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1. 77 Removing the lon Source Interface REPOS DESEE 78 Cleaning the Skimmer and Tube Lens on the LXQ and LTQ XL Mass SPECTRO MIC LEDS od up or ea as es a 79 Cleaning the Exit Lens and S Lens on the VelosPro 82 Cleaning the API Ion Transfer T beos oin debe a dena 84 Reinstalling the Ion Source nterface 0 89 O00 RE Lens Maintenance 3 4 baked Bee Be ae 89 Removing the Q00 RF Lens Assembly 90 Disassembling the Q00 RF Lens Assembly 92 Cleaning the Q00 RF Lens Assembly Components 93 Reassembling the Q00 RF Lens Assemb ly 94 Reinstalling the Q00 RF Lens Assembly 94 Thermo Scientific Thermo Scientific Chapter 6 Chapter 7 Contents QO and Q1 Ion Guides Maintenance 95 Removing the Top Cover of the Mass Spectrometer 96 Removing the Vacuum Manifold s Top Cover Plate 98 Removing the QO and QI Ion Guides 99 Cleaning the QO and Q1 Ion Guides Lens L1 and Split Gate Lens 104 Reinstalling the QO and QI Ion Guides 105 Reinstalling the Vacuum Manifold s Top Cover 109 Reinstalling the Top Cover of the Mass Spectrometer 110 Election Multiplier R
2. 111 Electron multipliers and shield retainers Velos Pro 112 Diagnostics dialog box shovving the Set Devicelist 113 Diagnostics dialog box showing the electron multiplier voltage parameters 114 Diagnostics dialog box showing the Mass Calibration page 115 Calibrate dialog box showing the Automatic page 116 Thermo Scientific Figures Figure 84 Semi Automatic page in the Calibrate dialog LXQ and LTQ XL 117 Figure 85 Semi Automatic page in the Calibrate dialog box Velos Pro 117 Figure 86 Diagnostics dialog box in sun eerte ER ELE RE LEE Sie son 122 Fioure 87 Diagnostic tesis Rad 122 Thermo Scientific LTO Series Hardware Manual xix Preface The LTQ Series Hardware Manual describes the modes of operation hardware components cleaning and maintenance for the following LTQ Series mass spectrometers MSs e LXQ a single segment 2D linear ion trap mass spectrometer e LIQ XL a three segment 2D linear ion trap mass spectrometer 5 P P e LTQ Velos a dual cell 2D linear ion trap mass spectrometer e Velos Pro a dual cell 2D linear ion trap mass spectrometer Note Unless otherwise noted For the LTQ mass spectrometer follow the LTQ XL information For the LTQ Velos mass spectrometer follow the Velos Pro information Contents Related Documentation Ge
3. 28 LXQ vacuum manifold with top cover plate and turbomolecular pump 29 Turbomoleculat Pump usar y sos s y yo bon 30 Tune Plus window om sce dud Ra a Eire aac 34 Vaud los 46 Source dialog Dos oss ayas Eois 49 ESL Source dialog 007 EE ETRE si pisi 50 Two piece fingertight fitting and loosened sample inlet adapter fitting 58 ESI probe with the nozzle removed us os sre or p Rte he daa Ares 59 ESLhoz e dnd nz d o o ys IHRER POE sesi 61 Front end of the ESI probe exploded view 62 Fused silica sample tube inserted through the front of the ESI probe 64 Natural PEEK safety sleeve installed in the sample inlet ESI probe 65 Natural PEEK adaptor fitting installed to secure the safety sleeve dual 0000060607 65 Fingertight fittings installed over the safety sleeve ESI probe 66 Grounding union positioned in the grounding bar 66 LTO Series Hardware Manual xvii Figures xviii Figure 38 Figure 39 Figure 40 Figure 41 Figure 42 Figure 43 Figure 44 Figure 45 Figure 46 Figure 47 Figure 48 Figure 49 Figure 50 Figure 51 Figure 52 Figure 53 Figure 54 Figure 55 Figure 56 Figure 57 Figure 58 Figure 59 Figure 60 Figure 61 Figure 62 Figure 63 Figure 64 Figure 65 Figure 66 Figure 67 Figure 68 Figure 69 Figure 7
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5. 8 SIDE Dim geraden er ee Eee 9 Syringe pump on off button qs bee ea d bob Ro EHE SOS RR E 10 Divert inject valve button and LEDs 11 Divert Positions o ouais toss papse een RP o P diee AT dir Rs 11 bey et vale 05 ST aod poe aaa kay duode E ode dita dad ea 12 Series front panel LEDS y era some yan zada PES TUR PPS 13 Power panel forthe EXO ae egent eor Br qox So Ves e bee Ba pecie dig 14 Povver panel for the LTQ XL and Velos Pro 14 LXQ ion source interface cross section 16 LTQ XL ion source interface cross section 17 Skimmer and tube lens back vievy 18 Velos Pro ion source interface cross section 18 Velos Pro exit lens and S lens back view 19 QO0 rf lens LTQ XL on the left and Velos Pro on the right 20 QO quadrupole for the LXQ and LTQ XL 21 QO quadrupole for the LTQ Velos X qud 21 QO quadrupole with beam stop post for the Velos Pro 21 101 OPCS es ouis E EE ana hd eee cae odd bdo d de 22 LTQ XL linear ion trap quadrupole rod assembly 23 Visual representation of mass analyzer operation 26 Functional block diagram of the vacuum system
6. 2011 Thermo Fisher Scientific Inc All rights reserved Ion Max ETQ XL Velos Velos Pro and ZoomScan are trademarks and Accela ETQ LXQ and Xcalibur are registered trademarks of Thermo Fisher Scientific nc in the United States Microsoft and VVindovvs are registered trademarks of Microsoft Corporation in the United States and other countries The following are registered trademarks in the United States and possibly other countries Agilent is a registered trademark of Agilent Technologies Inc Convectron is a registered trademark of Brooks Automation Kimwipes is a registered trademark of Kimberly Clark Corporation Liquinox is a registered trademark of Alconox Inc MICRO MESH is a registered trademark of Micro Surface Finishing Products Inc Nalgene is a registered trademark of Nalge Nunc International Corporation Teflon is a registered trademark of E I du Pont de Nemours amp Co Tygon is a registered trademark of the division of Saint Gobain Performance Plastics Corp Upchurch Scientific is a registered trademark of IDEX Health amp Science LLC Vespel is a registered trademark of E I du Pont de Nemours amp Co Viton is a registered trademark of DuPont Performance Elastomers LLC Waters is a registered trademark of Waters Corporation All other trademarks are the property of Thermo Fisher Scientific Inc and its subsidiaries Thermo Fisher Scientific Inc provides this document to its customers with a product purchase t
7. c Tighten the fingertight fitting to secure the safety sleeve and sample tube d Because the sample tube can move forward when tightening the sample inlet fitting ensure that the sample tube is initially recessed within the ESI needle If necessary loosen the red PEEK fitting and reposition the sample tube Figure 41 Sample tube position for flow rates greater than 100 uL min ESI probe 26 gauge electrospray needle sample inlet end of ESI probe 68 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Probe Maintenance Installing an Optional Metal Sample Tube You can configure the ESI probe to use a stainless steel metal sample tube rather than a fused silica sample tube Two kits are available one that includes a 32 gauge metal sample tube for typical flow rates used in ESI and another with a 34 gauge metal sample tube used for low flow applications Both kits include instructions for installing the stainless steel sample tube For part numbers see Ion Source Probes and Parts on page 126 HESI II Probe Maintenance The HESI II probe requires minimum maintenance If the metal sample tube is plugged replace it Replacing the metal sample tube requires a partial disassembly of the probe CAUTION HOT SURFACE At operating temperatures above 350 C 662 F the probe and API source housing can severely burn you Before removing the probe or API source housing allow the part t
8. 5 For positive ion polarity mode do the following a Select the first multiplier device name b In the Value box type the mass spectrometer s device value listed in Table 8 Table 8 Flectron multiplier device settings for positive ion polarity mode Device value Device name LXO LTO XL Velos Pro Multiplier 1 high gain V 800 900 1200 Multiplier 1 normal gain V 800 7 80 1300 c Click Set d Repeat step 5a through step 5c to set the remaining multiplier devices 114 LTO Series Hardware Manual Thermo Scientific 5 Maintenance Electron Multiplier Replacement 6 For negative ion polarity mode do the following a Select the first multiplier device name b In the Value box type the mass spectrometer s device value listed in Table 9 Table 9 Flectron multiplier device settings for negative ion polarity mode Device value Device name LXO LTO XL Velos Pro Multiplier 1 high gain V 900 1000 1300 Multiplier 1 normal gain V 900 900 1400 Multiplier 2 normal gain V 900 7 90 1400 c Click Set d Repeat step 6a through step 6c to set the remaining multiplier devices IMPORTANT Follow the next procedure to save the multiplier settings or they are lost if you reset the system To save the electron multiplier voltage settings 1 In the Tools list choose Mass Calibration to open the Mass Calibration page Figure 82 Figure 82 Diagnostics dialog box showing the Mass Calibr
9. You can configure plumb the divert inject valve in one of two ways as a divert valve for direct infusion high flow infusion or LC MS experiments or as a loop injector for flow injection analysis For procedures about plumbing the valve in the loop injector or configuring the divert valve refer to the LTQ Series Getting Started Guide You can use the divert inject valve button or the data system to control the divert inject valve Refer to the data system Help for instructions about operating the divert inject valve 10 LTO Series Hardware Manual Thermo Scientific 2 Functional Description Divert Inject Valve LEDs and Button The control button for the divert inject valve is located on the front panel above the divert inject valve It switches the valve between two positions The LEDs to the left of the button indicate the position of the valve Figure 4 Figure 4 Divert inject valve button and LEDs When the divert inject valve is set up for loop injections flow injection analysis FIA pressing the divert inject valve button switches the valve between the load and inject modes The Load and Inject LEDs indicate the position of the valve When the divert inject valve is set up for divert valve operation pressing the divert inject valve button switches the LC flow between the mass spectrometer and the waste container The Detector and Waste LEDs indicate the position of the valve Divert Valve Positions Use the divert
10. n the body of the e mail message paste the license key and type your name company name and phone number f you purchased the Trap HCD option locate the bar code on the License Trap HCD for Velos Pro card that came with the instrument In the body of the e mail message type the product key that appears below the bar code f you did not purchase the Trap HCD option with the instrument contact your local Thermo Fisher Scientific Technical Sales representative When Thermo Fisher Scientific Customer Support sends you a new license code see Installing a New License Code Thermo Scientific LTO Series Hardware Manual xxiii Preface Installing a New License Code After you receive your new license code follow this procedure To install the HCD license number 1 Open the LIQ License dialog box see step through step 4 on page xxii 2 In the License box paste a copy of the new license number from the e mail message and click Set LTO License rau are licensed for all standard LTO features Example license number License B7BB BS3OC 718F 3901 2FA8 CA31 C157 B88C 78BB a 3 Click OK when the following message appears The new license number has been set 4 n the Velos Pro Configuration dialog box verify the addition of the Ion Trap HCD Full feature and click OK Velos Pro Configuration Source a Display You are licensed for all standard LTO features Tune Plus and the followi
11. diera doce 70005 20514 Spill ar Oo 900 E 0077007077 97055 20023 Thumbscrews 10 32 97000 20235 128 LTO Series Hardware Manual Thermo Scientific 7 Replaceable Parts Electron Multipliers Velos Pro Lens DL 2222 700 0 ES A EEG E ES NER 97055 20022 Multipole bracket 008 70005 20780 SI EDU 70005 60276 euch MPPP 97055 60207 Onaditipole DEde BE uo iore rte ep PUT ERE PRU E indt dos are 70005 20514 Rod beam TEODOR saysa 70005 20781 SPULE TENS osos eben EP EE ER ERE RESP Ea 97055 20023 Thitnbserews 102932 2d 0040 BE a a pa ke dcs 97000 20235 Electron Multipliers Thermo Scientific 0 Electron multiplier assembly u sz rnm eR me s 96000 60036 Ohren P 97055 20342 LTO XL Electron multiplierassemibly s mal asas bodi du 96000 60036 Dual O 0 tei dub tds cube Fa d Sol gin x l t 97055 20018 LTO Velos Electron mu ltiplier assembly Loses texere s Edad pP raus 96000 60036 Brus 1007007 0277737 70 uua E ee 97055 20018 Velos Pro Electron multiplier assembly 0950 01 00137 Base shield part of the electron multiplier assembly 97655 20002 Shield retainer 97655 20003 l The Velos Pro electron multiplier assembly does not require a separ
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13. CAUTION HOT SURFACE At operating temperatures above 350 C 662 F the probe and API source housing can severely burn you Before removing the probe or API source housing allow the part to cool to room temperature approximately 20 minutes before touching it e f the mass spectrometer connects to an LC system leave the solvent flow from the LC pump on while the probe cools to room temperature Note For instructions about removing or reinstalling the API probe or source housing refer to Chapter 2 Setting Up the API Source in the L7Q Series Getting Started Guide Removing the lon Source Interface To remove the ion source interface 1 Shut down and vent the system Shutting Down the Mass Spectrometer Completely on page 26 and let it cool to room temperature It can take several minutes for the mass spectrometer to vent 2 Unplug the mass spectrometer power supply cord from the electrical outlet 3 Remove the API source housing 4 Grasp the ridges on either side of the ion source interface with your fingers and carefully pull it out of the vacuum manifold Figure 54 18 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Interface Maintenance Figure 54 lon source interface removed from the vacuum manifold Vacuum manifold lon source interface inside cage Outer cage installed 5 place the ion source interface on the clean lint free work surface Cle
14. Setting Up the API Source in the LTQ Series Getting Started Guide ESI Probe Maintenance The ESI probe requires minimum maintenance If the fused silica sample tube is plugged or broken replace it You can trim or replace the sample tube without disassembling the ESI probe However to clean the nozzle bore or the interior surfaces of the ESI manifold or to replace the electrospray needle or needle seal you must disassemble the ESI probe CAUTION HOT SURFACE At operating temperatures above 350 C 662 F the probe and API source housing can severely burn you Before removing the probe or API source housing allow the part to cool to room temperature approximately 20 minutes before touching it e f the mass spectrometer connects to an LC system leave the solvent flow from the LC pump on while the probe cools to room temperature To maintain the ESI probe follow these procedures e Flushing the Sample Transfer Line and Sample Tube Trimming the ESI Sample Tube Disassembling the ESI Probe on page 59 Cleaning or Replacing the ESI Probe Components on page 60 e Assembling the ESI Probe on page 62 Installing a Fused Silica Sample Tube and PEEK Safety Sleeve on page 63 Installing an Optional Metal Sample Tube on page 69 Flushing the Sample Transfer Line and Sample Tube Thermo Scientific You can minimize cleaning of the probe components by flushing the sample transfer line sample tube and probe at th
15. E ocius update us oe a treat 39 Resetting the Mass Spectrometer ars Y Peer node PE Cen GaSe 39 Resetting Tune and Calibration Parameters 40 Restartino the Data System eiie oie EHE ERR NAR eta oni 41 Turning Off Selected Mass Spectrometer Components 41 Daily Operation en ea l ebay lb n n 45 Before Operating the LEO Series System quies 222 SES REI REC SR 46 Checking the System Mode ere sx yasamal Reuse tat 46 Checking the Vacuum Levels so ux orte 22 014 0a ER HER 46 Checking the Gas Supplies sc tuns te ies ERAS RES ea 48 Checking the ESI Fused Silica Sample Tube for Elongation 48 After Operating the L TO Series System re kb pA EE Ri 48 Flushing the Sample Transfer Line Sample Tube and API Probe 49 Cleaning the Ion Sweep Cone Spray Cone and Ion Transfer Tube 51 Puteinp the Oil gm the Forepump ia nass er idera bep tdem 51 Emptying the Solvent Waste Container 52 Placing the System in Standby Mode 22 2 dies tee 232 Kran ala 52 MaintendlibB 3 aa R E etd eR Md a UU EE Ee s 53 Tools and SUpplics od oer FO eta Shae 55 Ion Source Probe Maintenance 56 ESI Probe Maintenalice 57 HESI II Probe Maintenance 69 APCE Probe Maintenalice 4 oss ood ln o o nud adds sc e a EROR 72 Ion Source Interface Maintenance
