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MT Explorer 50 User Manual

1. a a 21 5 11 COLLECT MS MS SPECTRA ISOLATION AND 8 22 5 12 RETURNING TO THE MS MODE FROM THE MS MS 24 5 13 qe a TU BI 24 5 14 OPTIONS DIALOG BOK 25 5 15 28 5 16 EXTERNAE ONT OM 28 5 17 ADVANCED SETTINGS POWER USER 31 6 SHUT DOWN PROCEDURE 32 7 MAINTENANCE AND TROUBLESHOOTING 2 34 7 1 SCHEDULED 225 6 34 YR TROUBLESHOOTING a rina 34 7 3 MASS RECALIBRATION POWER USER 35 7 4 ELECTRON MULTIPLIER VOLTAGE ADJUSTMENT POWER USER 40 8 WARRANTY INFORMATION ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccess 44 APPENDIX A QUICK GUIDES FOR NORMAL OPERATION 46 APPENDIX CHROME EXPLORER DATA VIEWER INSTRUCTIONS 52 APPENDIX REPLACING THE MH CARTRIDGE sccsccccccccccccccc
2. File Plot Tools Help 4 P Scan Parameters PS 9 8 A 2 od scans 1 6 RT Spectrum Status Figure 5 2 Modas Command Toolbar Setting up a Method File After startup the default_ms method file is recalled Click on Scan Parameters Scan Parameters Icon on the top panel of Modas It will open a window with the already loaded MS method file based on the conditions selected for the experiment Select the range for MS or precursor mass range fragmentation energy for MS MS and press apply The mass range is from 100 m z to 800 m z in the example below Figure 5 3 the ion polarity must be positive The Enable AGC checkbox should typically be checked unless state the circumstances when the box doesn t need to be checked 9 MassTech MT Explorer 50 Scan Description MSn Settings Scan Range m z Mass Range Normal Low Parent mass Isolation Fragmentation From To m z width m z width m z ampl MS Power MS MS MS 100 1950 lon Polarity Positive Scan Time Number of microscans 5 Inject Time ms 100 Enable AGC 100000 Min Injection Time ms 1 Max Injection Time ms 100 Input Method for m z Range From To Center Width Apply Figure 5 3 Scan Parameters Box Open default method file Click File
3. Filename tesfile Acquire Mode 3 Continously Sample Name testsample ons Comment testcomment Minutes 1 lt gt Open Chromatogram Look in O Data quisition Status Idle My Recent Documents Desktop My Documents gs My Computer My Network Fil test mtd x Places Files MT Explorer Chromatogram File E up one screen Figure A 2 Continuously recorded spectra diagram Creates a new folder the Record icon on Simple Plot view The Pop Up will appear Recorder Settings 2 Left Click on Destination icon LJ n Pop Up will appear Save Spectrum 3 Choose a location to save the file 4 Create a filename Example test 6 Left Click on SAVE the Pop Up will close Save Spectrum Left Click on START Note becomes bold when recording Left Click on STOP to end the recording MassTech MT Explorer 50 MIM To Review Saved Spectra Top Left Corner of Modas Control Interface Modas 3 0 default ms method Plot Tools Help 4 1 Default Method Scan Open Method d Save Method Export Print Documents 1G Desktop My Computer Network File name Places Files of type MT Explorer Chromatogram File Figure A 3 Saved spectra diagram 1
4. i zum m 5 Scan Parameters te 2 E m ans 2 2 RT Spectrum Status Report E Report IT 0 2 TIC 4 103E 03 SIC 0 000E 00 Vacuum 221 6 Turbo Pump R 2307 6 L 2 9E01 lon Optics Hexapole RF Main RF 238 7 R 2455 4 L 2 5E01 Power Supplies lon Detection System p Instrument Status 305 8 R 3225 5 2417 L 2 0E01 461 6 R 2507 9 R 4707 3 1 19 01 L 1 9E01 134 0 414 0 R 14509 R 4104 9 L 1 6E01 p L 1 6E01 389 0 gue pe 2197 8 L 1 2E01 00 0 4817 R 4257 5 R 5718 7 107 6 188 3 320 7 9 9E00 L 9 9E00 RE1243 6 1684 6 R 2875 8 139 0 00131 3 149 2 9 0E00 30718 aoE00 420 3 R 116R21320 3 R 3077 8 R45069 3 1 8 0 088 0 00 L 7 9E00 157 9 00 4374 R 5209 4 L 5 9E00 318 364 7 3813916 I R 341R 38B Q386 7 3 9 00 3 98020 10 3 0 00 L 3 9E00 Scans elapsed 1 Microscans remaining 0 Figure 7 10 The normal noise if the correct Multiplier voltage is achieved 8 Save the adjusted multiplier voltage as a default value Go to Tools gt Options gt Detector dialog Figure 7 7 Set the adjusted multiplier value in the appropriate field and then click the OK button The multiplier voltage is saved as the default MassTech MT Explorer 50 Hardware Positive Negative Name Voltage V w RT Plot _ _ Multiplier HV V 230 5 w Chromatogram Conversion Dynode HV V
5. Click on the CHROMATOGRAM tab 2 In the menu toolbar select FILE then OPEN CHROMATOGRAM The Pop Up will appear Open Chromatogram 3 Choose desired file click OPEN Note File name and basic info will appear if you choose but do not click as shown above MassTech 48 MT Explorer 50 ume Scan Parameters a e T scans 1 v daz 84 Scan Parameters Scan Description Settings Scan Range m z Mass Range Normal O Low Parent mass Isolation width Fragmentation From m z m z width m z Q mers 5 Oms 30 8 2 _ 8 21198500 Ion Polarity Positive Scan Time 3 Number of microscans 3 84 Inject Time ms AGC Enable AGC AGC Target au Min Injection Time ms Max Injection Time ms 0 Input Method for m z Range From To O Center Width Figure A 4 Collect MS MS spectra diagram Left Click STOP to end spectra collection Left Click on SCAN PARAMETERS Pop Up will appear Scan Parameters Choose sms Enter the PARENT MASS m z value for the ion to be fragmented Enter an upper value for the SCAN RANGE Recommended Add 10 to the Parent Mass m z value Enter a Fragmentation Amplitude value ampl Note 0 denotes Parent Mass m z ion isolat
6. ELKE a a C Documents and Settings user My Documents SampleData_M3TD 01_APCI MS_Pos_Liq_Carf db3 1 9 4 5v TEF perennem Pepea 4724 Click Here to Rescale undo zoom TiC 547786 95 Timestamp 6 5 2012 11 53 19 AM Click Here to Copy a Click to rescale Intensity only 700 750 300 Mem usage 15 33 MB Figure B 2 ChromExplorer running B Average Mass Spectra 1 Toggle Select on the Chromatogram Window top 2 Drag the mouse pointer on the Chromatogram for the region the user intends to average the region should be highlighted with thicker trace as shown below ChromExplorer 1 3 1 C Documents and Settings user My Documents SampleData_M3TD 01_APCI MS_Pos_Liq_Carf db3 Averaged Scans Figure B 3 ChromExplorer showing highlighted chromatogram MassTech 53 MT Explorer 50 3 The mass spectrum window should show average of the mass spectra of the highlighted scans Tip If you did not see highlighted region on the chromatogram and instead zoomed the Chromatogram simply click Rescale on the right hand side of the chromatogram window click Toggle on the left hand side of the chromatogram window try again MassTech 54 MT Explorer 50 APPENDIX C REPLACING THE MH CARTRIDGE Note Please refer to the User M
7. Mass Calibration Conversion Dynode HV V Detector Import Export 1 Change Password Figure 7 11 Save the Adjusted Multiplier Voltage as Default 9 Repeat the procedure for the opposite polarity 10 Restore the noise filter level back typical value 15 3 units See item 3 7 5 Export Import of the Calibration Parameters Power User Only The calibration parameters can be changed from time to time It is a good idea to save backup the calibration parameters before such changes and also during Modas software update so they can be recovered 1f necessary parameters are saved into a user defined file during the Export procedure so the recovery is straightforward during the Import procedure Note The calibration parameters are permanently changed during the Import procedure Always make a backup file before using the Import feature to have the option of reversing any undesirable changes MassTech 2 MT Explorer 50 I 8 WARRANTY INFORMATION Twelve Month Limited Warranty MassTech Inc provides to the original purchaser the following limited warranty from date of invoice MassTech Inc warrants each MT Explorer 50 instrument and its components to be free from defects in material and workmanship Liability under this warranty covers servicing of the instrument when it 1s returned pre paid from the customer s facility within the United States to our factory MassTech Inc will repair any
