenuation Home beam Limit switch at NA attenuator home Voltages and Delays Control Page Sets all voltages and delay times in linear and reflector modes NOTE After changing any of the settings on this control page you must apply them before they can take effect To do so click APPLY ALL Ramp Voltages Set Delays f you leave the Voltage and Delays control page without applying the changes you lose tne changes The values revert to the last applied settings Modes of operation NA NA Linear Reflector If you set and apply voltage for the source grid Fidis voltages eller vo taggs mirror or guide wire without enabling high voltage Source the diagnostics software programs only the Grid Grid corresponding DACs You can verify these output Mirror Mirror voltages with a voltmeter DAC voltages are shown Guide Wire Guide Wire in Table D 2 on page D 8 To detec
250. tion stops the laser from firing homes the laser attenuator and resets the attenuator minimum and maximum values to those stored in the Registry file Under Laser Type select the laser you are switching to Internal or External and then click Re Initialize 5 4 2 Laser Attenuation The attenuator of the internal laser is an optical disk with a 360 gradient of optical density Figure 5 26 on page 41 positioned between the laser and the prism The laser attenuator decreases or increases the intensity of the laser beam As the laser is triggering you adjust the attenuation by pressing the Control Page Up and Control Page Down keys with the Voyager Software Instrument Control Panel window active This rotates the laser attenuator to set the degree of optical density at the point the laser beam enters the attenuator The optical density determines the amount of energy that is delivered to the sample spot Attenuation is controlled by a stepper motor and is adjustable using the Voyager Control Panel laser step controls For information on setting the step size see the Voyager User Guide Digitizer Laser Parameters This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Laser System 100 of the original beam intensity passes through to the sample Home position 3 optical density marked with reflective tape 0 optical density Greater density
251. tors and Valves Use the Diagnostics Software Mechanical control page Figure 5 3 to manually control the valves linear actuators grabber and load eject cycles 5 11 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components Camera Mechanical Laser Voltages Delays xt Y Table DE Switch Box Direct Bus Access Valves Actuators Indicators Limit Switches CLOSE OPEN Closed Open RETRACT EXTEND Retracted Extended Flap Door 1 9 g Fr Linear 1 o C F ja Flap Door 2 e cC iv Linear 2 o 9 F Foreline Valve 1 v Grabber Foreline Yalve 2 C c OFF ON Vent Valve Lol C Q C m Load Eject Cycle r Single Iteration m Multiple Iterations Total Number of Complete Load Eject Cycles to Be Run 10 zi Initiate LOAD Cycle Initiate EJECT Cycle Number of Complete Load Eject Cycles Completed 0 Start ZEIT SHG r Options pe scum e n E Restart Faulted Vacuum Gauges Do Not Move X Y Stage From Load Position E Figure 5 3 Mechanical Control Page Opening and Closing Doors and Valves You may need to manually open and close the doors and valves in conjunction with the actuators and grabber to remove a sample plate lodged in the main source chamber To do so click the Open or Close radio button of the respective valve Observe the Do T
252. tputs a pulse of pre programmed width The circuit has 10 ns resolution and a 15 bit maximum delay 327 us Theory The circuit can be divided into the following blocks Figure 2 33 100 MHz clock Trigger buffer and sync Latches Counters Address decoder Drivers 100Mhz Clock opto laser voor Le T a synch Pulse t P Driver gt reset 16 bits M 15 bit Start 15 bit Down Pulse e _ gt B daa bus Register Counter latch Driver load ai reset ji Vv y Pulse Driver gt N 15 bit End N 15 bit Down reset Register 34 Counter load zT reset f 16 bit Config L Register Buffer ee load start address Address load end bus Decoding n es PB100843 Figure 2 33 Pulse Generator Board Block Diagram 2 63 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics 100 MHz Clock The clock generates a 10 ns time base used by the counters synchronizer and address decoder Trigger Buffer The trigger buffer takes a 3 to 12 V asynchronous pulse event buffers it to 5 V synchronizes it to the 100 MHz clock then presents it as an