16. lon Detection Systems The LTQ Series mass spectrometer has a high sensitivity off axis ion detection system The LXQ has one electron multiplier and the LTC XL and Velos Pro have two detectors The ion detection system produces a high signal to noise ratio S N and enables voltage polarity switching between positive ion and negative ion modes of operation The electron multipliers are located on opposite sides of the mass analyzer Each electron multiplier has a corresponding conversion dynode A conversion dynode is a concave metal surface located at a right angle to the ion beam Figure 21 A high positive potential 15 kV for negative ion detection or a high negative potential C15 kV for positive ion detection is applied to the conversion dynode For the LTQ XL and the Velos Pro mass spectrometers both conversion dynodes are physically connected and operate at the same voltage An ion striking the surface of the conversion dynode produces one or more secondary particles The curved surface of the conversion dynode focuses these secondary particles and the voltage gradient accelerates them into the electron multiplier The conversion dynode shields shield the vacuum manifold from the electric field that the conversion dynode produces 26 LTO Series Hardware Manual Thermo Scientific Thermo Scientific 2 Functional Description Mass Spectrometer The LXQ uses one and the LTQ XL and LTQ Velos use two continuous dynode electron multiplie
17. nability of the multiplier gain calibration procedure to achieve a gain of 4 x 10 electrons per ion with an electron multiplier voltage less than or equal to 2 5 kV You can read the current value of the electron multiplier voltage in the Ion Detection System dialog box In the Tune Plus window choose Setup Ion Detection System Note The LXQ mass spectrometer has only one electron multiplier Adjust the following procedure accordingly For Field Service use only Part number Electron multiplier anode and base shield See page 129 Electron multiplier shield retainer Velos Pro only 97655 20003 110 LTO Series Hardware Manual Thermo Scientific 5 Maintenance Electron Multiplier Replacement To remove the electron multiplier assembly 1 Shut down and vent the system Shutting Down the Mass Spectrometer Completely on page 36 and let it cool to room temperature Venting the mass spectrometer can take several minutes 2 Unplug the mass spectrometer s power supply cord from the electrical outlet Remove the top cover of the mass spectrometer see page 96 A O Remove the vacuum manifold s top cover plate see page 98 VA Put on a new pair of lint and povvder free gloves 6 Remove the two hex socket head screws securing one of the electron multipliers to the top cover plate by using the 5 64 in hex driver Figure 78 Note For the Velos Pro mass spectrometer the assembly includes a small plastic
18. retainer that becomes free after removing the electron multipliers screws Figure 79 Set it aside with the screws 7 Hold the electron multiplier with one hand and with the other hand hold the high voltage connector 8 Detach the high voltage connector from the high voltage feedthrough to remove the electron multiplier assembly The anode remains in the anode feedthrough in the top cover plate Figure 78 Electron multipliers and dual anode LTO XL Electron multipliers High voltage connector Anode shield Dual anode Anode feedthrough High voltage feedthrough Thermo Scientific LTO Series Hardware Manual 111 5 Maintenance Electron Multiplier Replacement 112 LTO Series Hardware Manual Figure 79 Electron multipliers and shield retainers Velos Pro Shield retainer Repeat step 6 to step 8 with the second electron multiplier To replace the electron multiplier assembly CAUTION Be careful not to damage the surface of the electron multiplier shield inside surface This shield has been electropolished to prevent field emission Attach the high voltage connectors to the electron multipliers For the Velos Pro mass spectrometer position the plastic retainer on the top cover over the screw holes for the electron multiplier Figure 79 With one hand holding the electron multiplier and the other hand holding the high voltage co
19. 29 Two piece fingertight fitting and loosened sample inlet adapter fitting Receiving port of the sample inlet adapter fitting mam Ferrule for 190 um OD tubing ne vving red Fused silica fingertight fitting sample tube Gently pull back on the sample tube to free it from the ferrule Push the sample tube forward so that it extends beyond the end of the electrospray needle Cut a small length 4 5 mm of sample tubing by using the fused silica cutting tool and then under magnification check that the end is squarely cut Pull the sample tube backwards until the exit end of the sample tube is flush with the ESI needle The optimal sample tube protrusion depends on the solvent flow rate as follows For flow rates less than or equal to 100 uL min set the sample tube protrusion to 1 mm past the ESI needle tip For flow rates greater than 100 pL min ensure that the sample tube is flush with the ESI needle tip or recessed inside the ESI needle by less than 1 mm Thermo Scientific 5 Maintenance lon Source Probe Maintenance 8 Tighten the two piece fingertight fitting securely to hold the sample tube in place 9 Because the sample tube can move forward when tightening the two piece fingertight fitting ensure that the sample tube is still set to the appropriate protrusion If necessary loosen the fitting and reposition the sample tube 10 Reinstall the ESI probe into the API source housin
20. Damping gas restrictor Q00 Q0 Analyzer rf lens lon guide region region region lon gauge Triple inlet turbomolecular pump Vent XZY Air filter valve eS Thermo Scientific Vacuum Manifold Thermo Scientific 2 Functional Description Mass Spectrometer The vacuum manifold Figure 23 encloses the ion source interface ion optics mass analyzer and ion detection system assemblies The vacuum manifold is a thick walled aluminum chamber with a removable top cover plate machined flanges on the front sides and bottom and various electrical feedthroughs and gas inlets The vacuum manifold is divided into four chambers by three baffles Figure 23 XO vacuum manifold with top cover plate and turbomolecular pump Top cover plate Vacuum manifold Turbomolecular pump LTO Series Hardware Manual 29 2 Functional Description Mass Spectrometer Turbomolecular Pump A triple inlet turbomolecular pump Figure 24 provides the vacuum for the Q00 rf lens QO ion guide and analyzer regions of the vacuum manifold The turbomolecular pump mounts under the vacuum manifold Figure 24 Turbomolecular pump High vacuum inlet Interstage inlet Molecular drag inlet Vent valve port lon gauge port The main power switch turns off the turbomolecular pump The electronics service switch has no effect on this pump Power to the turbomolecular pump automatically shuts off if the turbomolecular pumps temperature becom
21. Loosen the three hex socket head screws securing the ion source interface to the vacuum manifold s outer cage by using the 5 32 in hex ball driver Figure 64 Figure 64 000 rf lens assembly removal Vacuum manifold 3 25 in ID O ring Hex socket head Electrical connector Screws for the Q00 rf lens assembly Outer cage lon source interface inside cage 6 Carefully remove the Q00 rf lens assembly and place it on the clean lint free work surface Tip To remove the assembly more easily you can take two of the three removed screws and screw them into the two previously open not used screw holes Thermo Scientific LTO Series Hardware Manual 91 5 Maintenance 000 RF Lens Maintenance Disassembling the 000 RF Lens Assembly To disassemble the 000 rf lens assembly CAUTION Be careful not to bend or break the lead pins on the Q00 rf lens 1 Carefully remove the leads from the lead pins on the Q00 rf lens and lens LO Figure 65 Figure 65 000 quadrupole and lens LO wiring connections Top lead pin zo OP SAN 542 NX LO lead pin V Lens LO Q00 rf lens Bottom lead pin 2 Gently push lens LO from the back of the Q00 rf lens assembly Figure 66 If necessary first loosen the ball plungers by using the small slotted screwdriver 3 Gently push QO0 rf lens from the back of the outer cage Figure 66 If necessary first loosen the ball plungers by using the small s
22. Thermo Scientific The inlet gas hardware controls the flow of damping gas sheath gas auxiliary gas sweep gas and air during venting into the mass spectrometer The vent valve Figure 24 on page 30 allows the vacuum manifold to be vented to air that has been filtered through a sintered nylon filter The vent valve a solenoid operated valve is closed when the solenoid is energized The vacuum manifold vents when the mass spectrometer no longer receives external power as with a power failure or by turning off the main power switch Power is briefly provided to the vent valve after losing external power to protect against the accidental loss of power When power to the vent valve solenoid shuts off for more than a very brief period of time the vent valve opens and the manifold vents to filtered air LTO Series Hardware Manual 31 2 Functional Description Mass Spectrometer Damping Gas Inlet Assembly The damping gas inlet assembly controls the flow of helium into the mass analyzer cavity Helium 275 70 kPa 40 10 psi 99 999 ultra high purity enters the mass spectrometer through a 1 8 in port on the back of the mass spectrometer The mass spectrometer regulates the flow of helium and delivers it to the mass analyzer Helium in the mass analyzer cavity dampens ionic motion and improves the performance of the mass spectrometer See Helium Damping Gas on page 25 Sheath Gas Auxiliary Gas and Sweep Gas Valves The sheath
23. Viton 0 500 in ID 1 16 in thick 00107 05600 Sample tube O ring Viton 0 239 in ID 1 16 in thick 00107 04000 lon Source Interface Parts Thermo Scientific All Models O ring 2 033 Viton V884 2 in ID 1 16 in 00107 01 00006 O ring 2 039 Viton 2 74 in ID 0 063 in 00107 12550 O ring AS 146 Viton 2 625 in ID 0 094 in 00107 11002 O ring Vespel graphite 0 325 in ID 97055 20442 LXO lon source interlace assembly 53 3x acd cade eet saz d nalar d m bab esed 97055 60181 D r ben as 2 c s s om y dest PU es E 97055 20517 EL E osas Ms b b 97055 20516 T be lens auper 07 0 0 0 0 t aud 97055 20463 LTO XL lon source Interface assembly iu sinus haa da bre ee Rd Re d 97055 60040 Jon transfer tube sc cnc dd ee be ee eb a ORB oli oie be Bs BUR ee 97055 20198 SIMIC somete ERES ba a uns qui mdr Rd eR Ra SC bas b e dc 97055 20253 Tobeleis ETC 97055 20251 LTO Velos Pr len a 55 2 2 02775 0 d E rum ates Soares dus 70005 20419 lon source interface assembly due titan 0500700077 70005 60187 Ion trans Tul RUSSE EUREN S NEP RS ME Ru m ER RE 70005 20606 5250657222 75 0500210 Eq e RE ERI RU 70005 60182 Velos Pro 0915000227 0 0 E 70005 20419 lon source interface assembly nas ba ad n de rn PR RP d ard nda sas 70005 60290 lon tU escono ure Yaa Ra b rda B
24. autosampler and LC are usually installed to the left of the mass spectrometer The divert inject valve is integrated into the front panel of the mass spectrometer In a typical analysis by LC MS a sample is injected onto an LC column The sample then separates into its various components The components elute from the LC column and pass into the mass spectrometer for analysis Upon entering the atmospheric pressure ionization API source sample molecules are ionized and desolvated into the gas phase by any of these methods e Electrospray ionization ESI e Heated electrospray ionization H ESI e Atmospheric pressure chemical ionization APCI Thermo Scientific LTO Series Hardware Manual 7 2 Functional Description Overview Figure 1 e Atmospheric pressure photoionization APPI Nanospray ionization INSI The ion optics focus and accelerate the resulting gas phase sample ions into the mass analyzer where they are isolated and ejected according to their mass to charge ratios As the mass analyzer ejects the sample ions they are detected by a detection system that includes one or two electron multipliers and that produces a signal proportional to the number of ions detected The system electronics receive and amplify the ion current signal from the ion detection systems The signal then passes on to the data system for further processing storage and display The data system provides the primary mass spectromete
25. been subjected to heating and cooling Ensure that the cover plates of the vacuum manifold and O rings are properly positioned LTO Series Hardware Manual 47 A Daily Operation After Operating the LTO Series System Checking the Gas Supplies Check the helium gas supply on the regulator of the gas tank Ensure that there is sufficient gas for the analysis which is a minimum of 3447 kPa 500 psi on the high pressure gauge of the regulator If necessary replace the tank Verify that the pressure of helium reaching the mass spectrometer is 275 70 kPa 40 10 psi If necessary adjust the pressure with the tank pressure regulator Check the nitrogen gas supply on the regulator of the nitrogen gas tank or liquid nitrogen boil off tank Ensure that there is sufficient gas for the analysis If necessary replace the tank Verify that the pressure of nitrogen reaching the mass spectrometer is 689 138 kPa 100 20 psi If necessary adjust the pressure with the tank pressure regulator Note Typical daily nitrogen gas consumption when nitrogen is on 24 hours per day is 5560 26700 L 196 943 ft For more information about gas requirements including those fora MALDI LTQ XL system and the ETD reagent carrier gas for the LTQ XL ETD system refer to the LTQ Series Preinstallation Requirements Guide Checking the ESI Fused Silica Sample Tube for Elongation Using acetonitrile in the mobile phase can elongate the polyimide coating
26. cleaning 74 nozzle removing 73 reassembling 77 APCI sample tube dimensions 72 installing 76 removing 75 replacing 72 API gas valves description 32 API probe cleaning 49 API source description 15 ion source interface 15 atmospheric pressure ionization source description 15 autosampler starting up 39 auxiliary gas description 32 C calibration parameters resetting to factory defaults 40 cleaning procedures APCI probe components 72 ESI probe components 57 exit lens 82 lens LO 93 lens L1 104 Q00 rf lens 93 skimmer 80 S lens 82 split gate lens 104 tube lens 80 Communication LED 13 Thermo Scientific compliance FCC vii regulatory iii WEEE ix Convectron gauge description 31 conversion dynode description 26 cooling fans description 32 customer responsibility 53 D daily tasks 45 damping gas 25 damping gas inlet assembly description 32 data system starting up 38 diagnostics 121 divert inject valve button and LEDs 11 loop injection 10 12 positions 11 E electromagnetic compatibility vii electron multipliers description 26 location photo 98 replacing 110 voltages negative ion polarity mode 115 positive ion polarity mode 114 electronics service switch 15 EMC compliance iii emergency shutdown 33 ESI manifold cleaning 61 ESI nozzle cleaning 60 ESI probe assembling 62 cleaning 57 disassembling 59 flushing 57 LTO Series Hardware Manual 135 index F maintenance overview 5
27. computer Wait at least 20 seconds after the computer shuts down Press the Power button again Turning Off Selected Mass Spectrometer Components There are five ways that you can turn off some or all of the mass spectrometer components Turn off individual mass spectrometer components by using the Tune Plus window Turning off individual mass spectrometer components might be necessary when troubleshooting a problem or running certain diagnostic procedures Place the mass spectrometer in standby mode which is the normal state to leave the mass spectrometer in when it is not in use Place the mass spectrometer in off mode which is similar to standby except that all high voltage components of the mass spectrometer are off Place the electronics service switch in the Service Mode down position so that you can perform maintenance procedures involving nonvacuum system components of the mass spectrometer Turn off the Main Power switch which removes all power to the mass spectrometer including the vacuum system Table 5 summarizes the On Off status of mass spectrometer components voltages and gas flows Thermo Scientific LTO Series Hardware Manual 41 3 System Shutdown Startup and Reset Turning Off Selected Mass Spectrometer Components Table 5 On off status of mass spectrometer components voltages and gas flows Sheet 1 of 2 x es Main Povver svvitch Mass spectrometer component mode mode service svvitc