8. File Chromatogram Tools Help Admin Views Perspectives Chromatogram e e e 22 c N e e eo e e N SN sample 1 Some comment Run 4 100 150 450 Index 20 Parentlon 0 Injection Time 0 00100 C Users Konstantin Documents MTE50 Data test mtd Reset External Control Scans elapsed 0 Microscans remaining 0 d d Figure 5 27 Updated comment from run count 5 17 Advanced Settings Power User Only To maintain optimum configuration for the common user some settings are only available to Power Users Enabling the power user settings requires an administrative password which is provided during MT Explorer 50 training Modas in Power User mode is started by double clicking a separate icon Procedures for Power User settings Mass re calibration Electron multiplier voltage adjustment and Export Import of calibration parameters are described in section 7 3 and 7 4 MassTech 31 MT Explorer 50 SHUT DOWN PROCEDURE Prior to maintenance or transport the instrument needs to be shut down Below are the instructions 1 The instrument should be set to standby mode if not already so 2 Right click at the Standby button the standby menu should appear Power Off 3 Click on Power Off Reset lon Source PCB Status Report j Cancel Report 4
9. Savitzky Golay Filter Median Window Size Polynom Power M Number of Points to the Left NL Number of Points to the Right NR 3 Cancel Figure 7 7 Setting Noise Filter Level to Zero 4 Click IR Set Conversion Dynode to 10kV positive mode or MassTech 40 MT Explorer 50 M 10 in negative mode Set Multiplier to zero volts see Figure 7 8 ley Exit Lens DC offset V 60 Multiplier High Voltage kV 0d 5 Conversion Dynode High Voltage kV 10 00 Figure 7 8 Initial Detector Settings 5 Configure the scan MS mode m z 35 2000 1 microscan Injection any value for example 100ms 6 Acquire the spectrum The noise level should be around 5 10 as shown in Figure 7 9 File Plot Tools Help 9 2 2 1 619 03 SIC 0 000 00 9 MassTech MT Explorer 50 7 stepwise increase of the multiplier voltage Figure 7 7 from 1 8kV step 100 acquiring the spectrum at each step until the dark count spikes level in the range of 100 10001s achieved The typical spectrum is shown in Figure 7 5 This is the adjusted value for the Multiplier voltage DO NOT EXCEED the multiplier voltage above 2 5kV If the noise level at 2 5kV 1s still below 100 it is an indication that the detector needs to be replaced File Plot Tools Help
10. and reach the detection system where they produce a signal proportional to the number of ions detected The ion detection system consists of a conversion dynode electrode with high voltage up to 10 kV applied to it and a discrete dynode electron multiplier The ion current from the detection system is amplified by a pre amplifier and 15 then communicated to the data system for further processing storage and display Each sequence of loading the mass analyzer with ions followed by mass analysis of the ions is called a scan The MT Explorer 50 uses several different scan modes types to load fragment and eject ions from the mass analyzer this allows the user to do MS and tandem MS MS MS experiments This MT Explorer 50 s ability to vary the scan mode type ion polarity and having an interchangeable AP ionization source interface gives the user great flexibility in the instrumentation for solving complex analytical problems MassTech MT Explorer 50 This page 15 left intentionally blank MassTech MT Explorer 50 2 MAJOR COMPONENTS With external cover removed top view of the MT Explorer 50 15 shown in Figure 2 1 Figure 2 1 Major components diagram Cone with inlet capillary B MS analyzer Se Radio Frequency coils 4 dr D Metal Hydride MH a oW so L uu 0 cartridge E Po
11. gt Default Method The default method dialog box Figure 5 4 will appear Once the appropriate mode and polarity 15 selected 1t will recall the selected default method MS Positive MSMS Positive O MS Negative MSMS Negative Figure 5 4 Default Method Dialog Box Recalling a Previously Saved Used Method File Click File gt Recent Methods It has a list of most recent 10 method files with their path information see Figure 5 5 MassTech MT Explorer 50 Plot Tools Help Default Method a Scan Parameters Open Method Save Method O Open Chromatogram Export Print Recent Methods Recent Chromatograms Exit 5524 z E03 Figure 5 5 Opening Recent Method File 5 3 Ion Polarity Modes The MT Explorer 50 can operate in either one of the two ion polarity modes positive or negative It controls whether positive ions or negative ions are transmitted to the mass analyzer for mass analysis by changing the polarity of the potentials applied to the 10n source and ion optics Note that it 1s impossible to conduct a simultaneous positive and negative 10n spectrum collection on an ITMS The information obtained from a positive 10n mass spectrum is different and complementary to that obtained from a negative ion spectrum for the same analyte Thus the ability to obtain both a positive 10n and negative 10n mass spectra aids the qualitative analys
12. instrument is about 15 mTorr while the background air pressure in the second vacuum section is at 10 Torr range The ion guide optics focuses and accelerates the sample ions transmitted through the inlet capillary into the mass analyzer where they are trapped in stable orbits by a time varying electric field The polarity of the potentials applied to the ion source and ion optics elements determines whether the positively or negatively charged ions are transmitted to the mass analyzer this ion polarity mode is selected by the user The ion guide optics are hexapoles composed of six parallel rods equidistantly positioned around the hexapole central axis A superimposed radiofrequency RF potential is applied to the hexapole rods to create a trapping electric field confining ions near the hexapole center axis The ion transfer system of the instrument includes the inlet capillary and two hexapole ion guides one per each stage of the vacuum system which is separated by the conductance limiting diaphragms The conductance limiting diaphragms restrict the gas flow entering either section while minimizing the ion losses due to collisions Ions are propelled from the inlet capillary to the mass analyzer by applying small accelerating voltages to the ion guide elements typically 5 10 V Additionally these voltages are used to gate ions coming from IS so that they reach the mass analyzer during the injection period but only when the trap is fille
13. selector Figure 7 4 If a peak cannot be found in the calibration mixture selector then the theoretical m z value is set to zero like the peak 36 in Figure 7 4 To find the mass of this peak the user will need to enter the theoretical m z manually Compare the top two peaks in the Figure 7 4 Peak 30 has current measured m z 1122 42 which is by 0 42 higher then Theoretical value Error is 0 42 Th in the Error column Peak 31 has Current value by 1 Th higher Error in this case is 1 42 Obviously the peak 31 is C 13 isotopic satellite of 30 therefore is not included in the calibration The user s responsibility is to uncheck it into the Use column Repeat such an inspection for each peak in the table uncheck all of the peaks with too large Error THE NEW CALIBRATION WILL BE CALCULATED ONLY FOR THE CHECKED PEAKS If more peaks need to be added from another spectrum open or acquire it in MODAS and click Peak Peaks button again the user will be prompted to either append peaks or override the entire table 9 MassTech MT Explorer 50 Once finished with peak selection click Calibrate button newly calculated calibrations will be seen below the table see Figure 7 5 File Tools Help i amm si i Scan Parameters 4 SWE l o pam Mass Calibration RT Spectrum Status Report Report Pick Peaks Calibrate Agile