253. ts Une remarque fournit une information importante l op rateur er se pr sente ainsi REMARQUE Si on vous demande d ins rer la disquette de d marrage dans le lecteur ins rez la puis appuyez sur n importe quelle touche Une recommandation fournit une information destin e viter des d t riorations du syst me ou la perte de donn es RECOMMANDATION La lampe peut tre endommag e N y touchez pas Un avertissement fournit une information indispensable la s curit de l operateur et se pr sente ainsi AVERTISSEMENT Conformez vous toujours aux r glements du laboratoire quand vous utilisez votre syst me Safety Symbols The following symbols may be displayed on the system These symbols may also appear next to associated warnings in this document Electrical Symbols The following chart is an illustrated glossary of electrical symbols that may be displayed on your instrument Whenever such symbols appear on instruments please observe appropriate safety procedures This symbol indicates the on position of the main power switch This symbol indicates the off position of the main power switch This symbol indicates the on off position of a push push main power switch This symbol indicates that a terminal may be connected to another instrument s signal ground reference This is not a protected ground terminal This symbol indicates that this is a protective grounding terminal
254. ts and finish load eject operations To force the diagnostics software to ignore vacuum faults and finish load eject operations check the Ignore Vacuum Faults check box With this option enabled all vacuum faults are ignored and load eject operations automatically continue after the diagnostics software waits for the specified timeout period to expire CAUTION Using this option to ignore and override vacuum gauge faults when the system is operating under vacuum could damage the ion gauges O ring seals and vacuum pumps Resetting Faulted Vacuum Gauges After a vacuum fault occurs the diagnostics software turns off the vacuum gauges to protect them from damage caused by over pressurization You can restart the BA1 and BA2 ion gauges when TC2 registers 8 x 107 torr To restart the vacuum gauges click Festart Faulted Vacuum Gauges 5 2 7 Mechanical Control Page Errors and Warnings To determine the conditions generating display of an error or warning message review Table 5 4 An error is the result of a severe hazard and forces the operation to abort warning allows the option of continuing the operation with risk of damaging the instrument Table 5 4 Diagnostics Software Mechanical Control Page Warning and Error Conditions Action Selected in the Message dis Mechanical Control Page Type Condition Causing the Message Open Flap Door 1 Warning Vent valve is Open OR Flap Door 2 is Open Close
255. u suivant donne la signification de tous les symboles lectriques qui figurent sur les appareils En pr sence de l un de ces symboles il est imp ratif de se conformer aux consignes de s curit appropri es Position MARCHE de l interrupteur d alimentation principal Position ARR T de l interrupteur d alimentation principal poussoir Borne pouvant tre reli e la mise la terre d un autre appareil Ce n est pas une borne de mise la terre prot g e D Positions MARCHE ARR T de l interrupteur d alimentation principal bouton This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Safety and Compliance Information d effectuer tout autre raccordement lectrique l appareil Borne de mise la terre de protection devant tre reli e a la terre avant Borne recevant ou fournissant une tension ou un courant de type alternatif eS Borne pouvant recevoir ou fournir une tension ou un courant de types alternatif et continu Ce symbole appara t c t des valeurs des fusibles requis par le syst me AVERTISSEMENT Indique la pr sence d une haute tension et avertit l utilisateur de proc der avec pr caution AVERTISSEMENT Avertit l utilisateur de la n cessit de consulter le manuel pour obtenir davantage d informations et de proc der avec pr caution ET Symboles Non l
256. ubleshooting 5 32 Acquisition Error 6 9 Actuators see Linear actuators Address Decoder 2 17 2 64 Adjusting attenuator 5 41 extend oriface valve 5 25 grabber extension speed 5 25 microswitches 5 29 nitrogen laser repetition rate 1 13 5 39 nitrogen laser trigger 1 13 TIS voltage 5 42 Air compressor Load position fails to turn on 5 20 loss of operating pressure for actuators and valves 5 20 triggered by load switches 5 19 Aligning sample stage 5 13 source pedestal 5 24 AT Limit Feedback Circuit 2 31 ATM multigauge controller key 5 46 5 52 Attenuator see Laser attenuator Auto transformer connection to AC Distribution board 2 5 B BA gauge see also lon gauge degassing 5 54 E09 error 6 13 high reading 6 14 pressure range 5 46 range 5 45 shutdown 6 14 status bar display 4 11 Baud rate multigauge controller to Voyager 5 50 Bayard Alpert gauge see also lon gauge Beam guide wire 1 15 Beam laser see Laser beam path nitrogen Beam steering board 2 33 connectors 2 35 Input 2 35 input 2 35 location 2 34 output 2 35 overview 2 33 power 2 35 switches 2 35 test points 2 35 Co theory 2 34 Beam steering plates description 5 38 Bleed screw see Extend orifice valve Bradbury Nielson gate 1 15 5 42 Index 1 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted lt xmo2 Index C Cable for nitrogen laser externa