28. lead pin points toward the socket in the contact ring support b Insert the lead pin into the socket and firmly press it until it snaps into place Thermo Scientific LTO Series Hardware Manual 81 5 Maintenance lon Source Interface Maintenance Cleaning the Exit Lens and S Lens on the Velos Pro Chemicals can accumulate on the surfaces of the exit lens and S lens The use of an S Lens that incorporates an rf electric field however minimizes the harmful effects of this contamination The exit lens and S Lens require cleaning less often than the ion sweep cone and the ion transfer tube Remove the exit lens and S lens from the ion source interface cage before cleaning them No tools are needed to remove or install these components To clean the exit lens and S lens follow these procedures 1 To remove the exit lens and S lens 2 To dean the exit lens and S lens 3 To reinstall the S lens and exit lens To remove the exit lens and S lens 1 Remove the ion source interface see page 78 2 Loosen and extend the two thumbscrews that secure the exit lens and S lens Figure 57 Figure 57 Exit lens S lens and ion source interface cage for the Velos Pro S lens Exit lens lon source Interface cage 3 Remove the exit lens from the S lens and place it on the clean lint free work surface 4 Grasp the two thumbscrews and carefully pull out the S lens from the ion source interface cage and place it on the work su
29. lens During the tune procedure the Velos Pro determines the mass dependent rf amplitudes for optimum transmission of ions through the lens Figure 14 Velos Pro exit lens and S lens back view Exit lens S lens LTO Series Hardware Manual 19 2 Functional Description Mass Spectrometer lon Optics 000 lon Optics Q0 lon Optics The following ion optics focus the ions produced in the API source and transmit them to the mass analyzer e 000 Ion Optics e QO Ion Optics OI Ion Optics The Q00 ion optics are the optics located closest to the API source The Q00 ion optics include the Q00 rf lens and the lens LO For the LXQ LTQ XL and LTQ Velos mass spectrometer the QOO rf lens is a square array of metal elements that act as an ion focusing device first image in Figure 15 For the Velos Pro the Q00 rf lens is an array of eight cylindrical metal elements second image in Figure 15 An rf voltage applied to the elements creates an electric field that guides the ions along the axis of the lens A dc voltage offset from ground applied to Q00 called the Q00 offset voltage increases the translational kinetic energy of the ions emerging from the skimmer or exit lens During ion focusing the offset voltage is negative for positive ions and positive for negative ions Figure 15 000 rf lens LIQ XL on the left and Velos Pro on the right The lens LO is a metal plate with a small hole in one end through which the ion beam
30. of Liquinox in water Scrub the components with a chamois tip swab soaked in a 196 solution of Liquinox in Water Rinse the components thoroughly with tap water Sonicate the components for 10 min in methanol Scrub the components with a chamois tip swab soaked in methanol Rinse the components with methanol Dry the components with a rapid stream of oil free nitrogen gas Inspect the components under magnification for any lint or particulates Note Inspect the inside surfaces and edges to confirm that no lint or particulates are present Use tweezers or a similar tool to remove the lint or particulate To clean lens L1 and the split gate lens Inspect the components under magnification for any lint particulates and sample buildup or coatings Note After use the surfaces can be discolored which is normal and not to be confused with sample buildup or coatings Sonicate the components for 10 15 min in a 50 50 methanol water solution or a 196 solution of Liquinox in water If a sonicator is not available use a soft toothbrush with a 196 solution of Liquinox in water Clean the bore in each lens by using the 6000 grit MICRO MESH polishing swabs Rinse the components thoroughly with tap water Rinse the components with methanol Thermo Scientific 5 Maintenance Q0 and 01 lon Guides Maintenance 6 Dry the components with a rapid stream of oil free nitrogen gas 7 Inspect the
31. of the tube Thermo Scientific L LC pump A high pressure solvent pump in the liquid chromatograph LC that provides the pressure on the input side of a column to drive the eluent and sample through the column lens A metal disk with a circular hole in the center that allows the ion beam to pass mass analyzer A device that determines the mass to charge ratios of ions by one of a variety of techniques nanospray ionization NSI A type of electrospray ionization ESI that accommodates very low flow rates of sample and solvent on the order of 1 to 20 nL min for static nanospray or 100 to 1000 nL min for dynamic nanospray p parent ion An electrically charged molecular species that can dissociate to form fragments The fragments can be electrically charged or neutral species A parent ion can be a molecular ion or an electrically charged fragment of a molecular ion Also called a precursor ion product ion An electrically charged product of reaction of a selected parent ion In general product ions have a direct relationship to a particular parent ion and can correlate to a unique state of the parent ion rflens A multipole rod assembly that is operated with only radio frequency rf voltage on the rods In this type of device virtually all ions have stable trajectories and pass through the assembly Thermo Scientific Glossary S sample loop A loop of calibrated volume that is used to perform flow injectio
32. of the ions is called a scan The mass spectrometer uses several different scan modes and different scan types to load fragment and eject ions from the mass analyzer The ability to vary the scan mode and scan type as well as the ionization and ion polarity modes provides greater flexibility in the instrumentation for solving complex analytical problems For information about the electrospray ionization ESI and atmospheric pressure chemical ionization APCT techniques refer to the Jon Max and lon Max S API Source Hardware Manual For information about the atmospheric pressure photoionization APPI technique refer to the Jon Max APPI Source User Manual For more information about the nanospray ionization INSI technique refer to the manual that came with your NSI source LTO Series Hardware Manual 5 Oo m Functional Description This chapter describes the principal components of the L TC Series mass spectrometers and their functions Note Unless otherwise noted For the LTQ mass spectrometer follow the LTC XL information For the LTQ Velos mass spectrometer follow the Velos Pro information Contents Overview e Syringe Pump e Divert Inject Valve Mass Spectrometer Overview Figure 1 shows a functional block diagram of an LTQ Series system that uses either a liquid chromatograph with an autosampler or the syringe pump as the inlet A sample transfer line connects the LC to the mass spectrometer The
33. on the fused silica sample tube which can degrade both signal intensity and stability over time If you are using a fused silica sample tube in the ESI mode verify that the sample tube is not elongated past the tip of the ESI spray needle If the tube is elongated cut and reposition it See Trimming the ESI Sample Tube on page 58 After Operating the LTO Series System Follow these procedures every day after operating the LIQ Series system e Flushing the Sample Transfer Line Sample Tube and API Probe Cleaning the Ion Sweep Cone Spray Cone and Ion Transfer Tube on page 51 e Purging the Oil in the Forepump on page 51 Emptying the Solvent Waste Container on page 52 Placing the System in Standby Mode on page 52 48 LTO Series Hardware Manual Thermo Scientific A Daily Operation After Operating the LTO Series System Flushing the Sample Transfer Line Sample Tube and API Probe Flush the sample transfer line sample tube and API probe at the end of each work day or more often if you suspect they are contaminated with a 50 50 methanol water solution from the LC system through the API source at a flow rate of 200 400 uL min for approximately 15 minutes to remove contamination To flush the sample transfer line sample tube and API probe 1 Complete all data acquisition if any 2 Open the Tune Plus window see page 34 Al Il 3 Ensure that the On Standby button indicates the On mode and then do one of the n
34. plate 3 Reconnect the electrical leads to the QO quadrupole lens L1 split gate lens and O1 octapole according to the wiring diagram Figure 75 through Figure 77 as applicable 4 Check all leads to ensure that they are secure and attached to the correct electrodes Figure 75 through Figure 77 as applicable Thermo Scientific LTO Series Hardware Manual 105 5 Maintenance Q0 and Q1 lon Guides Maintenance Figure 75 00 and 01 ion guides wiring diagram for the 0 Wire 9 gray Wire 10 white Wire 1 brown Wire 8 violet Wire 11 blue Wire 2 red Wire 7 blue Wire 12 violet Wire 4 yellow Wire 5 green Wire 6 black Wire 3 orange 106 LTO Series Hardware Manual Thermo Scientific 5 Maintenance Q0 and 01 lon Guides Maintenance Figure 76 Q0 and 01 ion guides wiring diagram for the LTQ XL Wire 9 gray Wire 10 white Wire 1 brown Wire 8 violet Wire 11 blue Wire 2 red Wire 7 blue Wire 12 violet Mn nM Wire 4 yellow Wire 5 green Wire 6 black Wire 3 orange Thermo Scientific LTO Series Hardware Manual 107 5 Maintenance Q0 and Q1 lon Guides Maintenance Figure 77 Q0 and Q1 ion guides wiring diagram for the Velos Pro Wire 7 blue Wire 4 yellow Wire 14 gray Wire 8 violet Wire 13 white Wire 9 gray Wire 5 green Wire 10 white Wire 1 brown Wire 2 red Wire 11 blue Wire 12 violet left yellow right orange Wire 3 oran
35. resolution Before their ejection from the mass analyzer cavity sample ions collide with helium atoms These collisions reduce the kinetic energy of the ions which results in damping the amplitude of their oscillations The ions are then focused to the axis of the cavity rather than allowed to spread throughout the cavity which would spread their ejection times and degrade the mass spectral resolution Helium in the mass analyzer cavity also serves as a collision activation partner During the CID step of an SRM CRM or MS z 1 full scan analysis the resonance excitation ac voltage applied to the exit rods drives parent ions energetically into the helium atoms After gaining sufficient internal energy from the resulting collisions the parent ion dissociates into one or more product ions Summary of Mass Analyzer Operation The processes that occur in the mass analyzer can be broken down into four steps 1 Ion storage 2 Ion isolation SIM SRM CRM or MS z 1 full scan only 3 CID SRM CRM or MS n gt 1 full scan only 4 Ion scan out the ion detection step For SRM and MS MS full scan applications the mass analyzer performs the ion isolation and CID steps at the same time For CRM and MS z gt 1 full scan applications the ion isolation and CID steps are performed n 1 times For SIM SRM CRM or MS n gt 1 full scan the ion isolation waveform voltage is applied to the exit rods in combination with a
36. standby following If operating in APCI or APPI mode go to step 4 If operating in ESI mode go to step 5 4 To flush the APCI source a Choose Setup gt APCI Source to open the APCI Source dialog box Figure 27 Figure 27 APCI Source dialog box x Actual Vaponzer T emp C annon 449 90 Sheath Gas Flow Rate arb 80 asi Aux Bas Flow Rate arb 20 1835 Sweep Gas Flow Hate arb p 0 00 Discharge Current pA ion 4 ee Discharge Yoltage EM 4 53 Capillary Temp 20000 20020 Capilar Voltage 800 H 856 Tube Lens Offset 100 00 10015 Apply Cancel Help b Inthe Vaporizer Temp C box enter 500 c Inthe Sheath Gas Flow Rate arb box enter 30 d In the Aux Gas Flow Rate arb box enter 5 e Inthe Sweep Gas Flow Rate arb box enter 0 f Inthe Discharge Current box enter 0 Thermo Scientific LTO Series Hardware Manual 49 A Daily Operation After Operating the LTO Series System 50 g Click OK h Go to step 6 5 To flush the ESI source LTO Series Hardware Manual a Choose Setup ESI Source to open the ESI Source dialog box Figure 28 Figure 28 ESI Source dialog box ESI Source Actual Sheath Gas Flow Aate arb 2 0 01 Aus Gas Flow Rate 0 am Sweep Gas Flow Hate arb r an 0 02 Spray Voltage kv 500 002 Spray Current LA 1 03 Capillary Temp C 276 00 278 28 Capilary Voltag
37. that the electronics have power However the electron multipliers conversion dynodes 8 kV power to the API source main rf voltage and ion optic rf voltage remain off The embedded computer boots After several seconds the Communication LED turns yellow to indicate that the data system and the mass spectrometer have started to establish a communication link e After several more seconds the Communication LED turns green to indicate that the data system and the mass spectrometer have established a communication link Ensure that the instrument console window is active The data system transfers operational software to the mass spectrometer Thermo Scientific 3 System Shutdown Startup and Reset Resetting the Mass Spectrometer e After three minutes the System LED turns yellow to indicate the software transfer from the data system to the mass spectrometer is complete and that the mass spectrometer is in standby mode When you change the mode from standby to on the System LED turns green to indicate that the mass spectrometer is functional and the high voltages are on Note The Vacuum LED on the front panel illuminates green only if the pressure in the vacuum manifold is below the maximum allowable pressure 5 x 104 Torr in the analyzer region and 2 Torr in the ion transfer tube skimmer region Although you can calibrate the mass spectrometer after the vacuum LED turns green you must allow the mass spectrometer vacuum system to s
38. the LC system follow the startup procedure described in the manufacturer s manual If necessary configure the LC as described in the Z7Q Series Getting Connected Guide Note Do not turn on the liquid flow to the mass spectrometer at this point in the procedure Thermo Scientific LTO Series Hardware Manual 37 3 System Shutdown Startup and Reset starting the System after a Complete Shutdown Starting the Data System 4 To start the data system Turn on the computer monitor and printer if provided Starting the Mass Spectrometer Ensure that the data system is running before you start the mass spectrometer The mass spectrometer does not operate until it receives instructions from the data system l 38 LTO Series Hardware Manual To start the mass spectrometer Turn on the flows for the helium and nitrogen gases at their tanks if they are off Turn off the Main Power switch and place the electronics service switch in the Service Mode down position Plug in the power supply cord for the mass spectrometer Turn on the Main Power switch This turns on the one or two forepumps respectively and the turbomolecular pump AII LEDs on the front panel are off Wait at least 1 hour to allow the mass spectrometer to pump down Place the electronics service switch in the Electronics Normal up position The following occurs The Power LED on the front panel turns green to indicate
39. 0 Figure 71 Figure 72 Figure 73 Figure 74 Figure 75 Figure 76 Figure 77 Figure 78 Figure 79 Figure 80 Figure 81 Figure 82 Figure 83 LTO Series Hardware Manual Safety sleeve connection to the grounding union ESI probe 67 Sample tube securely tightened to the grounding union ESI probe 67 Adjusting the sample tube position ESI probe 68 Sample tube position for flow rates greater than 100 pL min ESI probe 68 Components of the metal ESI needle insert 70 Tip enlarged of the metal ESI needle insert 70 HESI II probe disassembled exploded view 71 HESI II probe nozzle tip enlarged sies a m l SERE ERAS 71 JUDA OD 0007070500 72 APCT probe cross You sr den dE RE SERRE PRSE KE aes 73 Sample inlet end of the APCI probe showing locked and unlocked 7577565775 74 APG probe nozzle a Semb y ai d ewe dara d ides 74 3 8 in open end wrench on the APCI flange fitting 75 APC sample tube connecti onae re 114 2 ee 76 Sample tubing connection to the APCI flange fitting 76 Sample tube extending past the APCI nozzle tip T Ion source interface removed from the vacuum manifold 79 Skimmer tube lens and ion source interface cage for the LXQ and DUO XE eo P TMFECTI Eee 80 ETO X Lion source
40. 0 and 01 lon Guides Maintenance Figure 72 00 and 01 ion guides for the LIQ XL exploded view Multipole brackets Thumbscrews Split gate lens Lens L1 a e quadrupole Baffle Guide post Thermo Scientific LTO Series Hardware Manual 101 5 Maintenance Q0 and Q1 lon Guides Maintenance Figure 73 00 and 01 ion guides for the LTO Velos exploded view Multipole brackets Thumbscrews Split gate 01 lens octapole Q0 Lens L1 quadrupole Baffle Guide post 102 LTO Series Hardware Manual Thermo Scientific Thermo Scientific 5 Maintenance Q0 and 01 lon Guides Maintenance Figure 74 00 and 01 ion guides for the Velos Pro exploded view Multipole brackets Thumbscrews m Split gate 01 lens octapole Q0 Lens L1 quadrupole Baffle Guide post LTO Series Hardware Manual 103 5 Maintenance Q0 and Q1 lon Guides Maintenance Cleaning the 00 and 01 lon Guides Lens L1 and Split Gate Lens 104 CAUTION Do not drop or bang the QO quadrupole and Q1 octapole against any surface COO N A A HM Series Hardware Manual To clean the Q0 and Q1 ion guides Inspect the components under magnification for any lint particulates and sample buildup or coatings Sonicate the components for 10 min in a 196 solution