14. subject to change without notice While every effort has been made to supply accurate and complete information MassTech Inc assumes no responsibility and will not be liable for any errors omissions damages or losses that might result from any use of this manual or the information contained therein even if this information is properly followed and problems still arise Revision History Version 1 0 Created January 2013 Version 1 1 Updated July 2013 Version 1 2 Updated October 2013 Software Edition Modas 3 2 Operating System Microsoft Windows XP Service Pack 3 or Windows 7 MassTech 111 MT Explorer 50 This page 15 left intentionally blank MassTech 1V MT Explorer 50 _ Table of Contents PREFACE coania 1 PRINCIPLE OF OPERATION esesesesesecesscscscseseseseseseseseseoscsoseseseseseseseseseosssoseseseseseses 1 2 MAJOR COMPONENT SS cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccsccsccscccccscccess 5 3 INSTALLATION AND STARTUP PROCEDURES cccccccccccccccccccccces 7 3 1 7 Jud INSTALLATION REQUIREMENTS epa else Fran agr equ eye ck va ipa vlov qa ep va guae 7 3 3 SYSTEM INT
15. ERFACE FRONT 20 0 1000 00 00 7 3 4 SYSTEM INTERFACE BACK PANEL ccsccsccscccecceccecceccceccsscecccscesccsscescescceccsscescescesscscescessence 8 3 5 MT EXPEOREBOO START LIB 40064060 a DN ERFURT as ud Ida 9 3 6 INSTALLATION OF MODAS MT EXPLORER 50 OPERATING SOFTWARE c cccceccecceccscescescescceecs 9 4 INSTALLING AN ION SOURUXQCE e eee eee eee eee eee eee eee eeseese eee eeseese eese sese ee 11 5 MODAS SOFTWARE AND OPERATIONAL INSTRUCTIONS 13 5 1 STARTING SOFTWARE OE eu dated od aUos ad oae qa 13 5 2 STARTING VIS OPERATION 13 5 3 TON MODES 16 5 4 ADIUST ION SOURCE VALUES 16 5 5 ADIUSTION OPTICS VALUES CERO 17 5 6 ADJUST DETECTOR VALUES ccccccecssccscccsccsccsccescesccsccsccescesccsccescescesccsccescesccsscsscescssesscecens 18 5 7 SELECTING METHOD OF MS 00 000000000000 19 5 8 CONTINUOUSLY SCAN MS SPECTRA 19 5 9 TRO eee een a eee 20 5 10
16. MT Explorer 50 Ion Trap Mass Spectrometer User Manual Version 1 2 MassTech Inc 6992 Columbia Gateway Drive Suite 160 Columbia MD 21046 USA Phone 1 443 539 1758 Fax 1 443 539 1759 Email 11515 apmaldi com Web www apmaldi com MassTech MT Explorer 50 0 ff Warning The MT Explorer 50 lon Trap Mass Spectrometer is produced with a variety of components which should only be serviced by qualified personnel For maintenance or repair issues please contact your sales agent or the manufacturer directly MassTech Inc 6992 Columbia Gateway Drive Suite 160 Columbia MD 21046 USA Phone 1 443 539 1758 Fax 1 443 539 1759 Email msms apmaldi com MassTech ii MT Explorer 50 COPYRIGHT NOTICE All rights reserved including the right of reproduction in whole or in part of any form This document may be electronically reproduced distributed or printed in its entirety provided this copyright and statement are attached Any modification or any other reproduction distribution or use of this document or portions hereof is strictly prohibited without the express written permission of MassTech Inc COPYRIGHT 2012 All rights reserved TECHNICAL NOTICE Technical information contained this publication 15 for reference purposes only Contents of this manual are
17. Section 5 2 or O Ion Source Icon See Section 5 4 or 4 Ion Optics Icon See Section 5 5 pz pa The scan parameters source settings and optics settings are all part of MS operation and will be saved into the method file see Section 5 2 5 8 Continuously Scan MS Spectra Mass Spectra are scanned during the operational mode The spectral scanning is controlled by Play Pause Stop buttons in the middle of the top panel To start scanning click Play 1 in the Scan box stands for an unlimited number of spectra to be scanned MassTech 19 MT Explorer 50 scans 1 EI 3 Figure 5 9 Play Pause Stop Panel If a specific number of spectra 15 desirable rate 1s few spectra second depending on injection time or signal intensity if AGC 15 selected the user can specify a number in the window Scanning will stop automatically after the specified number of spectra has been scanned The Pause button will pause and Stop button will stop scanning 5 9 Record Spectra Recording the mass spectra can be achieved If you are ready to record the spectra that are being collected press the Record button 3 A Recorder Settings window will open where you can specify the name of the file see Figure 5 10 Once recording is in progress the Record button will light up will remain so until the recording is over Filename Acquire Mo
18. The turbo pumps should spin downward which generates a high pitch to low pitch sound wait for the Parameter Value lon Source Figure 6 1 Shut Down Produce Box next step until the turbo pumps spin down to prolong their life around 15 minutes 5 Turn off the main switch in the back of the MT Explorer If maintenance needs to be done wait an additional 15 minutes to completely break vacuum 6 The system should be ready for maintenance or transport A Instrument will be turned off Are you sure Figure 6 2 Warning Box Figure 6 3 Power Off Box MassTech 32 MT Explorer 50 This page 15 left intentionally blank MassTech 33 50 _ 7 MAINTENANCE AND TROUBLESHOOTING 7 1 Scheduled Maintenance The empty MH cartridge should be replaced for a full one from time to time typically in one week or more for the new cartridge The replacement instructions are provided in Appendix C below Note Please refer to the User Manuals for HydroFill and HydroStik for important information regarding safe use of these units It is good practice to run methanol at the end of the day ITMS must be in Standby mode Since the vacuum pumps are oil free pumps they do not require scheduled maintenance DO NOT ATTEMPT any services or repair
19. alibration Type Quadratic Apply Scans elapsed Reset Figure 7 6 Apply Calibration As shown in Figure 7 5 three types of calibration curves are calculated linear quadratic and cubic Any of the calibrations can be used by MODAS Note linear calibration provides the RMS error of 0 455 Th across the spectrum while the quadratic RMS 16 ten times more precise The complex cubic approximation provides similar result Typically the quadratic approximation provides a more accurate mass compared with a linear function while cubic gives no essential advantage It is recommended selecting the calibration type Quadratic The RMS value is the mass precision expected after the recalibration If all the peaks in the table are identified with correct theoretical values the calculated RMS should be linear RMS lt 0 5 quadratic and cubic RMS lt 0 1 The large M 9 MassTech 39 MT Explorer 50 RMS is an indication that the peak selection identification error is made Try to correct the mistake s and press Calibrate button again The procedure can be repeated many times until a good RMS is achieved If it does not help the spectrum spectra quality may be not adequate For example the spectrum was recorded with too high of an injection time IT which resulted in peak broadening shift Finally choose mass range either Normal or Low polarity Positive Negative and ca
20. anuals for HydroFill and HydroStik for important information regarding safe use of these units If the MODAS window has a warning about the Buffer gas the MH cartridge should be replaced with a full cartridge Note Cartridges are reusable Do not discard Fila Plot Tools Help Admin Views Perspectives m o og 7 m Status Report Parameter Fault Flags pg Vacuum Ion Trap Chamber Air Torr 1 483 amp 04 Buffer Gas Warning Turbo Pump Stage One OK Stage Two gj lon Optics x Hexapole RF Re Scans elapsed 296 Microscans remaining 0 Figure Warning message at status report In the back panel Figure 3 3 locate the MH cartridge in the cartridge holder The cartridge is hand tightened no tools are necessary Turn it counter clockwise to loosen the depleted cartridge The MH cartridges can be recharged using HydroFILL station supplied with MT Explorer 50 please refer to HydroFILL manual on charging instructions After charging put the full cartridge straight back in the cartridge holder turn it clockwise to tighten MassTech