257. ument Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Accessing the Diagnostics Software 4 3 Accessing the Diagnostics Software Before Accessing Before accessing the diagnostics software close the ICP and shut down the IHC as follows 1 From the Start menu select Settings Control Panel 2 In Control Panel double click hy i Services The Services dialog box appears Figure 4 3 Services Service Status Startup Started Started Close Automatic Automatic Start di Started Automatic Started Automatic d Stop NAV Alert Started Manual N Auto Protect Started Automatic Pause Net Logon Started Automatic T NetMeeting Remote Desktop Sharing Manual Network DDE Manual Senp Network DDE DSDM Manual f L Hw Profiles ninde Hi Startup Parameters Help Figure 4 1 Services Dialog Box 3 Highlight the Instrument Hardware Controller program and click Stop Once the IHC has stopped close this dialog box Accessing To access the diagnostics software 1 From the Start menu select Programs Voyager and the appropriate Voyager diagnostics option The Voyager Diagnostics software for NT platform option is highlighted in Figure 4 2 gj User Guides m Data Explore F1 Diagnostics Cycle 1 Diagnostics Test 51 Run Voyager V4 5 T7 Uninstall Voyager e Voyager Control Panel FA
258. uments serial numbers 4153 and earlier had a guide wire and flight tube drift tube power supply Before shipment the beam steering circuit assembly is optimized for system performance If the instrument is disassembled or components are shifted out of factory alignment the optimization procedure can be repeated by a trained field service engineer For a description of this procedure see Chapter 5 Troubleshooting by Components The Beam Steering board assembly is installed where the V750061 Flight Tube Drift Tube Power assembly was located in earlier instruments Figure 2 21 on page 2 34 The Beam Steering board assembly uses the same power and control connections as the former Drift Tube Power assembly 2 33 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics steer eam ing board x Y Y PB100851 Figure 2 21 Beam Steering Board Location Operation of the beam steering voltage is transparent to the user When acceleration voltage is changed beam steering voltage tracks in a linear fashion Theory The beam steering assembly consists of X Y deflection plates and an adjustable programmable dual power supply board Figure 2 22
259. ur bits of the data value C i ck Write From the Address pulldown menu select 4 Control Register Enter a 16 bit value in the Data Value text field Clear bits 2 0 TIS frequency select to select a frequency of 100 MHz Setbit 4 TIS high voltage enable to enable high voltage Set bit 3 TIS counter enable to enable the counter which starts the TIS timer counters and activates the Timed lon Selector Remember you must write the entire sixteen bits of the Control register so enter a value that sets all components the Control register configures including DE and LMG parameters appropriately C i ck White i This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Index Numerics 100 MHz clock 2 64 16 bit Diagnostics software to test high voltage cable 5 30 18 MHz clock and divide by four 2 17 32 bit Diagnostics software see Diagnostics software 48 bit I O board 2 46 connectors 2 46 functions 2 46 LEDs 2 47 location 2 46 overview 2 46 6 theory 2 46 AC Distribution board block diagram 2 7 connection to auto transformer 2 5 fuses 2 5 2 7 J13 mirror turbo controller 3 6 J14 source turbo controller 3 6 LEDs 2 5 2 7 line voltages 2 5 location 2 5 output connectors 2 6 overview 2 5 stepper motor feedthroughs interconnect 5 27 theory 2 5 Accessing field service resources A 2 Acqiris digitizer 1 19 Acquisition tro