41. 0 grit Nitrogen gas clean dry and compressed Water LCMS grade and tap IMPORTANT Prepare a clean work surface by covering the area with lint free paper e Put on a new pair of lint and powder free gloves before starting each of these removal cleaning and reinstallation procedures CAUTION HOT SURFACE At operating temperatures above 350 C 662 F the probe and API source housing can severely burn you Before removing the probe or API source housing allow the part to cool to room temperature approximately 20 minutes before touching it e f the mass spectrometer connects to an LC system leave the solvent flow from the LC pump on while the probe cools to room temperature Removing the Q00 RF Lens Assembly For Field Service use only Part number O ring Viton 3 25 in ID 1 8 in thick 00107 13000 To remove the 000 rf lens assembly 1 Shut down and vent the system Shutting Down the Mass Spectrometer Completely on page 36 and let it cool to room temperature Venting the mass spectrometer can take several minutes 2 Unplug the mass spectrometer power supply cord from the electrical outlet 3 Remove the ion source interface see page 78 90 LTO Series Hardware Manual Thermo Scientific 5 Maintenance 000 RF Lens Maintenance 4 Reach into the opening in the vacuum manifold where the ion source interface was and disconnect the electrical connector to the C000 rf lens assembly 5
42. 01 lon Guides Maintenance CAUTION HOT SURFACE At operating temperatures above 350 C 662 F the probe and API source housing can severely burn you Before removing the probe or API source housing allow the part to cool to room temperature approximately 20 minutes before touching it If the mass spectrometer connects to an LC system leave the solvent flow from the LC pump on while the probe cools to room temperature Removing the Top Cover of the Mass Spectrometer To remove the top cover of the mass spectrometer 1 Shut down and vent the system Shutting Down the Mass Spectrometer Completely on page 36 and let it cool to room temperature Venting the mass spectrometer can take several minutes 2 Unplug the mass spectrometer s power supply cord from the electrical outlet 3 Disconnect any tubing between the syringe pump or LC system and the API source 4 Use the 1 4 in hex driver to loosen the latch on the front door Figure 67 Figure 67 Front door latch Door latch 5 Open the front door and loosen the two captive screws that secure the top cover by using the Phillips screwdriver Figure 68 96 LTO Series Hardware Manual Thermo Scientific 5 Maintenance Q0 and 01 lon Guides Maintenance Figure 68 Top cover screws Top cover screws 6 Slide the top cover back and off Figure 69 Figure 69 Top cover pushed back Top cover Thermo Scientific LTO Series Hardware Manual 9
43. 2001 A2 2005 EN 61000 4 5 2005 EN 61326 1 2006 EN 61000 4 6 2007 EN 61000 4 2 1995 A1 1999 A2 2001 EN 61000 4 11 2004 FCC Class A CFR 47 Part 15 2007 Low Voltage Safety Compliance This device complies with Low Voltage Directive 2006 95 EEC and harmonized standard EN 61010 1 2001 LTQ Velos ETD System November 2008 EMC Directive 2004 108 EEC EMC compliance has been evaluated by TUV Rheinland of North America Inc EN 61326 1 2006 EN 55011 2007 EN 61000 3 2 2006 EN 61000 3 3 2005 EN 61000 4 2 2001 EN 61000 4 3 2006 EN 61000 4 4 2004 EN 61000 4 5 2005 EN 61000 4 6 2007 EN 61000 4 11 2004 FCC Part 15 2007 Velos Pro Mass Spectrometer April 2011 EMC Directive 2004 108 EEC EMC compliance has been evaluated by TUV Rheinland of North America Inc EN 61326 1 2006 EN 55011 2007 A2 2007 CFR 47 FCC Part 15 Subpart B Class A 2009 EN 61000 3 2 2006 EN 61000 3 3 1995 A1 2001 A2 2005 EN 61000 4 2 1995 A1 1999 A2 2001 Lovv Voltage Safety Compliance EN 61000 4 3 2006 EN 61000 4 4 2004 EN 61000 4 5 2005 EN 61000 4 6 2007 EN 61000 4 11 2004 This device complies vvith Lovv Voltage Directive 2006 95 EEC and harmonized standard EN 61010 1 2001 Velos Pro ETD System April 2011 EMC Directive 2004 108 EEC EMC compliance has been evaluated by TUV Rheinland of North America Inc EN 61326 1 2006 EN 61000 4 3 2006 EN 55011 2007 A2 2007 EN 61000 4 4 2004 CF
44. 62 If the needle is damaged replace it If the sheath gas is leaking at the interface between the needle seal and the needle replace the needle seal To replace the needle needle seal or both 1 Disconnect the ESI nozzle from the ESI manifold see steps 3 5 in To disassemble the ESI probe on page 59 2 Pull the ESI needle out of the ESI manifold 3 To dislodge the needle seal gently tap the ESI manifold against a hard surface If necessary use the needle or another appropriate tool to push the needle seal out of the ESI manifold Tapping the manifold against a hard surface can also help to dislodge the resistor and battery contact 4 If necessary replace the needle seal the 26 gauge spray needle or both 5 Reassemble the ESI probe see steps 1 6 in To assemble the ESI probe on page 62 To clean and dry the ESI manifold 1 Disassemble the ESI probe see steps 3 5 in To disassemble the ESI probe on page 59 2 Rinse the ESI manifold with HPLC grade water and then with LCMS grade methanol 3 Remove excess methanol from the manifold with a lint free tissue and then dry it with nitrogen gas 4 Inspect the spray needle nozzle O ring high voltage socket O ring and needle seal 5 Replace any damaged parts 6 Reassemble the ESI probe see the following procedure Thermo Scientific LTO Series Hardware Manual 61 5 Maintenance lon Source Probe Maintenance Assembling the ESI Probe Follow this
45. 7 5 Maintenance Q0 and Q1 lon Guides Maintenance Removing the Vacuum Manifold s Top Cover Plate To access the QO and Q1 ion guides mass analyzer and ion detection system remove the top cover of the vacuum manifold The top cover is held in place by gravity and by the pressure differential between the vacuum manifold and atmospheric pressure Six cables connect to the top cover plate To remove the vacuum manifold s top cover plate 1 Disconnect the two electron multiplier high voltage coaxial cables at the back of the plate Figure 70 Figure 70 Electrical connections to the top cover plate of the vacuum manifold Electron multiplier high voltage cables Electrometer cable Top cover PCB cables Handle front 2 Disconnect the electrometer cable If necessary use a small slotted screwdriver to loosen the screws that secure the cable 3 Disconnect the three cables connected to the top cover PCB not visible 98 LTO Series Hardware Manual Thermo Scientific 5 Maintenance Q0 and 01 lon Guides Maintenance 4 Carefully lift up the top cover plate by its two handles and place it upside down supported on its handles on the clean lint free work surface CAUTION Do not pull the cover too hard Instead rock it back and forth to loosen it Lift it straight up and not at an angle to avoid damaging the bottom ion optics Try not to damage the components on the bottom side of the cover plate 5 Cover t
46. 7 stainless steel metal needle 69 ESI sample tube trimming 58 exit lens description 19 reinstalling 83 removing 82 F fan filters cleaning 119 FCC compliance vii flow injection analysis 11 forepump oil purging 51 forepumps description 31 oil purging 51 functional block diagram mass spectrometer 8 vacuum system 28 fused silica sample tube checking 48 for APCI probe installing 76 for ESI probe installing 63 trimming 58 G gas supply levels checking 48 gate lens See split gate lens grounding union connection 66 H HCD See Trap HCD license helium pressure 48 HESI II probe cleaning 69 flushing 69 needle insert replacing 69 inlet gases hardware description 31 ion detection system description 26 ion gauge description 31 ion guides description 20 drawings QO and Q1 LTQ Velos 102 QO and Q1 LTQ XL 101 136 LTO Series Hardware Manual QO and Q1 LXQ 100 QO and Q1 Velos Pro 103 tube lens 17 See also QO ion guide and Q1 ion guide ion isolation waveform voltage description 24 ion source interface description 15 ion transfer tube 15 reinstalling 89 removing 78 skimmer 17 19 ion sweep cone cleaning 51 description 15 figure of 86 ion transfer capillary See ion transfer tube ion transfer tube cleaning 51 88 description 15 removing 85 ionization technique definition 5 K kits ESI probe 126 HESI II probe 126 safety sleeve 126 L LC MS analysis description 4 LED
47. 95 A1 2001 EN 61000 4 5 1995 A1 2001 EN 61326 1 1997 A1 1998 A2 2001 A3 2003 EN 61000 4 6 2003 EN 61000 4 2 2001 EN 61000 4 11 1994 A1 2001 EN 61000 4 3 2002 CISPR 11 1999 A1 1999 A2 2002 FCC Class A CFR 47 Part 15 2005 Low Voltage Safety Compliance This device complies with Low Voltage Directive 73 23 EEC and harmonized standard EN 61010 1 2001 Thermo SCIENTIFIC MALDI LTQ XL System August 2007 EMC Directive 2004 108 EC EMC compliance has been evaluated by TUV Rheinland of North America Inc EN 55011 1998 A1 1999 A2 2002 EN 61000 4 3 2002 EN 61000 3 2 2000 EN 61000 4 4 1995 A1 2000 A2 2001 EN 61000 3 3 1995 A1 2001 EN 61000 4 5 2001 EN 61326 1 1998 A2 2001 A3 2003 EN 61000 4 6 2003 EN 61000 4 2 2001 EN 61000 4 11 2001 FCC Class A CFR 47 Part 15 2006 CISPR 11 1998 A1 1999 A2 2002 Low Voltage Safety Compliance This device complies with Low Voltage Directive 2006 95 EC and harmonized standard EN 61010 1 2001 Safety of Laser Products Compliance with safety of laser products is declared under Thermo Fisher Scientific sole responsibility This device complies with the harmonized standard IEC EN 60825 1 A2 2001 ETQ Velos Mass Spectrometer August 2008 EMC Directive 2004 108 EEC EMC compliance has been evaluated by TUV Rheinland of North America Inc EN 55011 2007 A2 2007 EN 61000 4 3 2006 EN 61000 3 2 2006 EN 61000 4 4 2004 EN 61000 3 3 1995 A1
48. CB Figure 70 on page 98 Oneor two electron multiplier high voltage coaxial cables as applicable e One electrometer cable Thermo Scientific LTO Series Hardware Manual 109 5 Maintenance Electron Multiplier Replacement Reinstalling the Top Cover of the Mass Spectrometer To reinstall the top cover of the mass spectrometer 1 Open the front door of the mass spectrometer by using the 1 4 in hex driver on the door latch Figure 68 on page 97 2 Place the top cover on the mass spectrometer and slide it forward until it is flush with the front panel 3 Tighten the two captive screws to secure the top cover by using the Phillips screwdriver 4 Close the front door of mass spectrometer and use the 1 4 in hex driver to tighten the latch 5 Reconnect any tubing between the syringe pump LC pump or LC and the API source to accommodate your instrument configuration Electron Multiplier Replacement Electron multipliers have finite lifetimes and their surfaces degrade over time causing more voltage to be required to achieve the specified gain Factors contributing to a decrease in the lifetime are air exposure causes oxidation electron flow produces internal heat heat poor vacuum conditions and water causes arcing You might need to replace one or both of the electron multipliers as applicable if either of these symptoms persists Excessive noise in the mass spectrum produced by the electron multiplier
49. R 47 FCC Part 15 Subpart B Class A 2009 EN 61000 4 5 2005 EN 61000 3 2 2006 EN 61000 4 6 2007 EN 61000 3 3 1995 A1 2001 A2 2005 EN 61000 4 11 2004 EN 61000 4 2 1995 A1 1999 A2 2001 Low Voltage Safety Compliance This device complies with Low Voltage Directive 2006 95 EEC and harmonized standard EN 61010 1 2001 FCC Compliance Statement THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES OPERATION IS SUBJECT TO THE FOLLOWING TWO CONDITIONS 1 THIS DEVICE MAY NOT CAUSE HARMFUL INTERFERENCE AND 2 THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION CAUTION Read and understand the various precautionary notes signs and symbols contained inside this manual pertaining to the safe use and operation of this product before using the device Notice on Lifting and Handling of Thermo Scientific Instruments For your safety and in compliance with international regulations the physical handling of this Thermo Fisher Scientific instrument requires a team effort to lift and or move the instrument This instrument is too heavy and or bulky for one person alone to handle safely Notice on the Proper Use of Thermo Scientific Instruments In compliance with international regulations Use of this instrument in a manner not specified by Thermo Fisher Scientific could impair any protection provided by the instrument Notice on the Susceptibility to Electromag
50. RICAL SHOCK Cover the fused silica sample tube with the PEEK safety sleeve and use the associated PEEK ferrules provided in the Safety Sleeve Kit before operating the mass spectrometer The PEEK tubing acts as a second level of protection against accidental electrical discharge Installing the fused silica sample tube with the PEEK safety sleeve requires the following parts Image Description Part number Ferrule natural PEEK 0 027 in ID 00101 18119 for use with the 0 024 in OD PEEK safety sleeve m Fitting adapter natural PEEK 10 32 to 1 4 28 00101 18080 for the ESI probe sample inlet Upchurch Scientific P 669 Fitting fingertight natural PEEK two wings 00101 18081 Tw for the 1 16 in OD high pressure tubing Upchurch Scientific F 300 Fitting fingertight red one wing 00101 18195 for the 1 16 in OD high pressure tubing Upchurch Scientific F 200 Fitting grounding union stainless steel 00101 18182 0 010 in thru hole Upchurch Scientific U 435 Safety sleeve natural PEEK tubing 00301 22806 230 um ID 610 um OD 25 4 cm long 0 009 in ID 0 024 in OD 10 in long Tubing fused silica 100 um ID 193 um OD 00106 10499 0 003 in ID 0 008 in OD Tubing red PEEK 127 um ID 1 16 in OD 00301 22912 0 005 in ID 1 6 mm OD To install the fused silica sample tube thread the sample tube through the ESI needle that protrudes from the ESI probe nozzle and the safety s
51. UIM uasiamnzuly uaBunsiaMuy zne Jazinuag Uap WN 39puaAJan nzep ulapJegne uongpue WI pJIM OqUJ G sesai 191 uaq ny s q uauoBeyey uspuauisJoA uap ul Jyo u lp 142489 aula 1491S3Q 53 448439 eureure y S iqzinuog aula s31eJar sap DunueM Jap 90 Japo ualjeyiwauy iu BueDuuf wiag ars ueDeJ 9 u unzz au ny uauuoy exrueg ul p Jepo uai exrueu 91711405 u bny Jap 1jejofisBunzjo 19A U ql n q uaser uaeJeqpunzjua uoa WeMuahay Ul WEIS S Sep I UU M USWYEUGeWS YIISIOA uabibejyasula rp arg ua1uoeeg l n ueqeu 1jumjeDqe uis eseip w py eu 15 uajuauoduloy 9171luJ8 BIS ugue Z M uJey euag uausgallyasa lon Uap Ul U NHU S ON Uap Puaygalds ug SajyoneqiaA eis blosluq uaijexiulau U9puazi9J U9puazie Japo ueueDejnui ueuaDoulzie uSuosixo yu Bue wn waq eungospueuzinuos als uaDeJ uay euiua uarjeyrueu auoi iuejeD UU 18 90 Sasaiq uaieyuauy Qb 1U2lu u yejd1 197 uoA Duny pqezinu s rp als uauluaN 9 99 ueueuiuoueqe yuu zy3lu uajaqiesBunueA ais uaqiamnag 1uu9J19D Z N WOA pun 193 euoseDqe 18491 sep ynw uayieg1esBunue Aw 40A ueuuo uauoesun18A uaDunzja J9A ueDunuuedsu2oH u p1 M 18490 WASAIP l 2042s04 J9 3 H ISG0A S3npolq son ues 3141 7U319S Jaysi4 ouuau 10 uoneziueBJo Yoddns 09129 E90 1n0 1951009 a qeuorsanb SI 9Jynpo90Jd e jo Ajgjes aui
52. able union fitting until the tip of the needle insert protrudes past the probe nozzle by 1 5 mm Figure 45 Figure 45 HESI ll probe nozzle tip enlarged ESI needle Metal needle 7 Place the end cover on the probe body insert the two hex socket head screws into the end cover and then tighten them by using the 3 mm hex driver Thermo Scientific LTO Series Hardware Manual 71 5 Maintenance lon Source Probe Maintenance APCI Probe Maintenance The APCI probe requires minimum maintenance Occasionally you must replace the internal APCI sample tube 150 um ID 0 006 in ID 390 um OD 0 015 in OD and 8 6 cm 3 4 in long fused silica tubing and clean the APCI nozzle CAUTION HOT SURFACE At operating temperatures above 350 C 662 F the probe and API source housing can severely burn you Before removing the probe or API source housing allow the part to cool to room temperature approximately 20 minutes before touching it e f the mass spectrometer connects to an LC system leave the solvent flow from the LC pump on while the probe cools to room temperature Figure 46 and Figure 47 show the major components of the APCI probe Figure 46 APCI probe Vaporizer heater cable socket Retention flanges Flat side on APCI nozzle head APCI nozzle assembly 12 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Probe Maintenance Figure 47 APCI probe cross sect