21. ard disk the peaks will be loaded automatically MassTech 37 MT Explorer 50 File Tools Help s 1 Scan Parameters x 27 Ta II 2 0 i OQ fsws cu Mass Calibration RT Spectrum Status Report Report Pick Peaks Calibrate DAC Current m z Theoretical m z Use Error Th 5145 31 226 87 0 00 0 00 lon Trap Chamber Air Torr 52 2m Calibration Mixture Buffer Gas 13963 26 601 49 601 98 Selector 4 Turbo Pump 16079 94 691 50 f Stage One 18759 89 805 49 Stage Two p lon Optics 18784 41 806 53 p Hexapole RF 24107 15 1033 09 1033 99 Report Main Repor 24129 05 1034 02 1033 99 0 Para lon Detection System on Source 30508 57 1305 80 0 00 p Power Supplies ESC Vacuu p Instrument Status 30530 75 1306 75 0 00 38185 94 1633 24 1633 95 38204 50 1634 03 1633 95 42226 74 1805 74 0 00 Polarity positive Calibration Type Quadratic Scans elapsed 0 Microscans remaining 0 Figure 7 4 Mass Calibration Tab If the RT and disk spectra are opened at the same time the user will be prompted to choose which one to use The DAC and current m z columns in the table were imported from the spectrum the theoretical m z column was built based on the calibration mixture
22. cees 55 MassTech MT Explorer 50 This page 15 left intentionally blank MassTech vl gt gt gt MT Explorer 50 _ The following symbols used this manual to indicate material that should especially be noted because it relates to safety issues This symbol in the manual margin is used to emphasize the presence of very important operating instructions related to safety especially during installation removal maintenance and troubleshooting Operators are strongly encouraged to read this manual before installation removal operation maintenance or troubleshooting Operators should pay special attention to paragraphs marked by DO NOT ATTEMPT services or repairs that are not covered in the Troubleshooting Section Section 7 of this manual For services and repairs beyond those specifically provided in the Troubleshooting section contact the manufacturer MassTech Inc 6992 Columbia Gateway Dr Suite 160 Columbia MD 21046 443 539 1758 MassTech MT Explorer 50 This Page is left intentionally blank MassTech MT Explorer 50 _ 1 PRINCIPLE OF OPERATION The MT Explorer 50 is a miniaturized Ion T
23. component s or part s that 1t finds to be defective during the period of this limited warranty which 15 twelve months from the date of 1nvoice Should a defect become apparent the original purchaser must first notify MassTech Inc of the suspected defect and request a Return Merchandise Authorization number RMA at the following number 443 539 1758 The instrument or suspected components should be carefully packaged in the original container if the original shipping container has been lost trashed or damaged another one must be purchased from MassTech Inc prior to shipping Then mark the original container with the RMA and ship the item s prepaid to MassTech Inc Attn Service Dept 6992 Columbia Gateway Dr Suite 160 Columbia MD 21046 The instrument will be repaired the shortest possible time and returned prepaid by the same shipping method as received by the factory During the warranty period no charge will be made to you for parts services or labor This limited warranty 1s void if the instrument has been damaged by accident misuse negligence act of God or serviced by any other person or manufacture not authorized by MassTech Inc The warranty also does not apply to units that have had the serial lot number altered defaced or removed MassTech P MT Explorer 50 _ This limit
24. d by the ions This function is controlled by an automatic gain control AGC of electronics that sets the optimum number of ions to the mass analyzer by altering the injection time The mass to charge ratios of the produced ions are measured by the ion trap mass analyzer Selected ions are stored in an evacuated cavity 1 e ion trap by applying the appropriate electric fields a very small amount of a light buffer gas H or He is supplied to the ion trap The main functions of the buffer gas required for ion trap operation includes ion cooling towards the center of the trap and ion fragmentation in collisions with the buffer gas molecules Ions can be ejected from the mass analyzer selectively according to their masse to charge ratio Schematically the layout of an ion trap resembles two electrodes called end caps which are either grounded or biased with DC or AC potentials and the third ring electrode is between the end caps a sinusoidal RF high voltage is applied to it MassTech MT Explorer 50 _ A batch of ions 1 the trap cell 15 constrained by this oscillating electric field Some of the ions will have stable trajectories and remain trapped whereas others will have unstable trajectories and will be ejected through a hole in the exit end cap electrode These ions will pass through exit lens
25. de 2 Continously Sample Name Test sample O Scans Comment Test sampe comment O Minutes Acquisition Status State Idle Scans Duration Figure 5 10 Recorder Settings Box 9 MassTech m MT Explorer 50 _ Recording Modes The Acquire Mode allows for the user to record the spectra either by number of Scans Minutes or Continuously until the Stop button is pressed Click Start to start the recording The Record button on the Modas tab will light up it will remain lit until recording is stopped View Acquisition Status to see the state of acquisition the number of scans in the file and the duration of collection None of the spectra will be recorded unless Record button is pressed lit see above for both forms of the button To Stop Recording Press Stop in Recorder Window to avoid keep writing spectra into the same file If the Continuous Acquire mode was selected recording will not automatically stop by stopping spectra acquisition or by pressing Close button in the Recorder Settings window Note The retention time on the chromatogram starts when the recording starts If scanning 15 paused or stopped and thereafter resumed the original start time will remain as the start time of the resumed scans as well The chromatogram will show a straight line for the duration of the pause or s
26. ectra Isolation and Fragmentation MassTech MT Explorer 50 The MS MS Spectra be obtained by opening the method window Figure 5 13 and selecting the Mass Range e g from 45 to 319 Precursor mass to be fragmented at 100 Isolation window 15 5 Da reasonable Fragmentation width is 2 Da reasonable Frag Amplitude Fragmentation Amplitude is 0 no fragmentation expected This ensures that the ion is stable enough to survive the stay in the ion trap As typically done with small molecules one must adjust the Frag Amplitude for each Parent mass by trial and error For peptides a more universal value of 25 can be applied for most species The starting point of will show you the height of the peak at 100 then the starting point of fragmentation could be 50 and then the user should view the reduction of the peak at 100 and rise of the fragments adjusting the Frag Amplitude until the peak at 100 is low but still visible at about 10 of the spectrum and fragmentation peak s are consistently visible across multiple scans multiple spectra Main Scan Scan Description MSn Settings Scan Range m z From To Mass Range Normal Low Parent mass Isolation Fragmentation m z width m z width m z ampl Q MS Power O MS MS MS 100 500 150 8 2 0 04 lon Polarity Positive Scan Time Number of microscans 5 Inject Time ms 10 AGC Enable AGC AGC Target au Min Injec