260. urce Clips Source clips guide the sample plate onto the sample stage Source side clips should be smooth all the way out to their leading ends with no burrs bends or dimples If the clips are damaged either replace them or smooth them with a small flat file and MicroFinish cloth If a new source clip is not available you may be able to switch the two side clips Switching the clips side to side allows the good trailing edge of one clip to become the leading edge on the other side of the source To switch clips side to side replace Clip 1 with Clip 3 Then replace Clip 3 with Clip 1 Figure 5 10 Trailing edge Leading edge Figure 5 10 Switching Source Clips After replacing the clips inspect all sample plates used in the system Sample plates that have either been dropped damaged during loading or otherwise mishandled may develop dimples or dents on their edges that cause the plates to bind in the source Repair or replace any sample plates with damaged edges 5 23 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components 5 3 2 Source Pedestal Aligning the Source Pedestal Materials T handle allen wrench To align the source pedestal NOTE Before aligning the pedestal be certain that both poles of the grabber are of equal length If not replace the grabber 1 With a
261. ure on the switch button a resistance usually about 10 to 20 ohms will occur in the switch contacts This resistance is sufficient to drop the 5 V logic signal low enough to cause the 5 V load logic to fail but not enough to cause the 24 V compressor control to fail As such the compressor runs but the logic faults To adjust the load position microswitch 1 Move the Load Switch bracket Figure 5 17 closer to the feedthrough sensor bobbin CAUTION Moving the switch too close to the bobbin may cause excessive wear and premature switch failure 2 Adjust the Load Switch bracket such that the switch and the bobbin are centered Figure 5 18 on page 5 29 and close enough that the switch is activated by contact with the bobbin Microswitch Bobbin PB100860 Correct alignment Figure 5 18 Adjusting the Load Position Microswitch Top View If the problem persists replace the switch 5 29 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter5 Troubleshooting by Components 5 3 4 Sample Plate and Grid Voltage The ion source can be relatively easy to troubleshoot if high voltage is present at the sample plate and the grid assembly However measuring and verifying these voltages can be difficult because the power supplies are safety interlocked and isolated to prevent accidental expos
262. ure to potentially lethal high voltages You can measure source and grid voltages directly or indirectly Directly Vent the instrument and disable the vacuum system Use a high voltage probe to measure the voltages Indirectly Use a high voltage Y adapter Before optimizing the variable voltage grid setting Grid Voltage adjust laser intensity until you obtain a signal to noise ratio of approximately 50 1 5 3 5 Internal High Voltage Cable You can test the integrity of the high voltage HV cable with the system under vacuum This process takes advantage of the Linear Actuator 1 being grounded In this test you determine if the internal high voltage cable feedthrough is maintained from the sample plate to the high voltage connectors Using the 16 bit Diagnostic Software To test the HV cable using the 16 bit diagnostics software 1 Load the sample plate into the sample plate holder 2 Exit Voyager Control software and manually turn off the ion gauge tubes 3 Start the service mode software 4 Initialize the autosampler then move the sample plate to the load position 5 Close Foreline Valve 1 6 Open Flap Door 1 and extend the Linear 1 actuator This completes the circuit As you extend the Linear 1 actuator watch the video monitor If you see movement of the plate the grabber assembly is touching the plate 7 Connect a small feeler gauge to the shaft of the Linear 1 actuator and the high voltage feedthrough
263. us If status is correct the BA1 cable is defective and needs replacement E07 Over Temperature inside Verify that the fan is operational temperature the multigauge Replace if necessary controller is over 65 C E08 Multigauge Board logic failure Power down then power up the mass controller spectrometer board Reset the multigauge controller unit by pressing F Vac then A81 If necessary replace the multigauge controller unit E09 Vacuum Catastrophic leak in Toggle through the channels to locate system the vacuum system the gauge that is shut down Check the integrity of the Foreline hose connections Copper seals O ring seals Feedthroughs Weldments E14 Keypad Keypad locked Unlock the keypad by pressing F Vac then A33 6 17 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter6 Troubleshooting by Symptoms 6 3 LED Indicators LED indicators reflect the status of the system Table 6 7 describes LED states and any actions needed to correct the fault Table 6 7 LED Indicators LED Location mae System Status Comment State Voyager Yellow Turbo initial Turbos initiated workstation top start up panel or Yellow Turbo building Turbo is at 80 of full speed D12 on MALDI and up speed Consolidated green Control Board Green Turbo at full Turbo is at normal operating conditions speed 56 krpm Red