53. and precision aligned hyperbolic rods In the LXQ and LTQ XL mass spectrometers the two rods in the x dimension have slots In the Velos Pro mass spectrometer all rods have a slot Ions are ejected only through the x rods during scan out In each trap rods opposite each other in the array are connected electrically You can consider the four rods of each section to be two pairs of two rods each LXO and LTO XL The mass analyzer in the LXQ and LTQ XL mass spectrometers consists of a front lens linear ion trap and back lens The front and back lenses are metal plates with a circular hole in the center through which the ion beam passes The front and back lenses provide conductance limits The LXQ rods have one section and the LTQ XL rods have three sections Figure 20 shows the basic design of the linear ion trap Figure 20 TO XL linear ion trap quadrupole rod assembly Back section lt Center section Front section Thermo Scientific LTO Series Hardware Manual 23 2 Functional Description Mass Spectrometer Velos Pro The mass analyzer in the Velos Pro mass spectrometer consists of a front lens a high pressure linear ion trap cell a center lens a second low pressure linear ion trap cell and a back lens The front center and back lenses are metal plates with a circular hole in the center through which the ion beam passes The front center and back lenses provide conductance limits he Velos Pro rods have three s
54. aning the Skimmer and Tube Lens on the LXO and LTO XL Mass Spectrometers Chemicals accumulating on the surfaces of the skimmer and tube lens form an insulating layer that can modify the electrical fields controlling ion transmission The skimmer and tube lens require cleaning less often than the ion sweep cone and the ion transfer tube No tools are needed to remove or install these components CAUTION Do not scratch the outside of the skimmer cone To clean the skimmer and tube lens follow these procedures 1 To remove and clean the tube lens and skimmer 2 To reinstall the tube lens and skimmer on page 81 Thermo Scientific LTO Series Hardware Manual 19 5 Maintenance lon Source Interface Maintenance Figure 55 shows the skimmer and tube lens removed from the ion source interface cage Figure 55 Skimmer tube lens and ion source interface cage for the LXO and LIQ XL Ball plunger holes for one side LXO Tube lens Contact ring lon source interface cage support okimmer Ball plunger holes for one side LTO XL Tube lens Contact ring lon source interface support outer cage Skimmer To remove and clean the tube lens and skimmer 1 Remove the ion source interface see page 78 2 Gently press the skimmer out of the contact ring support and then place it on the clean lint free work surface If necessary first loosen the ball plungers a little by using the small slotted screwdriver F
55. ant mutagenic or toxic chemicals Use only approved containers and procedures for disposing of waste oil Eye Hazard Eye damage could occur from splattered chemicals or airborne particles Wear safety glasses when handling chemicals or of Pe servicing the instrument Thermo Scientific LTO Series Hardware Manual XXV Preface Contacting Us There are several ways to contact Thermo Fisher Scientific for the information you need To contact Technical Support Phone 800 532 4752 Fax 561 688 8736 E mail us techsupport analyze thermofisher com Knowledge base www thermokb com Find software updates and utilities to download at mssupport thermo com To contact Customer Service for ordering information Phone 800 532 4752 Fax 561 688 8731 E mail us customer support analyze thermofisher com Web site www thermo com ms To get local contact information for sales or service Go to www thermoscientific com wps portal ts contactus To copy manuals from the nternet Go to mssupport thermo com agree to the Terms and Conditions and then click Customer Manuals in the left margin of the window To suggest changes to documentation or to Help Fill out a reader survey online at www surveymonkey com s PQM6P62 e Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com XXVI LTO Series Hardware Manual Thermo Scientific UU BN Introduction The LTQ Series linear ion t
56. ate anode component LTO Series Hardware Manual 129 7 Replaceable Parts Miscellaneous Parts Miscellaneous Parts Ferrules Ferrule natural PEEK 0 027 in ID for use with the PEEK safety sleeve 00101 18119 Fittings Fitting adapter natural PEEK 10 32 to 1 4 28 0 040 in 1 0 mm thru hole for the ESI probe sample inlet Upchurch Scientific P 669 00101 18080 Fitting fingertight natural PEEK two wings for the 1 16 in OD high pressure tubing Upchurch Scientific F 300 00101 18081 Fitting fingertight red one wing for the 1 16 in OD high pressure tubing Upchurch Scientific F 200 00101 18195 Fitting grounding union stainless steel 0 010 in thru hole Upchurch Scientific U 435 tes dI PRI EA RR E RR deba 00101 18182 Forepumps Lorena LL uoscenceseroicessqibekc Q rice Ars de S 00301 15101 Sample Loops BL stainless Steel 44 46 nee een 7 00110 22010 I0 uL Gta less steel aus nee bop eed as peewee 7 00110 22012 Eni 77 7 TENUES 00110 22014 DOL Stainless Steel ETT 00110 22016 LOO Stainless oo Ls an eh dara to 00110 22018 DOOM is Sess steal os ewer pt EBENE SER RER EEE TREES 00110 22020 0 0 00110 22022 Tubing Safety sleeve natural PEEK tubing 230 pm ID 610 pm OD 25 4 cm long 0 009 in ID 0 024 in OD 10 in long 00301 22806 Sample tube fused si
57. ation page Diagnostics E Tests R Manual coarse calibration Plot readback Set device Ealibrate current scan type HF tune F bara Expected low mass 195 10 Observed low mass 194 90 _ Display settings Expected high mass 1 822 00 Observed high mass 1 818 1 Toggles Im Triggers Set 4GC mode Execute Mass calibration ne Guster evaluation r Estimate other calibration modes using eurrent Full scan Execute pu Cancel 2 Click Save and then click OK To complete the process of changing the electron multipliers calibrate the electron multiplier voltage as described in the next procedure Thermo Scientific LTO Series Hardware Manual 115 5 Maintenance Electron Multiplier Replacement To calibrate the electron multiplier voltages 1 Allow the system to pump down for at least two hours before turning on the high voltages Thermo Fisher Scientific Product Support recommends 15 hours or more 2 Set up for infusing the tuning solution into the mass spectrometer as described in the LTQ Series Getting Started Guide E 3 In the Tune Plus window click the Calibrate button to open the Calibrate dialog box Figure 83 Figure 83 Calibrate dialog box showing the Automatic page B Calibrate Mass Range Mormal High Automatic Semi Automatic Check Calibration Items Multipole AF Frequency Main AF Frequ
58. by Underwriters Laboratories Inc EN 55011 1998 EN 61000 4 3 2002 A1 2002 EN 61000 3 2 1995 A1 1998 A2 1998 A14 2000 EN 61000 4 4 1995 A1 2001 A2 2001 EN 61000 3 3 1995 EN 61000 4 5 1995 A1 2001 EN 61326 1 1997 EN 61000 4 6 1996 A1 2001 EN 61000 4 2 1995 A1 1998 A2 2001 EN 61000 4 11 1994 A1 2001 FCC Class A CFR 47 Part 15 Subpart B 2004 CISPR 11 1999 A1 1999 A2 2002 Low Voltage Safety Compliance This device complies with Low Voltage Directive 73 23 EEC and harmonized standard EN 61010 1 2001 Thermo SCIENTIFIC LTQ XL Mass Spectrometer September 2006 EMC Directive 89 336 EEC EMC compliance has been evaluated by TUV Rheinland of North America Inc EN 55011 1998 Al 1999 A2 2002 EN 61000 4 3 2002 EN 61000 3 2 1995 A1 1998 A2 1998 A14 2000 EN 61000 4 4 1995 A1 2001 A2 2001 EN 61000 3 3 1995 A1 2001 EN 61000 4 5 1995 A1 2001 EN 61326 1 1997 A1 1998 A2 2001 A3 2003 EN 61000 4 6 2003 EN 61000 4 2 2001 EN 61000 4 11 2001 FCC Class A CFR 47 Part 15 2005 CISPR 11 1999 A1 1999 A2 2002 Low Voltage Safety Compliance This device complies with Low Voltage Directive 73 23 EEC and harmonized standard EN 61010 1 2001 LTQ XL ETD System January 2007 EMC Directive 89 336 EEC EMC compliance has been evaluated by TUV Rheinland of North America Inc EN 61000 3 2 1995 A1 1998 A2 1998 A14 2000 EN 61000 4 4 1995 A1 2000 A2 2001 EN 61000 3 3 19
59. calibrations might produce incorrect calibration results To reset the tune and calibration parameters to their default values 1 Open the Tune Plus window see page 34 2 Save a copy of the master calibration file 3 Do one of the following To restore the default calibration parameters choose File Restore Factory Calibration To restore the default tune parameters choose File Restore Factory Tune Method 4 To calibrate or tune the mass spectrometer follow the procedures described in the LTQ Series Getting Started Guide 40 LTO Series Hardware Manual Thermo Scientific 3 System Shutdown Startup and Reset Restarting the Data System Restarting the Data System If possible use the Windows restart procedure to shut down and restart the data system so that Windows can properly close applications and save changes to files Note The communications link between the data system and the mass spectrometer should automatically reestablish after resetting the data system When this occurs the Communication LED turns yellow and then green If the system is unable to reestablish the communications link press and hold the Reset button for three seconds To restart the data system by using Windows soft reboot On the Windows taskbar choose Start Shut Down Select Restart and then click OK To restart the data system by using the power button hard reboot Press the Power button on the data system
60. components under magnification for any lint or particulates Note Inspect the orifices to confirm that no lint or particulates are present in the bore of the orifices Use tweezers or a similar tool to remove the lint or particulate Reinstalling the Q0 and Q1 lon Guides To reinstall the 00 and 01 ion guides CAUTION Be careful not to bend or break the lead pins on the QO quadrupole and QI octapole 1 Reinstall the QO ion guide as follows a Insert lens L1 into the opening in the baffle Figure 71 on page 100 through Figure 74 on page 103 b With one hand hold the QO quadrupole against the lens L1 and press L1 against the opening in the baffle with the contact pin up and away from the top cover plate c With the other hand install the Q0 ion guide mounting bracket at the other end of the Q0 quadrupole Note If the QO quadrupole is not positioned correctly it could be too far forward and make contact with the manifold d Tighten the two thumbscrews securing the QO ion guide mounting bracket to the top cover plate 2 Reinstall the Q1 ion guide as follows a Insert the split gate lens into the opening in lens L1 Figure 71 through Figure 74 b With one hand hold the Q1 octapole against the split gate lens and with the other hand install the Q1 ion guide mounting bracket at the other end of the Q1 octapole c Tighten the two thumbscrews securing the Q1 ion guide mounting bracket to the top cover
61. ct 9 Disconnect the high voltage socket from the ESI probe by using the 1 2 in open end wrench 10 Unscrew the fitting from the sheath liquid inlet 11 If the ESI manifold needs cleaning follow the procedure To clean and dry the ESI manifold on page 61 12 To reassemble the ESI probe see Assembling the ESI Probe on page 62 Cleaning or Replacing the ESI Probe Components Maintaining the ESI probe requires occasional replacement of the 26 gauge needle the needle seal the ESI nozzle and the high voltage socket O rings In addition the ESI nozzle and manifold occasionally require cleaning For Field Service use only Part number ESI 26 gauge spray needle 00950 00990 ESI needle seal 00950 00952 ESI nozzle O ring Viton 0 676 in ID 00107 0710 ESI high voltage socket O ring 00107 02550 To clean the ESI nozzle 1 Disconnect the ESI nozzle from the ESI manifold see steps 3 5 in To disassemble the ESI probe on page 59 2 Clean the bore of the ESI nozzle with LCMS grade methanol The choice of solvent depends on the solubility of the chemical deposits 3 Rinse the nozzle with methanol and dry with nitrogen gas 60 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Probe Maintenance 4 nspect the ESI nozzle O ring and replace it if necessary Figure 31 Figure 31 ESI nozzle and O ring ESI nozzle O ring 5 Reconnect the ESI nozzle to the ESI manifold see page
62. dware Manual 15 2 Functional Description Mass Spectrometer The heater block contains two heater cartridges surrounds the ion transfer tube and heats the tube to temperatures up to 400 C 752 F A probe sensor measures the temperature of the heater block A decreasing pressure gradient draws ions into the ion transfer tube in the atmospheric pressure region and transports them to the ion transfer tube skimmer or ion transfer tube S lens region as applicable of the vacuum manifold The vent prevent ball stops air from entering the vacuum manifold when the tube is removed so that you can remove the ion transfer tube for cleaning without venting the system LXO and LTO XL The ion source interface in the LXQ and LTQ XL includes an ion transfer tube two cartridge heaters a heater block a sensor a vent prevent ball an ion sweep cone an AP tube lens and a skimmer Figure 10 and Figure 11 The tube lens and skimmer mount to the ion source interface cage Figure 10 XO ion source interface cross section Vent prevent ball Tube lens lon sweep cone T i Ks D Skimmer spray cone immediately behind 5 the sweep cone Heater block 16 LTO Series Hardware Manual Thermo Scientific 2 Functional Description Mass Spectrometer Figure 11 LTO XL ion source interface cross section Vent prevent ball Tube lens lon sweep cone okimmer opray cone immediately behind lon transfer tube th
63. e 35 00 34 73 Tube Lens Vk 110 00 1474 Apply Lancel Help b In the Sheath Gas Flow Rate arb box enter 30 c Inthe Aux Gas Flow Rate arb box enter 5 d Inthe Sweep Gas Flow Rate arb box enter 0 e Inthe Spray Voltage kV box enter 0 f Click OK To set up and start a flow of 50 50 methanol water solution from the LC system to the API source a ChooseSetup Inlet Direct Control to open the Inlet Direct Control dialog box The Xcalibur data system controls the LC pumps from several manufacturers including Thermo Fisher Scientific Inc Agilent Technologies and Waters Corporation Contact your Thermo Fisher Scientific sales representative for information about the liquid chromatography systems compatible with the LTQ Series mass spectrometer Click the LC Pump tab Set the solvent proportions to 5096 methanol and 5096 water Start the solvent flow Thermo Scientific A Daily Operation After Operating the LTO Series System 7 Let the solution flow through the sample transfer line sample tube and API probe for 15 minutes 8 After 15 minutes turn off the flow of liquid from the LC to the API source as follows a Leave the API source including the APCI vaporizer sheath gas and auxiliary gas on for an additional 5 minutes mn b Click the Pump Off or Stop Pump button Al m 9 After another 5 minutes click the On Standby button to select the Standby mode On Standby Cleaning the l
64. e 63 Figure 62 lon source interface components for the LXO and LIU XL opray cone lon sweep cone lon transfer tube Figure 63 lon source interface components for the Velos Pro opray cone lon sweep cone lon transfer tube 5 Clean the O ring with methanol or replace it if necessary 6 Position the O ring in the spray cone CAUTION Be careful not to bend the ion transfer tube Rotate the tube as you insert it 88 LTO Series Hardware Manual Thermo Scientific 5 Maintenance 000 RF Lens Maintenance Insert the ion transfer tube into the heater block rotating it clockwise by using the ion transfer removal tool as you insert it and until it is fingertight Reinstall the ion sweep cone onto the ion source interface Place the electronics service switch in the Electronics Normal up position to turn on the nonvacuum system voltages Note If you successfully unblocked the ion transfer tube the Convectron gauge pressure should increase to a normal value approximately 1 Torr If trying this method does not clear the blockage replace the ion transfer tube Reinstalling the lon Source Interface To reinstall the ion source interface Orient the ion source interface as shown in Figure 55 on page 80 Carefully insert the ion source interface into the vacuum manifold until it is positioned in the Q00 rf lens Reinstall the API ion source housing Start up the system as d