27. ed warranty contains the entire obligation of MassTech Inc and no other warranties expressed implied or statutory are given No representative or employee of MassTech Inc 15 authorized to assume any further liability or grant any further watranties except as set herein MassTech Inc disclaims liability for indirect incidental or consequential damages The exclusion or limitation of incidental or consequential damages are not permitted by some states and this limitation or exclusion may not apply to you Warranty rights vary from state to state therefore you may have other rights addition to those provided by this warranty MassTech MT Explorer 50 MMI APPENDIX A QUICK GUIDES FOR NORMAL OPERATION To Start Normal Operation 1 Left Click on the icon to automatically start up the ITMS will become and PLAY will become accessible 2 Left Click on PLAY to start mass spectra generation Figure Start normal operation diagram MassTech MT Explorer 50 To Continuously Record Modas 3 0 default ms method File Plot Tools Help Scan Parameters zn 4 st Dow 4 nm xis Q scans v Spectrum N Parameter Value Ion Source T 000 Source ID NSI 0 0008 000 MUN 0 022 NSI C 0 uA Recorder Settings
28. ffset V Hexapole RF amplitude V Figure 5 7 Ion Optics Box 5 6 Adjust Detector Values Detector voltages can be set at the Detector window Click y to access the detector window s Exit Lens DC offset V Multiplier High Voltage kV Conversion Dynode High Voltage kV Figure 5 8 Adjust Detector Values Box Note the changes to the electron multiplier and conversion dynode voltages made in this window are valid only for the current session Permanent changes of these voltage settings can only be done by the Power User Section 5 15 MassTech MT Explorer 50 _ 5 7 Selecting Method of MS Operation A method of MS operation is kept in special files extension mtm There are two ways to select a method file 1 Open default method file through the dialog box File gt Default Method After Modas startup the default MS method 15 loaded 2 Open any user saved method file The current MS method can be saved into a method file at any time through File gt Save Method dialogue Opening the saved method file is done through File gt Open Method dialogue After selecting the method file the user can make any adjustments by clicking on the following icons scan parameters source and optics icon Scan Parameters Scan Parameters Icon See
29. he MS system with a laptop PC RJ 45 30 m maximum length 1 8 m cable is supplied with the system e Exhaust line 7 I D plastic hose or tubing connected to a chemical hood or an appropriate fume ventilation system a barb connector is provided with the system 33 System Interface Front Panel Figure 3 2 is a picture of the interface front panel of the ITMS The alignment rails and alignment stubs are used to correctly mount and position an ion source to the ITMS The 15 pin connector and HV1 port connect directly to an ion source 44 pin D sub and HV2 connect and serve as an external control for some ionization sources additional temperature controls and HV output see your specifications MassTech MT Explorer 50 Five light emitting diodes LEDs located the upper right side of the ITMS front panel serve as indicators Front Panel Indicators Power illuminates when the electronic assemblies and vacuum systems are supplied with power 44 pin Vacuum illuminates when D sub the vacuum pressures inside ITMS are within operational ranges Ready illuminates when the HV interlock is engaged and the system is ready to operate Standby illuminates when the user places ITMS in Stand by mode most control voltages are down Operation illuminates when the ITMS 1s collecting the mass spectra 1 in full operation of ITMS Figure 3 2 Front panel 3 4 System I
30. he vacuum of the mass analyzer This ion delivery process has to occur with minimal ion loss for further mass spectrometry analysis A block diagram with the main components of the optics vacuum system and electronics of the MT Explorer 50 is presented in Figure 1 1 MS Detector Ion Guide Mass De 2S Optics Analyzer Personal Computer Acquisition Figure 1 1 Block diagram for MT Explorer 50 and its major components Ion Ions produced in the source are introduced to the mass spectrometer MS through a heated stainless steel inlet capillary which has 180 um 1 4 The air intake is 80 100 cc min depending on the inlet capillary temperature MassTech MT Explorer 50 _ The instrument has two vacuum sections Each section is evacuated by a turbo pump The turbo pump in the first vacuum section and is backed by a diaphragm pump The exhaust of the turbo pump in the second vacuum section which is connected to the first vacuum section of the instrument provides low backing pressure for its operation The majority of the gas flow from the heated inlet capillary is pumped out through the first vacuum section making the gas flow that reaches the second vacuum section of the instrument negligible With the inlet capillary temperature at 200 C the pressure the first vacuum section of the
31. ion of the Ion Source the system should be either at the OFF or STANDBY mode Do not attempt to switch the ion source when the system is ON SCAN mode MassTech 11 MT Explorer 50 This page 15 left intentionally blank MassTech 12 MT Explorer 50 5 MODAS SOFTWARE AND OPERATIONAL INSTRUCTIONS The Modas software has different levels of use The user mode refers to maintain optimum configuration for the common user some settings are only available to Power Users Enabling Power User mode requires an administrative password which is provided during MT Explorer 50 training 5 1 Starting Software Open the Modas software by double clicking the y icon a Modas To access the Power User option click the Modas Power User icon followed by password prompt Note Clicking Help will open the electronic version of this manual 5 2 Starting MS Operation File Plot Tools Help t i Scan Parameters E zl OQ scans Ji i 35 eee L Automatic Start Up Shut Down Figure 5 1 MS Starting Operation Box MassTech 13 MT Explorer 50 Press the button in the upper right corner of the screen to begin the automatic system startup procedure oodo o Transition Sequence Upon startup the RT Spectrum Real Time Spectrum tab appears as well as the Status Report tab on the right
32. ion only Suggested Fragmentation Amplitude start value 3 Left Click APPLY Left Click OK Left Click E to start MS MS collection m MassTech MT Explorer 50 To Return From MS MS Mode Modas 3 0 default_ms method File Plot Tools Help Scan Parameters m Py gt 2 y A Scan Parameters Scan Description 5 Settings Mass Range 2 Normal Low Parent mass Isolation width Fragmentation m z m z width m z ampl 9 MS OMS MS Positive Inject Time ms 2 AGC Enable AGC AGC Target au 2000000 Min Injection Time m Max Injection Time ms Input Method for m z Range From To Center Width Figure 5 Return to MS from MS MS diagram Left Click STOP to end spectra collection 2 Left Click on SCAN PARAMETERS Pop Up will appear Scan Parameters Choose s 4 Under FROM enter desired low mass enter desired high mass 8 Right Click in the RT Spectrum and Left Click on FIT TO VIEW MassTech m MT Explorer 50 Shut Down Procedures Modas 3 0 default_ms method NSI_HV_O kv NSI C 0 uA Capillary Temperature C Fault Flags Vacuum Ion Trap Chamber Air Torr Buffer Gas Turbo Pump Stage One Stage Two Figure A 6 Shut down procedure diagram 1 Left Clic
33. is of the sample Switching between positive and negative 10n modes can be done in the Ion Source window see below Note the change of the ion source icon when polarity is switched from x x to 5 4 Adjust Ion Source Values The ion source high voltage values can be adjusted under the Ion source window which recognizes the type of source attached to MT 50 9 MassTech MT Explorer 50 access 1on source window click NSI Source xdi Operational Standby Operational Standby lon Polarity Positive lon Polarity Positive Set Actual NSI HV 0 kV 1 NSI HV 0 kV 0 0 C 0 uA NSI C 0 10 9 7 Capillary Temperature 5 48 Capillary Temperature 120 118 9 Figure 5 6 Ion source window operational tab and standby tab In this one a nanospray ion source NSI is attached Both Operational and Standby values for high voltage current limit and temperatures can be set for the operational mode it also shows the actual readout 5 5 Adjust Ion Optics Values r OM i a 4 i ef To access the ion optics window click To adjust ion source values simply click on the appropriate number box and type appropriate values Then click Apply or OK MassTech MT Explorer 50 Capillary DC Offset V Hexapole 1 DC Offset V Conductance Limit 1 DC Offset V Hexapole 2 DC O