264. us is used in three places Internally to the CPLDs for trigger generation and DE TIS pulse generators On the control board itself for 16 bit DACs As a buffered output from the Control Board to drive external DAC PCAs reflector and Beam Guide in a STR and the DVDT PCA Detector Voltage Delay Timer or Low Mass Gate delay timer DAC HVPS control The MALDI consolidated board contains up to four 16 bit DACs U16 U22 U27 U44 and associated control signals to control high voltage power supplies HVPSs The DACs which are controlled via the Voyager bus output a 0 to 10 V signal to control the HVPSs The V750102 001 configuration STR configuration has two populated DACs U16 source control DAC and U22 grid control DAC The other two DACs are unpopulated because beam steering and mirror HVPSs are controlled by discrete DAC PCAs See Section 2 2 2 DAC Digital to Analog Converter Board V750025 In addition to the DACs two discrete outputs are associated with HVPS control Enable and Polarity U19 a precision voltage source generates a 5 V reference for the 16 bit DACs Laser trigger generation Laser trigger is generated from one of two sources Legacy discrete IC trigger generator A 555 based oscillator controlled by pot R 46 To select this circuit set dipswitch S1 to LASTRGOLD This circuit can be set from 1 Hz to 200 Hz but is not programmable by the software Output from this circuit runs through the
265. ust be installed and maintained by an Applied Biosystems Technical Representative Top front back and side panels must be installed during operation When front and side panels are installed there should be no detectable radiation present If front or side panels are removed when the laser is operational you may be exposed to laser emissions in excess of Class 1 rating Do not remove labels or disable safety interlocks Additional Safety Information Refer to the user manual provided with the laser for additional information on government and industry safety regulations 3 1 2 Required Customer Provided YAG Laser Safety Measures Before servicing a system using the YAG laser the customer is required to provide safety precautions The YAG accessory supplied with the Voyager DE STR is a class laser which is considered not capable of producing damaging radiation levels during operation When maintenance requires an Applied Biosystems field service engineer to defeat the interlocks protection system for the instrument the YAG laser is classified as a class IV laser A class IV laser poses hazards to the eye and skin not only from the direct beam but in some cases also from the diffuse reflection These lasers can be considered a fire hazard and may also produce laser generated air contaminants and hazardous plasma radiation Therefore before you can perform maintenance or service on the YAG Laser while at the customer facility the cu
266. ut of 0 to 10 V to match the DC DC converter requirement of 0 to 5 V Output Each axis has available 0 to 500 V dc For the deflector plates however the output is current limited to 400 pA so no damage results from a continuous short circuit The DC DC converters specify a no load ripple of less than 0 002 or 20 ppm Load regulation for 0 to 100 current is 0 01 and line regulation from 11 5 V to 16 0 V input is 0 196 Connectors Switches and Test Points Table 2 8 Connectors Switches and Test Points on the Beam Steering Board Item Name Function Type Connectors J1 Power output 14 pin Mini Fit Horizontal 0 to 500 V and Return Vertical O to 500 V and Return J2 HV Enable Post Leg lon Polarity 8 pin MTA locking header 24 V Relay Power 0 1 inch spacing J3 12 V power for dual DC DC 2 pin MTA locking header 500 V converters 0 1 inch spacing 2 85 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 2 Electronics Table 2 8 Connectors Switches and Test Points on the Beam Steering Board Continued Item Name Function Type J4 DC DC program input from DAC 4 pin MTA locking header 0 1 inch spacing Switches Swi Vertical deflection polarity switch SPDT VERTICAL and SW2 Horizontal deflection polarity SPDT HORIZONTAL switch and Test Points
267. ways Use the Technical Publications Customer Survey at http www appliedbiosystems com contact html Send e mail to techpubs appliedbiosystems com Xix This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted How to Use This Guide XX This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted 1 System Overview This chapter contains the following sections 1 4 Voyager DE STR Biospectrometry Workstation Overview 1 2 1 2 Voyager DE STR Laser Safety 1 4 1 8 Voyager DE STR Workstation Components 1 6 1 8 1 Sample Loading Chamber 1 7 1 3 2 Main Source Chamber sss 1 8 1 3 3 Laser System sss 1 11 1 3 4 Flight Tube Drift Tube 1 15 1 8 5 Mirror Chamber sseseseeeeeeeee 1 16 1 3 6 Digitizer entente 1 19 1 8 7 Computer and Video Systems 1 19 1 4 Voyager DE STR Workstation Supporting SySIOITIS 1 oe Le ta et pio a nt 1 20 This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Chapter 1 System Overview 1 1 Voyager DE STR Biospectrometry 1 Workstation Overview The Voyager D