65. e 72 2 Hold the APCI probe body with one hand and with the other hand grasp the head of the APCI nozzle assembly and rotate it counterclockwise until the flat sides of the head align with the retention flanges Figure 48 Thermo Scientific LTO Series Hardware Manual 73 5 Maintenance lon Source Probe Maintenance Figure 48 Sample inlet end of the APCI probe showing locked and unlocked nozzles Hetention flanges Locked nozzle Unlocked nozzle 3 Carefully pull out the nozzle assembly CAUTION If the sample tube hits the sides of the vaporizer it can break To prevent breakage carefully pull the APCI nozzle straight back from the APCI probe 4 Place the nozzle assembly on the clean lint free work surface Cleaning the APCI Nozzle For Field Service use only Part number O ring silicone 0 312 in ID 1 16 in thick 00107 04500 O ring Viton 0 500 in ID 1 16 in thick 00107 05600 To clean the APCI nozzle 1 Remove the nozzle from the APCI probe body see page 73 2 Check the condition of the O rings on the APCI nozzle Figure 49 Figure 49 APCI probe nozzle assembly 0 312 in ID O ring 0 500 in ID 0 ring 3 Clean the interior APCI components excluding the ceramic heater with a 50 50 solution of LCMS grade methanol LCMS grade water and a lint free swab Dry the components with nitrogen gas and place them on the clean lint free work surface 74 LTO Series Hardware Manual Thermo Scientif
66. e SA D RE Ed iu Eas 9 Divert Inject Vakie ze seasea E E 10 LEDs and Button 24200 ern ee 7 11 Divert Valve Positiones ais pakante pedenn p iar k eE A Ea Ea 11 Injection Valve Operation ssis neo aa IAS SP EUR TS 12 Mass OCCHOMICECE Bae ceentoceh se iee 7 ee aes 12 EDS rm 13 nennen E er dd 14 ALL Olu sd sopa ras eee eae 15 leit Source TIGE os x b rd vacare rad T 15 mag 20 11117 1 00 EEE EEE TERN Ea E LS 23 lon Detection Systems a acea ped ed 7 anes 26 VALUE SYS nn ee en Ghawdee ds 28 Inlet Gases G een testet ers 31 ps i gene 32 Chapter3 System Shutdown Startup and Reset 33 Shutting Down the System in an Emergency 33 Opening the Tune Plus Window leen 34 Placing the Mass Spectrometer in Standby Mode 35 Turning On the Mass Spectrometer sun ner sangen doe gg R done te 36 Thermo Scientific LTO Series Hardware Manual xiii Contents xiv Chapter 4 Chapter 5 LTO Series Hardware Manual Shutting Down the Mass Spectrometer Completely 36 Starting the System after a Complete Shutdown 37 Starting tie LO Syse ieee aa eb aa epulis 37 Starting the ars 38 Starting the Mass Spectrometer us erc este 38 Starting the AULOSSEIDIG
67. e components are essential to properly operate the mass spectrometer The Q1 ion guides require cleaning less often than the QO ion guide The cleaning frequency depends on the type and quantity of the compounds that you analyze To clean or replace the QO and Q1 ion guide components follow these procedures 1 Removing the Top Cover of the Mass Spectrometer 2 Removing the Vacuum Manifold s Top Cover Plate on page 98 3 Removing the Q0 and Q1 Ion Guides on page 99 4 Cleaning the QO and Q1 Ion Guides Lens L1 and Split Gate Lens on page 104 5 Reinstalling the Q0 and Q1 Ion Guides on page 105 6 Reinstalling the Top Cover of the Mass Spectrometer on page 110 You need the following tools and supplies from Table 7 on page 55 Tools Supplies 1 4 in hex driver Chamois tip swabs 5 64 in hex ball driver Detergent for example Liquinox Magnification device Gloves lint and power free Phillips screwdriver Graduated cylinder for use with methanol Sonicator Kimvvipes or lint free industrial tissues Optional Tweezers or similar tool Methanol LCMS grade Nitrogen gas clean dry and compressed Water HPLC grade or higher and tap IMPORTANT e Prepare a clean work surface by covering the area with lint free paper e Put on a new pair of lint and powder free gloves before starting each of these removal cleaning and reinstallation procedures Thermo Scientific LTO Series Hardware Manual 95 5 Maintenance Q0 and
68. e end of each work day or more often if you suspect they are contaminated To remove contamination use a 50 50 methanol water solution flushing for approximately 15 minutes from the LC system through the API source For instructions see Flushing the Sample Transfer Line Sample Tube and API Probe on page 49 LTO Series Hardware Manual 57 5 Maintenance lon Source Probe Maintenance Trimming the ESI Sample Tube Operating the mass spectrometer with acetonitrile in the mobile phase can cause elongation of the polyimide coating on the fused silica sample tube If the polyimide coating has elongated past the end of the electrospray needle cut and reposition the end of the sample tube l 58 LTO Series Hardware Manual To cut and reposition the end of the sample tube Place the mass spectrometer in Standby mode see page 55 and let it cool to room temperature See the temperature cautionary statement on page 57 Remove the ESI probe from the API source housing Loosen the red fitting of the two piece fingertight fitting that secures the position of the sample tube and the safety sleeve at the ESI probe sample inlet Figure 29 Note When the nut and ferrule assembly are properly positioned in the receiving port the receiving port compresses the ferrule so that it fits snugly to the tubing When you loosen the fitting the receiving port does not compress the ferrule and the tubing is free to move Figure
69. e it if necessary 3 Cut approximately 13 cm 5 in of fused silica tubing by using the fused silica cutting tool and then under magnification check that the end is cut squarely 4 Connect the sample tubing to the APCI flange fitting as follows a Slide the nut and then the ferrule onto the sample tubing Figure 52 Figure 52 Sample tubing connection to the APCI flange fitting u Sample tubing u Male nut APCI flange fitting j Ferrule 0 239 in ID O ring b While pressing the sample tubing into the externally threaded end of the APCI flange fitting finger tighten the nut and fitting 5 Carefully insert the free end of the sample tubing into the back of the APCI nozzle and out the nozzle tip and then finger tighten the APCI flange fitting 16 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Interface Maintenance 6 Tighten the APCI flange fitting an additional quarter turn by using the 3 8 in open end wrench Figure 50 on page 75 7 Cut the sample tube approximately 1 mm past the tip of the APCI nozzle by using the fused silica cutting tool Figure 53 Figure 53 Sample tube extending past the APCI nozzle tip APCI flange fitting A 224 uu APCI nozzle tip Reassembling the APCI Probe To reassemble the APCI probe 1 Hold the APCI probe body with one hand and with the other hand carefully insert the APCI nozzle into the APCI probe 2 Align the flat sides of
70. e items to check before operating the system and the cleaning procedures to perform after completing the analyses Contents Before Operating the LTQ Series System e After Operating the LTQ Series System Note You do not need to tune optimize the tune parameters for the ESI calibration solution and calibrate the ETQ Series system as part of your daily routine Generally calibration parameters are instrument parameters that affect the mass accuracy and resolution Tune parameters are instrument parameters that affect the intensity of the ion signal You calibrate the L TC Series system by using the ESI calibration solution about once every month Do some calibrations such as for the electron multiplier gain more often You must optimize the tune parameters create a new tune method whenever you change the type of experiment the specific compound or the compound class Pump down times of less than 15 hours on new instruments or after venting the mass spectrometer might cause incorrect calibration and might increase the aging of the electron multipliers For information about tuning and calibration refer to the LTQ Series Getting Started Guide Thermo Scientific LTO Series Hardware Manual 45 A Daily Operation Before Operating the LTO Series System Before Operating the LTO Series System Follow these procedures every day before beginning the first analysis Checking the System Mode Checking the Vacuum Levels Ch
71. e sweep cone Heater block Ions from the ion transfer tube enter the tube lens The tube lens has a potential applied to it to focus the ions toward the opening of the skimmer When you tune the LXQ or LIQ XL mass spectrometer adjust the tube lens potential to maximize sensitivity by balancing desolvation with fragmentation Ions from the tube lens pass through the skimmer and move toward the Q00 rf lens The skimmer acts as a vacuum baffle between the higher pressure ion source interface region and the lower pressure QO0 rf lens region of the vacuum manifold For the LXQ and LTQ XL ions from the ion transfer tube enter the tube lens Figure 12 The API tube lens offset voltage applied to the tube lens accelerates the ions into the background gas that is present in the ion transfer tube skimmer region Collisions with the background gas aid in the desolvation of the ions and increase sensitivity However if the tube lens offset voltage is too high collisions with the background gas can be energetic enough to cause ion fragmentation This fragmentation called ion source collision induced dissociation CID decreases sensitivity When you tune the LXQ or LTQ XL mass spectrometer adjust the tube lens offset voltage to maximize sensitivity by balancing desolvation with fragmentation Thermo Scientific LTO Series Hardware Manual 17 2 Functional Description Mass Spectrometer Figure 12 Skimmer and tube lens back view Tube lens S
72. e to position it in the cage 2 Insert lens LO through the back of the cage to position it CAUTION Be careful not to bend or break the lead pins on the Q00 rf lens If this happens you must replace the Q00 rf lens 3 Carefully reconnect the leads to the lead pins on the QO0 rf lens and lens LO as shown in Figure 65 on page 92 Reinstalling the 000 RF Lens Assembly For Field Service use only Part number O ring 2 148 Viton 884 2 737 in ID 00107 15542 To reinstall the 000 rf lens assembly into the vacuum manifold 1 Ensure that the two O rings are properly installed on the back of the outer cage Figure 66 on page 93 2 Orient the outer cage assembly Figure 66 on page 93 3 Carefully insert the outer cage assembly into the vacuum manifold 4 Tighten the three hex socket head screws that secure the assembly to the vacuum manifold by using the 5 32 in hex ball driver 5 Reconnect the electrical connector inside the vacuum manifold Figure 64 on page 91 6 Reinstall the ion source interface see page 89 7 Start up the system as described in Starting the System after a Complete Shutdown on page 37 94 LTO Series Hardware Manual Thermo Scientific 5 Maintenance Q0 and 01 lon Guides Maintenance 00 and 01 lon Guides Maintenance Chemicals accumulating on the surfaces of the Q0 and Q1 ion guides form an insulating layer that can modify the electrical fields controlling ion transmission Clean ion guid
73. eceives line power at 230 Vac 10 15 A for the LTC XL and Velos Pro or 10 A for the LXQ 50 60 Hz through the right side power panel see Figure 8 The power panel provides system power control a contact closure interface Peripheral Control an Ethernet 100Base T connection from the mass spectrometer to the data system computer and a system Reset button The power panel accepts line power filters it and provides it to various components of the mass spectrometer 14 LTO Series Hardware Manual Thermo Scientific Main Power Switch 2 Functional Description Mass Spectrometer In the Off position the Main Power circuit breaker switch removes all power to the mass spectrometer including the external forepump or forepumps In the On position power is supplied to the mass spectrometer In the standard operational mode the switch stays in the On position CAUTION To shut off all power to the mass spectrometer in an emergency place the main power circuit breaker switch labeled Main Power in the Off down position Do not use the electronics service switch Electronics Service Switch Reset Button API Source The electronics service switch is a circuit breaker In the Service Mode position the switch removes power to all components of the mass spectrometer except for the fans and vacuum system This setting allows you to service nonvacuum system components with the vacuum system still operating In the Electronics N
74. ecking the Gas Supplies on page 48 Checking the ESI Fused Silica Sample Tube for Elongation on page 48 Checking the System Mode Ensure that the system is turned on see Turning On the Mass Spectrometer on page 36 Checking the Vacuum Levels Before you begin daily operation check the vacuum pressure levels in the system and check for major air leaks in the system If there is a major air leak the system does not pump down to sufficient levels to turn on the system CAUTION For proper performance operate the L TQ Series system at the proper vacuum levels Operating the system with poor vacuum levels can cause reduced sensitivity tuning problems and reduced electron multiplier life check the vacuum pressure 1 Open the Tune Plus window see page 34 2 Choose Setup Vacuum to open the Vacuum dialog box Figure 26 Figure 26 Vacuum dialog box Vacuum lan Trap lon Gauge On C Off lon Gauge Pressure E 5 Tor 0 73 Convectron Gauge Pressure 0 32 3 Check the Ion Gauge Pressure readback This readback displays the current pressure in the analyzer region 46 LTO Series Hardware Manual Thermo Scientific Thermo Scientific A Daily Operation Before Operating the LTO Series System 4 Check the Convectron Gauge Pressure readback This readback displays the current pressure in the ion transfer tube skimmer and foreline region 5 Compare the current values of the pressures i
75. ections Axial Trapping Voltages The LXQ mass analyzer uses three dc axial trapping voltages one for each lens and one for the trap These voltages establish axial trapping by creating a potential well These dc axial trapping voltages allow the mass analyzer to perform its storage and scan out functions The LTQ XL mass spectrometer also uses three dc axial trapping voltages one for each rod section The Velos Pro mass spectrometer uses six dc axial trapping voltages one for each rod section on both linear ion traps These voltages establish axial trapping by creating potential wells AC Voltages Applied to the Exit Rods The ion isolation waveform voltage resonance excitation ac voltage and resonance ejection ac voltage are applied to the exit rods to stimulate motion of the ions in the direction of the ion detection system When the ac frequency applied to the rods equals the frequency of the motion of the trapped ion which depends on its mass the ion gains kinetic energy If the magnitude of the applied voltage is large enough or the ion is given sufficient time the ion is ejected from the mass analyzer in the direction of the ion detection system X direction The ion isolation waveform voltage is a multifrequency resonance ejection waveform that acts during the ion isolation step of SIM SRM CRM or MS z 1 full scan applications The ion isolation waveform voltage combined with the main rf voltage ejects all ions except
76. ed end facing away from the sample inlet onto the safety sleeve Figure 36 Fingertight fittings installed over the safety sleeve ESI probe Natural PEEK ferrules A Yr V IAI e CS One wing red Two wings fingertight fitting natural PEEK fingertight fitting 7 Connect the safety sleeve and sample tube assembly to the grounding union as follows a 66 LTO Series Hardware Manual Adjust the position of the sample tube so that it is flush with the end of the safety sleeve that protrudes from the back of the probe To provide leverage when tightening the fitting to the union position the grounding union in the grounding union bar of the ion source housing Figure 37 Figure 37 Grounding union positioned in the grounding bar sample inlet Grounding union A tta 3 To prevent the sample tube from slipping through the grounding union thru hole and out the other end connect a fingertight fitting and red PEEK tubing to the other end of the grounding union Thermo Scientific 5 Maintenance lon Source Probe Maintenance d While holding the safety sleeve and sample tube firmly against the grounding union receiving port manually tighten the fitting as tight as you can Figure 38 a
77. em Shutdown Startup and Reset Opening the Tune Plus Window Opening the Tune Plus Window There are several ways to open the Tune Plus window Figure 25 To open the Tune Plus window Do one of the following On the Windows taskbar choose Start Programs Thermo Instruments LTQ model Tune where model is your specific LTQ Series model Note For LTQ Series version 2 5 0 or earlier choose Start Programs x Xcalibur gt model Tune e n the Xcalibur application choose Roadmap view gt Instrument Setup gt model left pane Tune Plus e In the Xcalibur application choose Roadmap view gt Instrument Setup model menu toolbar Start Tune Plus Figure 25 Tune Plus window F Thermo Tune Plus Untitled mfx File View Control ScanMode Display Setup Diagnostics Help mva ve zie ef Clem b En 9 ie c 22 145 Heated ESI Source Spray Voltage KV Spray Current LA Vaporizer Thermocouple Vaporizer Temp C Sheath Gas Flow Rate Aux Gas Flow Rate Sweep Gas Flow Rate Capillary Temp OK Capillary Voltage V Capillary Temp Tube Lens V X X v v X v v v v v v Vacuum Vacuum OK lon Gauge Pressure OK lon Gauge lon Gauge E 5 Torr Convectron Pressure OK Convectron Gauge Torr No spectral data available Turbo Pump Status Running Life hours 12947 Speed Hz Power watts Temperature C lon Optics Multi