34. k STOP 2 Left Click on the icon to automatically shut down the ITMS will become and PLAY will become inaccessible i To Completely Shut Down MTE 50 Pumps OFF m fa E 3 Hold and Left Click on the icon Select POWER OFF WARNING pop up appears Reset Ion Source PCB Power Off AN Instrument will be turned off Are you sure Cancel Figure A 7 Shut down dialog boxes Left Click on YES MassTech MT Explorer 50 9 APPENDIX B CHROME EXPLORER DATA VIEWER INSTRUCTIONS To open data files under Windows Explorer extension db3 1 Find the file with Windows Explorer and double click the filename 2 If multiple filenames are opened will each open in a separate ChromExplorer 1 3 1 window To open data files while ChromExplorer 1 3 1 is running extension mtd 1 Click the File Icon at the top of the ChromExplorer window Wl ChromExplorer 1 3 1 Figure ChromExplorer running A 2 A File Operations Window will open Click Browse and a Windows file browser will open Browse for the file and double click Windows file browser will close and the file will be selected 3 Click Load to finish opening the data file View and Copy Operations Useful view and copy operations are shown in the figure below MassTech MT Explorer 50 ChromExplorer 1 3 1 1 3 1
35. kyDrive Print Chromatogram Libraries Development Recent Methods Recent Chromatograms Exit em Save as type mzML Chromatogram MassTech 1 80000000 MT Explorer 50 Figure 5 15 Export Chromatogram Option 1 Konstantin Novoselov My Documents MTESO Data File Plot Tools Help Admin Views Perspectives Organize v New folder Default Method Scan Parameters Open Method Save Method 2 Downloads gt Recent places Open Chromatogram amp SkyDrive Export b Spectrum J Libraries Print Chromatogram 29 Development 24 Documents Recent Methods Music i Pictures Recent Chromatograms d Subversion 5 4 c Videos lt 7 Exit 1474 8 8 2 03 femme Save astype ASCII Spectrum Data File v Figure 5 16 Export Spectrum Option In addition the data can be exported as a screenshot or image via Copy Paste procedure Figure 5 17 File Plot Tools show Chromatogram Scan Parameters Show Titles Show RT Show Spectrum Legend Copy as bitmap Copy as vector Clear Chromatogram 190 1 e R 6552 4 0 miami i Figure 5 17 Export Plot image Options 5 14 Options Dialog Box A number of instrument diagnostics can be accessed by the user with the
36. lding AC power system grounding is provided via the AC power cable When operating from a generator or external battery inverter the system requires a safety ground connection to avoid charge buildup The grounding connection shall be made to the designated grounding stud on the MT Explorer system chassis This shall be connected to an earth ground point e g grounding rod with minimum 16 AWG wire or braided ground strap NEC 250 may be used as a guide for acceptable erounding systems however local safety codes regarding wiring and grounding shall apply and override this document where applicable On the back panel of the MT Explorer 50 refer to Figure 3 3 1 Connect the power cord A to a standard 110 120 VAC wall outlet or as specified 2 Set up the laptop PC provided with the instrument and then connect the Ethernet cable to the PC and the ITMS C 3 Connect an exhaust line to the back of the ITMS B The exhaust line should vent to a chemical hood or other appropriate ventilation location 4 Flip the power on switch A to the position 5 Wait until the operational vacuum is reached as indicated by the front panel indicator LEDs refer to Figure 3 2 This process should take approximately 10 minutes 3 6 Installation of Modas MT Explorer 50 Operating Software The Modas software 15 provided with the laptop computer that comes with the MT Explorer 50 The computer is configured to communicate with the MT Ex
37. libration type it is recommended to use the Quadratic function After the user clicks Apply Figure 7 6 the new calibration is saved and is effective for all users and for all further MODAS sessions 7 4 Electron Multiplier Voltage Adjustment Power User Only The ordinary user has the possibility to tune the detector voltages settings see section 5 6 although it is not recommended The detector voltages changed by the ordinary user are not saved in the method file next time the MODAS is run the detector voltages will be set to the default values The power user can save the properly adjusted voltages so that next time the MODAS is restarted the adjusted values are restored The electron multiplier which 1s the part of the detector is deteriorating with time several month or more time scale depending on the instrument usage which results the data quality decrease In this case the Power user is to perform the readjustment as described below 1 Start MODAS in the power user mode 2 The Ion Source should be OFF set the ionization voltage to zero 3 Set Noise Filter Level to zero Go to Tools gt Options gt RT Plot gt Post Processing as shown in Figure 7 7 then click OK Hardware General Peak Detection Post Processing Peak Labels Remove baseli RT Plot T Noise Filter Level 0 00 Chromatogram Mass Calibration Filtering Detector None Import Export Median Filter Gangs
38. line and will start acquisition MODAS will acquire requested number of spectra and will stop Then MODAS will check the state of the StartIn line and will start next acquisition sequence when line state will equal to configured value 9 MassTech MT Explorer 50 Run Duration The same as Number of scans mode but acquisition duration will be used instead of number of spectra to acquire User can interrupt data acquisition at any moment by pressing Stop toolbar button Warning message will appear on the screen Figure 5 26 Spectrum data can be saved in one or multiple data files MODAS will generate filename appending numbers run count to the user supplied filename if Merge all runs in one file check box is unchecked MODAS will append counter value to the Comment field in the data file Figure 5 27 Status Report i Report E Parameter Value len Source p Vacuum p Turbo Pump p lon Optics to Hexapole RF Main RF lon Detection System Power Supplies Instrument Status DSP Version 0 7 5 FPGA Version Serial Number 13 Client 127 0 0 1 MODAS State Reset Controller State Reset Control Link Error Count 0 Data Link Error Count 0 AWG Sample Rate Hz 5000000 Digitizer Sample Rate Hz 97656 startin Low Figure 5 25 StartIn Status A Interrupt external run Figure 5 26 Warning Message Box MassTech 30 MT Explorer 50
39. ns Dialog Box RT Plot Under Chromatogram several options are available to customize the views and processing of the chromatogram Figure 5 21 General Peak Detection Post Processing Peak Labels Time Units Seconds Enable Vertical Autoscale Figure 5 21 Options Dialog Box Chromatogram 9 MassTech MT Explorer 50 _ 5 15 Reports Instrument Status Report dialog be invoked with help of Report toolbar button in the top part of Status Report tab u Status Report 6 EJ E Instrument Status Report 11 07 2013 16 35 55 Instrument Status Report Ion Source Ion Source ID None HV None C Capillary Temperature C Fault Flags Vacuum Name Value Ion Trap Chamber Air Torr 0 000600 Buffer Gas Turbo Pump Type text to find Figure 5 22 Instrument Status Report 5 16 External Control External Control configuration can be found in the Scan Parameters dialog Figure 5 23 In this dialog user can enable disable external control select operational mode configure in and out digital lines and set filename and save options Note Please note that these settings will be reset to the default values after MODAS is restarted Text label with text External Control will be displayed in the main window status bar when ex