268. y No Unauthorized Copying Permitted Flap valves description 1 7 Flat signal 6 2 6 3 Flight tube description 1 15 function 1 15 Flight tube power supply input 2 61 power 2 61 Flight tube power supply output 2 61 theory 2 61 Flowchart Source troubleshooting 5 21 Fore pump failure 6 14 function 5 44 pressure range 5 44 typical pressure 5 44 Foreline valve 1 conditions to meet before opening or closing 5 9 5 10 relative location inthe vacuum system 5 8 Foreline valve 2 conditions to meet before opening or closing 5 10 relative location inthe vacuum system 5 8 TC2 pressure to meet before opening 5 10 Foreline valves conditions to meet before opening or closing 5 10 error message displayed in Mechanical control page 5 17 Mechanical control page error and warning messages 5 17 warning message displayed in Mechanical control page 5 17 Fuses AC Distribution board 2 5 2 7 Fusing F1A B Through F15A B 2 5 Index G Grabber and Linear 1 actuator 5 12 and sample plate 5 12 and source pedestal alignment 5 24 conditions to meet before powering off 5 11 error message displayed in Mechanical control page 5 17 fails to contact sample plate 6 8 fails to hold sample plate 6 4 fails to pull sample plate during ejection 6 6 keeping stationary when testing 5 13 Mechanical control page error and warning messages 5 17 powering on off 5 12 remains powered on 5 12 testing alignment 5 13 voltage 5 13 warning message
269. y storage capacitors are charged and the laser is ready to fire at any time When you perform service on the laser in External Trigger mode remove jewelry and other items that can reflect the beam into your eyes or the eyes of others Wear laser safety goggles and protect others from exposure to the beam Post a laser warning sign WARNING ELECTRICAL SHOCK AND LASER HAZARD When instrument covers are removed high voltage contacts are exposed and the laser emits ultraviolet radiation Wear laser safety goggles and post a laser warning sign at the entrance to the laboratory when you remove covers for service WARNING LASER HAZARD Exposure to direct or reflected laser light can burn the retina and leave permanent blind spots Never look directly into the laser beam Remove jewelry and other items that can reflect the beam into your eyes Wear laser safety goggles during laser alignment Protect others from exposure to the beam Post a laser warning sign while performing service This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted Voyager DE STR Laser Safety Laser Safety Requirements To ensure safe laser operation note the following The system must be installed and maintained by an Applied Biosystems Technical Representative Top front back and side panels must be installed during instrument operation When front
270. ystem includes an Tektronix oscilloscope use this document to learn about functions not described in the Voyage DE Biospectrometry Workstation User Guide Printer documentation depends on the printer customer purchases Use this documentation to set up and service the printer Microsoft Windows NT User Guide and related documents Use this guide to learn detailed information about the Microsoft Windows NT user interface Reference Documentation These reference documents are shipped with each Voyager DE STR system Varian Turbopump Instruction Manual Varian Turbocontroller Instruction Manual Varian Multigauge Controller Manual Mechanical Pump Operating Instructions LSI Nitrogen Laser Manual Omega DIO PC 48 Manual Power Single Output SPL Series Data Sheet GAST Compressor Operating and Maintenance Instructions The customer also receives the appropriate manual for the digitizer included with the system Xviii LeCroy Embedded Signal Analysis Products Operator s Manual LSA1000 Series and LeCroy Embedded Signal Analysis Products Remote Control Manual LSA1000 Series GPIB Software Reference Manual Tek Manuals This Document Contains CONFIDENTIAL Material of Applied Biosystems For Internal Use Only No Unauthorized Copying Permitted How to Use This Guide Send Us Your Comments The Technical Communication Department welcomes your suggestions for improving our manuals You can send us your comments in two

"user manual"

Contents

Download Pdf Manuals

Related Search

Related Contents

&quot;user manual&quot;

Contents

Download Pdf Manuals

Related Search

Related Contents

"user manual"