78. ency Electron Multiplier Gain Mass and Resolution for Normal and Enhanced Scan Types Mass and Resolution Far oomScan and Ultrazoom Types Isolation and Activation SV aveferms Status Set Instrument to Standby when Finished Cancel Print Help 4 Click the Semi Automatic tab Figure 84 for the LXQ and L TO XL or Figure 85 for the Velos Pro 116 LTO Series Hardware Manual Thermo Scientific 5 Maintenance Electron Multiplier Replacement Figure 84 Semi Automatic page in the Calibrate dialog box LXO and LTO XL Bl Calibrate Mass Range High Automatic Semi Automatic Check V hat to Calibrate Result Last Cal Date select Al Multipole RF Frequency 12 117 2008 Main RF Frequency 12 11 2008 Positive lens Electron Multiplier Gain 12 12 2008 Negative lons Electron Multiplier Mass Calibration L Normal Scan Rate Types 12 12 2008 Enhanced Scan Rate Types 12 72 2008 D Zoom Scan Rate Types 12 72 2008 UltraZoom Scan Rate Types 12 12 2008 1 kis m Busan F7 lile binas amp lili Status Set Instrument to Standby when Finished Start Cancel Print Help Figure 85 Semi Automatic page in the Calibrate dialog box Velos Pro Bl Calibrate Mass Range Normal High Automatic Semr amp utomatic Check Last Cal Date L Select All L Multipole RF Frequency 4 23 2009 Main RF Freque
79. ens L1 and the split gate lens Daily or more often depending on analytical conditions Weekly or if the ion transfer tube bore is contaminated or obstructed If the ion transfer tube bore is corroded As needed depending on analytical conditions As needed depending on analytical conditions As needed depending on analytical conditions page 77 page 95 Clean the Q00 quadrupole and Q00 rf lens and lens LO lens LO As needed depending on analytical conditions page 89 For instructions about maintaining the LC modules refer to that instruments manual 54 LTO Series Hardware Manual Thermo Scientific Tools and Supplies 5 Maintenance Tools and Supplies The LTQ Series mass spectrometer requires very few tools to perform routine maintenance procedures You can remove and disassemble many of the components by hand Table 7 lists the tools equipment and chemicals you need to provide for the maintenance of the API source ion guides mass analyzer and ion detection system Iwo of the parts are in the kits Table 7 Tools equipment and chemicals Sheet 1 of 2 Description Tools Fused silica cutting tool Hex ball driver 3 mm Hex driver or ball driver 1 4 in Hex ball driver 5 32 in long handle Hex ball driver set 0 050 in 1 16 in 5 64 in 3 32 in 7 64 in 1 8 in 9 64 in 5 32 in and 3 16 in Ion transfer tube removal tool Open end wrenches 5 16 in 3 8
80. eplacement o vede m l M 110 Lorepunmp Maintenance a deese uter ete de seele 118 Han Filter Marmtelialee exero vene bue Eh eR ume dades 119 Dianqiosuese ERE ans Sets es aa eee a 121 Heplaceable Pals s em RE EPA EEPRMPC terete 125 t ede Sogni gib e ala Sis 7 die a dd er eft 126 20017 Si cC rrr 126 EHER k bal c l bal o assi 126 Ton Source Probes and Parts 126 Jon Source Interface Parts ea a ds 127 QUU DehsuP AE Sarees epit detta olds edet uo aded ar ide ds teta reed 128 O and Ol Ton Guide Parse sn o eio o edo C ERU cce 128 Electron Mult pliers sc xos tees ay s a o ES 129 Miscellaneous 130 kit nho ula o udi 130 Horepumpesss qs d sa TELE 130 Vacuum Manifold Parts eem c 130 Ulossana ab SITE 131 h Ts 135 LTO Series Hardware Manual XV Figures Thermo Scientific Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 Figure 13 Figure 14 Figure 15 Figure 16 Figure 17 Figure 18 Figure 19 Figure 20 Figure 21 Figure 22 Figure 23 Figure 24 Figure 25 Figure 26 Figure 27 Figure 28 Figure 29 Figure 30 Figure 31 Figure 32 Figure 33 Figure 34 Figure 35 Figure 36 Figure 37 Functional block diagram of an LTQ Series system
81. es too high The turbomolecular pump sends status information such as its temperature or rotational speed to the data system computer 30 LTO Series Hardware Manual Thermo Scientific Forepumps Convectron Gauge lon Gauge 2 Functional Description Mass Spectrometer The LXQ mass spectrometer has one forepump and the LTQ XL and Velos Pro mass spectrometers have two forepumps Forepumps create the vacuum necessary for the proper operation of the turbomolecular pump The forepumps also evacuate the ion transfer tube region of the vacuum manifold The power cords of the forepumps plug into the auxiliary power outlet labeled Mech Pumps on the power panel Figure 8 and Figure 9 on page 14 The main power switch labeled Power In controls this outlet not the electronics service switch CAUTION Always plug the forepump power cords into the outlet labeled Mech Pumps on the right side of the mass spectrometer Never plug them into a wall outlet The LXQ and LTQ XL mass spectrometers contain a Convectron gauge that measures the pressure in the ion transfer tube in the vacuum manifold and the foreline which connects the turbomolecular pump and the forepump The source PCB monitors the pressure measured by the vacuum gauge An ion gauge measures the pressure in the analyzer region of the vacuum manifold and is also used for vacuum protection Figure 24 on page 30 shows the ion gauge port Inlet Gases Hardware Vent Valve
82. escribed in Starting the System after a Complete Shutdown on page 37 Q00 RF Lens Maintenance Chemicals accumulating on the surfaces of the Q00 multi pole and lens LO form an insulating layer that can modify the electrical fields controlling ion transmission Clean ion guide components are essential to properly operate the mass spectrometer The Q00 rf lens and lens LO require cleaning less often than the tube lens and skimmer in the LXQ and LTQ XL mass spectrometers or the S lens in the Velos Pro mass spectrometer The cleaning frequency depends on the type and quantity of the compounds that you analyze To clean or replace the C900 rf lens components follow these procedures 1 Thermo Scientific Removing the Q00 RF Lens Assembly Disassembling the Q00 RF Lens Assembly on page 92 Cleaning the Q00 RF Lens Assembly Components on page 93 Reassembling the Q00 RF Lens Assembly on page 94 Reinstalling the Q00 RF Lens Assembly on page 94 LTO Series Hardware Manual 89 5 Maintenance 000 RF Lens Maintenance You need the following tools and supplies from Table 7 on page 55 Tools Supplies 5 32 in hex ball driver Chamois tip swabs Phillips screwdriver Detergent for example Liquinox Magnification device Gloves lint and power free Slotted screwdriver Graduated cylinder for use with methanol Sonicator Kimvvipes or lint free industrial tissues Methanol LCMS grade MICRO MESH polishing swab 600
83. euoduioo pajeau Aue MO E JUBWNIISUI aur BuiaiAJ8s L H lo sem 8sodsip 0 saJnpaooJd Jadoid pue suauiejuod paAoJdde ST S EO U U JULI JO 9AIS01J02 JO guabeinw diuaboulges 31x0 Buljpuey U UM s9A 0 D S eoIulgu snopJezeu uiejuoo 1ufiu 1u vinnsul stu 1831349 9004 UJ0JJ S19A02 aAOWAL 104 oq 1uauingjsui 3y Burjejedo l UO do y d y AOd li W04 1uaunJjsul BY I9UUOISIP pue 1uauinijsul y umop 1159 121 Aunfui jeuosiad asned ued zey S E110A uDiu s sn JUBWNJISU SIU yIOYS 9119917 NOILNYI 4 4 da joquiAs NOILNYI LEE Contents didi C xxi Related Documentation es cda em mr iad vnm ERE a BA xxii Gering a Traps HCO LIENE ss eos ea arena xxii Getting a New License E REPE Beb Bu a E xxii Installing a New License Codes osos ste BR Enten xxiv Safety and Special Notices 1 dede s ruote n Reb t XXV D T xxvi Chapter 1 luni mre 4 2a nee bb sub BB R d 1 LIQ Series Mass SpecttOmeters aud za a da deeded SII EPA P Ens 1 Overview of an LC MS 2 2 4 Chapter2 Functional Description 7 S lll HU 7 DUE TED o REI du add oe ce
84. g Disassembling the ESI Probe To replace or clean the ESI probe components disassemble the ESI probe 9 l Thermo Scientific To disassemble the ESI probe Place the mass spectrometer in Standby mode see page 55 and let it cool to room temperature Remove the ESI probe from the API source housing Unscrew the red fitting of the two piece fingertight fitting from the sample inlet adapter fitting and remove the sample tube from the ESI probe Because the ESI manifold contains loose components battery contact and resistor subassembly hold the ESI probe with the nozzle facing upward Remove the ESI nozzle from the ESI manifold by using the 5 16 in open end wrench see Figure 32 on page 62 If the nozzle requires cleaning follow the procedure To clean the ESI nozzle on page 60 Pull the ESI needle out of the ESI manifold Figure 30 Figure 30 ES probe with the nozzle removed Resistor High voltage socket iz ym sample inlet adapter fitting sheath liquid inlet fitting ESI needle Needle ESI seal manifold LTO Series Hardware Manual 59 5 Maintenance lon Source Probe Maintenance 8 To dislodge the needle seal gently tap the ESI manifold against a hard surface If necessary use the needle or another appropriate tool to push the needle seal out of the ESI manifold Tapping the manifold against a hard surface can also dislodge the resistor and battery conta
85. g 99 QI ion optics See Q1 ion guide QI octapole See Q1 ion guide regulatory compliance iii reset button 15 resonance ejection rf voltage 24 resonance excitation rf voltage 24 S safety standards iii sample transfer line flushing 49 57 69 73 sample tube APCI installing 76 ESI installing 64 flushing 49 57 69 sample tube dimensions 72 scan definition 5 scanning LED 13 sheath gas description 32 shutdown emergency 33 mass spectrometer 36 skimmer cleaning 79 description 17 19 reinstalling 81 LTO Series Hardware Manual 137 Index T S lens cleaning 83 description 19 reinstalling 85 removing 82 solvent waste container emptying 52 solvents 55 split gate lens cleaning 104 description 22 reinstalling Q1 ion guide and 105 removing Q1 ion guide and 99 spray cone cleaning 51 Standby mode 35 sweep gas description 32 syringe pump description 9 LED 9 system LED 13 startup 27 T top cover removing 96 Trap HCD license xxii troubleshooting 121 tube lens cleaning 79 80 description 17 offset voltage tuning 17 reinstalling 81 voltages 17 tune parameters resetting to factory defaults 40 turbomolecular pump 30 V vacuum LED colors and states 13 note about pressure 39 vacuum levels checking 46 vacuum manifold description 29 pressure 39 top cover removing 98 vacuum pump See turbomolecular pump vacuum system Convectron gauge 31 description 28 functional block diagram 28 p
86. gas auxiliary gas and sweep gas valves control the flow of nitrogen into the API source Figure 22 on page 28 Sheath gas is the inner coaxial nitrogen gas of the API probe that sprays nebulizes the sample solution into a fine mist as it exits the sample tube Auxiliary gas is the outer coaxial nitrogen gas that assists the sheath gas in the nebulizing and evaporating sample solutions Sweep gas flows out from behind the sweep cone in the ion source interface Sweep gas aids in solvent declustering and adduct reduction Dry nitrogen 689 138 kPa 1100 20 psi 99 purity enters the mass spectrometer through a 1 4 in port on the back of the mass spectrometer The data system controls the valves that regulate the nitrogen pressure You can set the flow rates from the Tune Plus window Cooling Fans Five fans provide cooling for the mass spectrometer One 2 8 CMM 100 CFM fan cools the rf voltage coil One 0 59 CMM 21 CFM fan cools the turbomolecular pump Three 2 8 CMM 100 CFM fans cool the electronics in the tower The back of the mass spectrometer draws air in The exhaust air exits from the vent slots on the sides of the mass spectrometer CAUTION To ensure safety and proper cooling always operate the mass spectrometer with its covers in place This is also necessary to comply with product safety and electromagnetic interference regulations 32 LTO Series Hardware Manual Thermo Scientific ge System Shutdown Start
87. ge Wire 6 black Wire 5 green 108 LTO Series Hardware Manual Thermo Scientific 5 Maintenance Q0 and 01 lon Guides Maintenance Reinstalling the Vacuum Manifold s Top Cover For Field Service use only Part number Split chamber O ring 12 33 x 6 65 x 3 21 in x w x 2 97055 40005 To reinstall the vacuum manifold s top cover 1 Remove and discard the tissue from the vacuum manifold s top opening 2 Check the vacuum manifold s split chamber O ring for signs of wear and replace it if necessary Enure that the O ring is positioned properly Note Periodically remove any contamination that might be on the inner walls of the manifold or conversion dynode surfaces by wiping them with a lint free cloth soaked in HPLC grade methanol Use a chamois tip swab soaked in methanol to clean around the inlets and feedthroughs 3 Carefully lift the top cover plate up by its two handles and turn it over 4 Orient the top cover plate so that the one or two electron multipliers as applicable are over the conversion dynodes 5 Carefully insert the four guide posts on the bottom of the top cover plate into the holes in the vacuum manifold 6 Hold the top cover plate parallel to the opening in the vacuum manifold and carefully lower it onto the opening in the vacuum manifold CAUTION Do not damage the O ring or the components on the bottom of the top cover plate 7 Reconnect the following Three cables to the top cover P
88. gnostics can often locate it The diagnostics do not diagnose problems that are not electrical in nature For example they do not diagnose poor sensitivity due to misaligned or dirty components or improper tuning For such reasons have someone who is familiar with systems operation and basic hardware theory run the diagnostics to find and isolate any problems or contact your local Thermo Fisher Scientific field service engineer Before running the diagnostics consider the following Did the system fail when you were running samples Did problems occur after you performed maintenance on the mass spectrometer data system or peripherals Did you change the systems configuration cables or peripherals just before the problem occurred If the answer is yes to the first question there is the possibility of a hardware failure and running the diagnostics is appropriate If the answer is yes to one of the last two questions the problem is probably mechanical not electrical Check again that alignment configurations and cable connections are correct before you run the diagnostics Thermo Scientific LTO Series Hardware Manual 121 6 Diagnostics Torun the diagnostics 1 Open the Tune Plus window see page 24 2 Choose Diagnostics Diagnostics to open the Diagnostics dialog box Figure 86 Figure 86 Diagnostics dialog box Diagnostics Readback NES 310 V ref Set Device Value 15 V tap cover 15 W powe
89. h 27 Off 0 position nl l Service Mode position Vent valve Closed Closed Closed Open 5 sec Fan turbomolecular pump Fans electronics tower APCI corona discharge needle APCI vaporizer Conversion dynode Electron multiplier ESI needle Gas auxiliary Gas sheath Off Gas sweep Ion optics multipoles rf voltages Mass analyzer rf waveform voltages Off Power supply 8 kV Power supply electron multipliers conversion dynodes on API ion transfer tube dc offset API tube lens E Ion optics lens Ion optics multipoles dc offset voltages Mass analyzer dc offset voltage Power supply 300 Vdc API ion transfer tube heater Fan rf coil On Gauge Convectron Gauge ion Power supply PS1 On Forepump Power supply PS2 42 LTO Series Hardware Manual Thermo Scientific 3 System Shutdown Startup and Reset Turning Off Selected Mass Spectrometer Components Table 5 n off status of mass spectrometer components voltages and gas flows Sheet 2 of 2 Stan n Electronics Main Power switch Mass spectrometer component mode mode service switch Off 0 position Service Mode position P Turbomolecular pump Off Turbomolecular pump controller On On On On Gas helium Thermo Scientific LTO Series Hardware Manual 43 UU BN Daily Operation To ensure the proper operation of the LIQ Series system Thermo Fisher Scientific recommends that you perform daily preventive maintenance This chapter specifies th