40. nt Neg Parameter p lon Source DAC Current m z Theoretical m z Use Error Th 5145 31 226 87 0 00 a Vacuum lon Trap Chamber Air Torr 9 863e 06 7888 49 343 36 Buffer Gas OK 13963 26 601 49 Turbo Pump 16079 94 691 50 Stage One OK 18759 89 805 49 f Stage Two OK lon Optics 18784 41 806 53 Hexapole RF Main RF 24129 05 1034 02 1033 99 U lon Detection System 24107 15 1033 09 1033 99 wo T i 30508 57 1305 80 0 00 Power Supplies 30530 75 1306 75 0 00 Instrument Status 38185 94 1633 24 1633 95 38204 50 1634 03 1633 95 4 n 42226 74 1805 74 0 00 Linear RMS 0 4410 6 9341E 0 4 2595E 2 x Quadratic RMS 0 3869 9 0236E 0 4 2421E 2 x 3 1845E 9 x 2 Cubic RMS 0 3753 5 4889E42 3 2762E 2 x 3 2046 6 x 2 4 1971E 11 x 3 Mass Range Low Polarity Positive Calibration Type Quadratic Reset Scans elapsed 0 Microscans remaining 0 Figure 7 5 The Calibration Values are Calculated Linear 2 RMS 0 4410 6 9341E 0 4 2595E 2 x Quadratic RMS 0 3869 9 0236E40 4 2421E 2 x 3 1845E 9 x 2 Cubic RMS 0 3753 5 4889 2 3 2762E 2 x 3 2046 6 x 2 4 1971 11 x 3 Mass Range Low Polarity Positive C
41. nterface Back Panel Figure 3 3 is a picture of the interfaces located on the back panel bottom rear of the ITMS MT Explorer 50 has several interfaces which need to be connected in order to establish the power and communications as well as safely operate the system Figure 3 3 The back panel A Power switch and cord connection B Exhaust connection C Ethernet cable to laptop PC D DB 9 RS 232 COM Port E DB 15 external control port F MH Cartridge Holder Descriptions and Notations for Figure 3 3 9 MassTech MT Explorer 50 M 09 A The depressed side of the switch denotes actuation The power switch box also contains the main power fuse refer to the operational voltage label The standard power cord is a 110 120 VAC with a NEMA 6 15 connector B The pump exhaust exits the ITMS via a 4 ID hose barb C A standard ethernet cable 1s connected between the ITMS and the control laptop or PC This cable should be no longer than 100 feet 30 meters length D If applicable the DB 9 Serial RS 232 Communication Port connects the ITMS and an external device e g AP MALDI ion source E The DB 15 External Control Port connects the ITMS and an external device for synchronous control and operation e g AP MALDI source or LC F MH Cartridge Holder See Appendix D for instructions on replacing 3 5 MT Explorer 50 Start Up System Grounding When operating from bui
42. o restore the temperatures Once completed continue with the experiment Make sure to pay close attention to the Read Back Values as they should stabilize after the reset has been performed 7 3 Mass Recalibration Power User Only Before the Mass Recalibration procedure is performed it 1s strongly recommended to save the existing mass calibration The Power User can access the dialog window for saving Export and loading Import of mass calibration through Tools gt Options gt Import Export as shown in Figure 7 2 MassTech 35 MT Explorer 50 ke Hardware Calibrations B Gromstngeam Mass Calibration Detector TJ Import Export S Change Password Figure 7 2 Dialog Box for the Mass Calibration Saving Export and Loading Import The MODAS software provides flexibility to calibrate the instrument based on a single or multiple spectrum spectra The spectrum or spectra used for calibration can be either acquired in real time RT or saved on hard disk MODAS maintains four types of calibrations Low Mass Normal Mass Positive Negative 10n modes that can be saved loaded as a single calibration file Figure 7 2 For the proper mass calibration it s critically important to acquire a high quality and unsaturated spectra The user must run the data acquisition over a long enough period of time to make sure that the chosen ion source generates a stable MS signal It
43. options box Figure 5 18 Options box is accessed by clicking Tools gt Options Hardware Boards tab shows the internal diagnostic status 5 m MT Explorer 50 fee Hardware Boards Power Cycle Board Power Comm RT Plot HW Controller True True Chromatogram MS Controller 1 True True Main RF PCB True True Hex RF PCB True True lon Source PCB True True Cancel Figure 5 18 Options Dialog Box Hardware Boards If necessary any of the controllers can be power cycled through the Power Cycle tab Figure 5 19 Boards Power Cycle MS Controller lon Source PCB Figure 5 19 Options Dialogue Box Hardware Power Cycle Under the RT Plot several options are available to customize the views and processing of the mass spectrum Figure 5 20 MassTech MT Explorer 50 M General Peak Detection Post Processing Peak Labels Remove baseline Noise Filter Level 3 00 3 00 Filtering None Median Filter Savitzky Golay Filter Median Window Size 3 Polynom Power M 2 Number of Points to the Left 3 Number of Points to the Right NR 3 Genel Pe Label Print Position Print Resolution Print Intensity No Labels Format String 0 0 0 nR 1 0 0 nL 2 0 0E00 Preview 1000 0 R 2000 0 L 3 0E03 Figure 5 20 Optio
44. plorer 50 during the factory setup therefore no other computers should be connected to communicate with the MT Explorer 50 MassTech MT Explorer 50 This page 15 left intentionally blank MassTech 10 MT Explorer 50 4 INSTALLING AN ION SOURCE 1 Position 1 source IS near the front of the ITMS The two locking knobs on the top of an IS control the alignment rail lock they should be in a perpendicular position to the MS front panel unlocked position 2 Align the MS system alignment stubs with the corresponding IS alignment holes the two alignment rails mount to slots on the front panel of the ion source Push the IS against the ITMS until there is virtually no gap between the two surfaces 3 Using both hands simultaneously turn the left amp right locking knobs 90 to engage the locking mechanism see Figure 4 1 Parallel position in relation to ITMS front panel denotes the 1 source 15 locked to the ITMS Figure 4 1 Ion source locking knobs External Control 4 If the IS includes an external control cable plug it into either the DB 9 for RS 232 COM Port or the DB 15 Port on the rear panel of the ITMS see Figure 3 3 Use whichever port is applicable to the IS see your IS manual 5 If necessary 44 pin D sub 2 connections can be utilized for external control of an ion source see your IS manual WARNING During installat
45. rap Mass Spectrometer ITMS Its major features include atmospheric pressure interface API to use various atmospheric pressure ionization sources high mass range up to 2500 Da with some options small size 12x17x20 inches and low power consumption It consists of API atmospheric pressure ionization optics to deliver ions to the mass analyzer ion trap mass analyzer and the ion detection system enclosed within the vacuum manifold At the front end the interchangeable atmospheric pressure AP ionization source IS is attached externally to the ITMS which is a standard feature of the modern laboratory mass spectrometers The AP ionization sources are efficient and can encompass analysis of a wide range of chemicals using the same mass analyzer ionization of the sample takes place in the AP IS The specific front end method used to ionize the sample is referred to as the ionization technique and can include the following chemical ionization APCD electrospray ionization ESI secondary electrospray ionization 5 ESD matrix assisted laser desorption ionization MALDI direct analysis in real time DART desorption electrospray ionization DESI and other methods of atmospheric pressure ionization As the mass analyzers operate 1n the vacuum an atmospheric pressure interface serves as the function of an ion delivery from the atmospheric ambient pressure conditions existing in the 10n source of a mass spectrometer to t
46. s recommended to acquire the data for the mass calibration with the AGC off In order to achieve the highest resolution gradually decrease the injection time IT If IT 15 too large the peaks in the mass spectrum will be broad and the mass shift will be skewed After the proper IT is selected set large enough number of microscans typically 30 100 to obtain the high quality spectrum This spectrum can be either recorded on the hard drive or directly used for calibration as RT spectrum Stop the data acquisition Figure 7 3 represents a good quality ESI spectrum of MassTech s calibration 9 MassTech MT Explorer 50 File Chromatogram Tools Help Mass Calibration Chromatogram 2500000 2000000 NL 2 697E 06 1633 3 gt 1 R 2287 7 L 3 2E04 RT 00 00 00 SN 1305 8 R 2911 4 L 2 4E04 1033 1 22324 L 2 0E04 805 5 R 1615 8 L 2 0E04 6015 1805 7 343 3 R 2607 2 8 R 6239 5 R 2901 9 L 6 6E03 6915 m 03740 3454 L 7 2E03 1 24 9 03 R 1896 7 3 72 L 41E03 44 03 400 1400 1600 1800 Injection Time 0 05000 C Users Konstantin Documents MTE50 Data 2 Agilent mix negative 10 scans 10 uscans mtd Scans elapsed 0 Microscans remaining 0 v d d Figure 7 3 ESI mass spectrum of the calibration mixture Open the mass calibration tab through Tools gt Mass Calibration Builder Figure 7 4 and click Pick Peaks button If only one spectrum is opened RT or loaded from h
47. s that are not covered in this Maintenance and Troubleshooting section For services and repairs beyond those specifically provided in the Troubleshooting section contact the manufacturer MassTech Inc 6992 Columbia Gateway Dr Suite 160 Columbia MD 21046 Phone 443 539 1758 2 Troubleshooting If at any point the software does not respond try the following to recover the software 1 Close the Modas software and wait for minute Then re open the software 2 Close the Modas software and shut down the PC Wait for 1 minute Then start up the PC and re open the software We are ready to provide you with any technical assistance Call us at 443 539 1758 or e mail the problem to Support apmaldi com MassTech 34 MT Explorer 50 0 Ion Source PCB Reset In rare cases when the observed Read Back voltage does not approach the Set Value voltage the Ion Source PCB needs to be reset In order to reset the Ion Source first change the Ports to Standby and Sources to None in the Experimental Selection screen Next press and hold the Power off Button and select the Reset Ion Source PCB option in the drop down menu that appears Reset lon Source PCB Status Report Cancel Report Parameter Value p lon Source Figure 7 1 Ion Source PCB Reset Button After the reset has been completed go back to the Experimental Selection and click Set t
48. ternal control is active Figure 5 24 User should select method and start acquisition after activation of the external control In this case MODAS will perform initial steps of the scan sequence method and waveforms upload etc and will stop just before sending scan start trigger to the MS controller At that moment MODAS will check the state of the StartIn digital line and if this state is equal to configured one MODAS will send the start trigger to mass spectrometer User can check the current state of the StartIn line in the Instrument section of the Status Report view Figure 5 25 MassTech 28 MT Explorer 50 Main Scan External Control External Control Chromatogram File Start from external device Filename Startln signal Sample name Comment ReadyOut signal Continuous run Number of scans Run duration min Merge all runs one file Figure 5 23 External Control Tab 8 8 10 External Control Scans elapsed 0 Microscans remaining 0 Figure 5 24 External control status bar label Three operational modes are supported a Continuous run In this mode MODAS will wait corresponding value at StartIn digital line and will start acquisition MODAS will acquire spectra until user stops acquisition All subsequent changes of the StartIn line state will be ignored b Number of scans In this mode Modas will wait corresponding value at StartIn digital
49. tion Time ms Max Injection Time ms 100 Input Method for m z Range From To O Center Width OK Cancel Apply Figure 5 13 Scan Parameters Box During MS MS Operation Note The software will warn the user if the mass scan range 15 selected beyond the limitations of the 10n trap mass spectrometry it will highlight the value in red Figure 5 14 9 MassTech m MT Explorer 50 scan Range m z From To H 050 ntation 35 o 0 4 Figure 5 14 Mass Range Warning at Scan Parameters Box During MS MS Operation 5 12 Returning to the MS mode from the MS MS Mode Switching back to the MS mode can be done by pushing the radio button for MS the Scan Range should also be checked and adjusted as necessary Alternatively a previously saved MS method can be recalled see section 5 2 5 13 Exporting Data Several options are available for exporting data Both the chromatogram Figure 5 15 and the mass spectrum Figure 5 16 can be exported The mzML format is available for exporting chromatogram while the ASCII format is available for mass spectrum Chromatogram Tools Help Admin Views Perspectives Default Method Open Method Save Method a ate Ft Favorites Open Chromatogram Desktop z MZML File M M Jg Downloads z MZML File Export Spectrum Recent places MZML File S
50. top 5 10 Review Saved Spectra The Spectra be opened by selecting File gt Open Chromatogram SeeAppendix A for Review Saved Spectra Alternatively ChromExplorer software be used See Appendix B Total chromatogram TIC and selected ion chromatogram SIC be viewed in the same window under Modas Figure 5 11 See section 5 14 for additional options MassTech MT Explorer 50 File Plot Tools Help i k UE Scan Parameters ge 0 zo scans 1 T gt RT Spectrum Status Report Report Parameter lon Source Vacuum Turbo Pump lon Optics Hexapole RF Main RF lon Detection System Power Supplies Instrument Status 1367 3 R 3109 8 L 5 5E03 1410 Scans elapsed 253 Microscans remaining 0 Figure 5 11 RT Chromatogram with TIC and SIC Spectrum properties report allows user to review some acquisition parameters selected scan properties and voltages It can be accessed by Chromatogram gt Spectrum Properties menu item 11 07 2013 16 39 21 Spectrum Properties General C Users Konstantin Documents MTE50 Data 2 Agilent mix negative 10 scans 10 uscans mtd 00 00 26 4260000 2323781 09134579 Scan Parameters Value Mass Range Mode Normal Mass Range m 7 10N Type text to find 4 Figure 5 12 Spectrum Properties Window 5 11 Collect MS MS Sp
51. wer and electronics assemblies F Diaphragm pump G Instrument control modules A cross sectional view of the internal components under vacuum of the MS analyzer is shown in Figure 2 2 Figure 2 2 A Cone heating elements and inlet capillary B Ion optics inlet hexapole guide and conductance limit orifice Ion optics MS analyzer hexapole ion guide D Ion trap mass analyzer E Conversion dynode and electron multiplier Pre amplifier MassTech MT Explorer 50 This page 15 left intentionally blank MassTech MT Explorer 50 3 INSTALLATION AND STARTUP PROCEDURES 3 1 Unpacking Lift the MT Explorer 50 out of the box and carefully set it onto a sturdy and flat surface Use the handles located on both sides of the MT Explorer 50 to lift and set the instrument into the desired position as seen in Figure 3 1 Figure 3 1 Location of handles on MT Explorer 50 Remove the wire from the MS inlet capillary Gf supplied Note The MT Explorer 50 weighs approximately 75 pounds 34 kg Two people may be necessary to lift it 1 e one person per handle 3 2 Installation Requirements e Dry environment on a desk or other solid surface for system set up Power outlets 115 220 VAC and or 28 VDC see your system specifications at the distance that can be reached by the MS system and laptop PC power cables 1 8 m power cables are provided e Ethernet cable to connect t

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