90. he opening in the top of the vacuum manifold with a large lint free tissue Removing the Q0 and Q1 lon Guides To remove the Q0 and 01 ion guides from the top cover plate CAUTION Be careful not to bend or break the lead pins on the QO quadrupole and QI octapole 1 Disconnect the electrical leads to the QO quadrupole lens L1 split gate lens and Q1 octapole Figure 71 Figure 72 on page 101 Figure 73 on page 102 or Figure 74 on page 103 2 Remove the Q1 ion guide as follows a Hold the Q1 octapole and split gate lens with one hand and with the other hand loosen and remove the two thumbscrews securing the Q1 ion guide mounting bracket to the top cover plate b Remove the Q1 octapole and split gate lens and place them on the clean lint free work surface 3 Remove the QO ion guide as follows a Hold the Q0 quadrupole and lens L1 with one hand and with the other hand loosen and remove the two thumbscrews securing the QO ion guide mounting bracket to the top cover plate b Remove the Q0 quadrupole and lens L1 and place them on the work surface Thermo Scientific LTO Series Hardware Manual 99 5 Maintenance Q0 and Q1 lon Guides Maintenance Figure 71 00 and 01 ion guides for the LXO exploded view Multipole brackets Thumbscrews Split gate Lens L1 Q0 quadrupole Guide post 100 LTO Series Hardware Manual Thermo Scientific 5 Maintenance 0
91. ic 5 Maintenance lon Source Probe Maintenance 4 Reinstall any O rings removed while cleaning 5 Do one of the following e f you do not want to replace the sample tube follow the procedure reassemble the APCI probe on page 77 e f you want to replace the sample tube follow the procedure To remove the APCI sample tube on page 75 Removing the APCI Sample Tube To remove the APCI sample tube 1 Remove the APCI nozzle from the APCI probe see page 72 2 Loosen the APCI flange fitting by using the 3 8 in open end wrench and then pull the sample inlet fitting exit nut ferrule and sample tube assembly from the APCI nozzle Figure 50 3 8 in open end wrench 3 Remove the sample tube nut and ferrule assembly from the APCI flange fitting Figure 51 Thermo Scientific LTO Series Hardware Manual 75 5 Maintenance lon Source Probe Maintenance Figure 51 APCI sample tube connection sample tube 10 32 male nut natural PEEK APCI nozzle 0 239 in ID Viton O ring 0 016 in ID ferrule natural PEEK Mu APCI flange fitting 4 Discard the used sample tube Installing the New APCI Sample Tube For Field Service use only Part number O ring Viton 0 239 in ID 1 16 in thick 00107 04000 To install a new APCI sample tube 1 Remove the APCI sample tube from the APCI nozzle see page 75 2 Check the condition of the O ring on the APCI flange fitting Figure 52 and replac
92. icates a problem perform the maintenance procedure indicated For more information about the diagnostics see the data system Help Thermo Scientific LTO Series Hardware Manual 123 7 Replaceable Parts This chapter provides the part numbers for the chemical and accessory kits that come with the LTQ Series mass spectrometers It also lists the replaceable and consumable parts for each mass spectrometer and their corresponding part numbers Note Accessory kits for the ETD module and MALDI source are listed in their respective Getting Started guides Contents e MS Ship Kit Accessory Kits Chemicals Kit on Source Probes and Parts on Source Interface Parts e 900 Lens Parts e QO and QI Ion Guide Parts e Electron Multipliers e Miscellaneous Parts Thermo Scientific LTO Series Hardware Manual 125 7 Replaceable Parts MS Ship Kit MS Ship Kit MS Ship Kit 70111 62033 Accessory Kits MS Accessory Kit all models 70111 62034 ETD Accessory Kit only for MS ETD systems 98000 62002 LXQ Special Acoso 1 6 0277000070 7 97055 62045 Vacuum Hose Accessory Kit su eur nennen rennen 97055 60135 LTO XL Special Accessory Wt eruat ae a arii are 7 97055 62044 Vacuum Hose Accessory Kits ou paco aurata ane eee pete e tee area teed 97055 62007 LTO Velos Special Accessory Kit Ems bd Capi sees sete ees er i a 97055 62044 Vacuum Hose Accessory K
93. igure 55 3 Push the tube lens from the back out of the contact ring support and then place it on the work surface 80 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Interface Maintenance 4 Wipe or scrub the skimmer with a Kimwipe soaked in a 50 50 methanol water solution 5 Sonicate the skimmer and tube lens in LCMS grade methanol Note If using buffers or salt solutions in the mass spectrometer you might need to use an aqueous solution for cleaning If using an aqueous solution flush the items with LCMS grade water and then with LCMS grade methanol 6 Air dry the components or blow them dry with nitrogen gas 7 Ensure that all the solvent has evaporated from the components before reinstalling them To reinstall the tube lens and skimmer 1 Reinstall the tube lens into the ion source interface cage as follows a Orient the ion source interface cage as shown in Figure 56 and align the tube lens so that the lead pin points toward the correct socket in the contact ring support b Insert the lead pin into the socket and firmly press it until it snaps into place Figure 56 LIQ XL ion source interface cage lon source interface cage Contact ring support skimmer lead pin socket Tube lens lead pin socket CAUTION Do not scratch the outside of the skimmer cone 2 Reinstall the skimmer into the ion source interface cage as follows a Align the skimmer so that the
94. il su iae edem ber kk ERES 97455 62007 Velos Pro DDGCLEILAGOBSSOE a 1877000000 7070007777 97055 62044 Vacuum 97455 62007 15 Chemicals Kit all models 97455 62045 lon Source Probes and Parts 126 ESI Probe Kit soxa em rennen OPTON 20011 Pabchy Sleeve 25 2004 mee eee d dent ed Erba Pen REIR MERE dE 70005 62015 Stainless Steel Needle Kit 32 gauge is ense eem BOB u Ba OPTON 53003 Stainless Steel Needle Kit 54 gauge isis e Rr bI sees OPTON 30004 HESI II Probe Kit uacua dak ar SERA RA A Bara bus OPTON 20037 High flow Needle Insert Assembly 5 2000 uL min 32 gauge metal sample tube OPTON 53010 Low flow Needle Insert Assembly 1 10 uL min 34 gauge metal sample tube OPTON 53011 APCI Probe lS ene s b aban UE IET ba E Me OPTON 20012 APC Probe Nozzle Assembly ux Lees tace mar ae 97055 60089 LTO Series Hardware Manual Thermo Scientific 7 Replaceable Parts lon Source nterface Parts ESI Probe High voltage socket O ring REA Tec ba ma Re se 00107 02550 B aa m E aa adan Md b 00950 00952 Nozzle ESI nozzle O ring Viton 0 676 in ID 00107 05710 Spray needle 26 0 3UB8 5 au ssepe acted Quos han loss dp Neues 00950 00990 APCI Probe Nozzle O ring silicone 0 312 in ID 1 16 in thick 00107 04500 Nozzle O ring
95. in and 1 2 in Phillips screwdriver small Slotted screwdrivers large and small Equipment Chamois tip swabs Gloves lint free and powder free Graduated cylinder or beaker for use with methanol Kimwipes or lint free industrial tissues Magnification device MICRO MESH polishing swab 6000 grit light purple color 2 25 in long Sonicator Chemicals Detergent for example Liquinox Methanol LCMS grade Nitrogen gas clean dry and compressed Part number 00725 00048 00025 10020 00025 03025 70111 20258 00301 01912 00301 01911 Fisher Scientific P N A456 1 Thermo Scientific LTO Series Hardware Manual 55 5 Maintenance lon Source Probe Maintenance Table 7 Tools equipment and chemicals Sheet 2 of 2 Description Part number Water LCMS grade Fisher Scientific P N W6 1 Water tap Provided in the HESI II Probe Kit b Provided in the MS Accessory Kit CAUTION AVOID EXPOSURE TO POTENTIALLY HARMFUL MATERIALS By law producers and suppliers of chemical compounds are required to provide their customers with the most current health and safety information in the form of Material ep Safety Data Sheets MSDSs The MSDSs describe the chemicals and must be freely available to lab personnel to examine at any time MSDSs provide summarized information on the hazard and toxicity of specific chemical compounds MSDSs also provide information on the proper handling of compounds f
96. inject valve to divert the solvent flow between the mass spectrometer and the waste container Figure 5 The divert valve has two positions Detector position Solvent flow from the LC pump enters the valve through port 2 and exits through port 3 to the union tee e Waste position Solvent flow from the LC pump enters the valve through port 2 and exits through port 1 to the waste container Figure 5 Divert valve positions To union tee detector To union tee detector From LC Plug Plug Optional Optional To waste To waste Detector position Waste position Thermo Scientific LTO Series Hardware Manual 11 2 Functional Description Mass Spectrometer Injection Valve Operation In the loop injection configuration Figure 6 use the divert inject valve button to switch between load and inject modes The injector valve has two positions Load position The injected sample enters the valve through port 5 and exits the sample loop through ports 4 and 1 respectively As you overfill the sample loop the sample solution exits the valve through port 6 Solvent flow from the LC pump enters and exits the valve through ports 2 and 3 respectively Inject position After you fill the sample loop press the blue button above the injection valve or use the controls available in Tune Plus Solvent flow from the LC pump backflushes sample out of the sample loop and then out of the valve through port 3 toward the detector Figure 6 I
97. interlace iad alas l Exit lens S lens and ion source interface cage for the Velos Pro 82 Vaculimdial e box se sa Meee lr 84 Inlet Direct Control dialog box for an Accela 1250 Pump 85 on SWEEP CONES area der et 9 de Pons sehen eaae 86 lon transfer tube removal tool bed Bay LR 87 Ion source interface components for the LXQ and LTQ XL 88 Ion source interface components for the Velos Pro 88 Q00 rf lens assembly removal 91 Q00 quadrupole and lens LO wiring connections 92 CODO rf lens assembly een 93 EronedeoElteit en m Summis x deoa e dr es 96 100 0065 deltas oe las ae i 97 Rep cover pushed bac a s d descent Rd 97 Electrical connections to the top cover plate of the vacuum manifold 98 QO and Q1 ion guides for the LXQ exploded view 100 QO and Q1 ion guides for the LTQ XL exploded vievv 101 QO and QI ion guides for the LTQ Velos exploded vievv 102 QO and Q1 ion guides for the Velos Pro exploded view 103 QO and QI ion guides wiring diagram for the LXQ 106 QO and QI ion guides wiring diagram for the LTQ XL 107 QO and Q1 ion guides wiring diagram for the Velos Pro 108 Electron multipliers and dual anode LTQ XL
98. ion 0 312 in ID O ring Ceramic Vaporizer heater N IM heater tube cable socket 1 IM tel a 0 500 in ID Viton O ring S x BD SDR er ra ua pu A ee o ENS H 000 CPC ZA PA I LLL T ii ETT TT l 0 ekx x Xxx o 7 gt plum 77 al orori APCI nozzle sample tube APCI flange fitting To maintain the APCI probe follow these procedures 1 Flushing the Sample Transfer Line and Sample Tube Removing the APCI Nozzle Cleaning the APCI Nozzle A oO N Removing the APCI Sample Tube on page 75 VA Installing the New APCI Sample Tube on page 76 6 Reassembling the APCI Probe on page 77 Flushing the Sample Transfer Line and Sample Tube You can minimize cleaning of the probe components by flushing the sample transfer line sample tube and probe at the end of each work day or more often if you suspect they are contaminated To remove contamination use a 50 50 methanol water solution flushing for approximately 15 minutes from the LC system through the API source For instructions see Flushing the Sample Transfer Line Sample Tube and API Probe on page 49 Removing the APCI Nozzle To remove the APCI nozzle from the APCI probe 1 Place the mass spectrometer in Standby mode see page 55 and let it cool to room temperature See the temperature cautionary statement on pag
99. irst aid for accidental exposure and procedures for the remedy of spills or leaks Read the MSDS for each chemical you use Store and handle all chemicals in accordance with standard safety procedures Always wear protective gloves and safety glasses when you use solvents or corrosives Also contain waste streams use proper ventilation and dispose of all laboratory reagents according to the directions in the MSDS lon Source Probe Maintenance This section contains information for maintaining the ion source probes ESI Probe Maintenance on page 57 e HESI II Probe Maintenance on page 69 e APCI Probe Maintenance on page 72 You need the following tools and supplies from Table 7 on page 55 Tools Supplies Fused silica cutting tool Chamois tip swabs Magnification device Gloves lint free and powder free 7 64 in hex driver Kimvvipes or lint free industrial tissues 5 16 in open end wrench Methanol LCMS grade 3 8 in open end wrench Nitrogen gas 1 2 in open end wrench Water HPLC grade or higher 56 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Probe Maintenance IMPORTANT Prepare a clean work surface by covering the area with lint free paper e Put on a new pair of lint and powder free gloves before starting each of these removal cleaning and reinstallation procedures Note For instructions about removing or reinstalling the API probe or source housing refer to Chapter 2
100. ision gas filled tube A voltage offset between the C Trap and HCD collision cell accelerates parent ions into the collision gas inside the HCD cell which causes the ions to fragment into product ions The product ions are then returned to the orbitrap mass analyzer for mass analysis HCD produces triple quadrupole like product ion mass spectra ion detection system The ion detection system is a high sensitivity off axis system for detecting ions It produces a high signal to noise ratio and allows for switching of the voltage polarity between positive ion and negative ion modes of operation The ion detection system includes a 15 kV conversion dynode and a channel electron multiplier ion isolation A step in an ion trap mass analysis where all ions but the ions of interest are ejected from the mass analyzer ion isolation waveform voltage In a Thermo Scientific ion trap a waveform voltage that is applied during the MS SIM mode and during the parent ion isolation step s of mass analysis for the MS MS Full MS Full MS MS SRM MS CRM and all of the ZoomScan modes for example all modes except MS Full The ion isolation waveform voltage ejects all ions but the SIM ion or parent ion of interest ion optics Focuses and transmits ions from the API source to the mass analyzer ion sweep cone A removable cone shaped metal cover that fits on top of the API ion transfer tube and acts as a physical barrier to protect the entrance
101. it DEEE Ce produit doit tre conforme la directive europ enne 2002 96 EC des D chets d Equipements Electriques et Electroniques DEEE Il est marqu par le symbole suivant Thermo Fisher Scientific s est associ avec une ou plusieurs compagnies de recyclage dans chaque tat membre de l union europ enne et ce produit devrait tre collect ou recycl par celles ci Davantage d informations sur la conformit de Thermo Fisher Scientific ces directives les recycleurs dans votre pays et les informations sur les produits Thermo Fisher Scientific qui peuvent aider la d tection des substances sujettes la directive RoHS sont disponibles sur www thermo com WEEERoHS 990 URS 211142124 JAYSI4 4 Ip nopoud Jad 620 31U29 ezuajsissy Ip 0171 402 ul IsIaaWw ip eDaud IS lpnunuo2 Ip ewid eunpaoo4d eun Jad PZZaINIIS Ip eJnsiul ej olqqnp ul opueng lpnupul QU 911149s9p IUOIZhJ SI 9 9Je3 nsuoo Ip 9 ug1n je aiejeubas s d oru299eJedde ns 9Jjout ojezzi n 9 ojoquiis ojsang auoDajeo n p id En OSaidwod uou 0091194 09H U B olysdauedde ns 9UOIZU9 nUeUI Ip 1 U3A9 UI IS 0 1JIWIYI nyopoud oueiDDaueu Is opuenb iA 910Jd I e14290 aJessopu e1slA ejje luuep a1esneo oJeqqaJ1od eue jau InuasaJd ajjaaiwed ajjap o rorum Opod Ip IZZI9S D B3S A e 13d 0 091194 ngewweijui se p ezuasaJd ul euiajsi
102. kimmer LXO LTO XL Velos Pro The ion source interface in the Velos Pro Figure 13 includes an ion transfer tube two cartridge heaters a heater block a sensor a vent prevent ball an ion sweep cone an S lens and an exit lens The S lens and exit lens mount to the ion source interface cage Figure 13 Velos Pro ion source interface cross section Vent prevent ball lon sweep cone cs 4 S lens Exit lens Mi m transfer tube R Spray cone directly behind the sweep cone Heater block 18 LTO Series Hardware Manual Thermo Scientific Thermo Scientific 2 Functional Description Mass Spectrometer Ions from the ion transfer tube enter the S lens Rf is applied to the S lens to focus the ions toward the opening of the exit lens When you tune the Velos Pro mass spectrometer adjust the S lens rf to maximize sensitivity The Velos Pro uses an S lens and exit lens rather than a tube lens and skimmer The exit lens acts as a vacuum baffle between the higher pressure ion source interface region and the lower pressure QO0 rf lens region of the vacuum manifold The S lens is an ion transmission device consisting of progressively spaced stainless steel electrodes Figure 14 An rf voltage is applied to the electrodes and adjacent electrodes have voltages of opposite phase As the rf amplitude increases ions of progressively higher mass to charge ratios pass through to the exit lens and move toward the QO0 rf
103. le is referred to as the ionization technique The ion optics transmit the ions produced in the API source 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 API source and ion optics determines whether positively charged ions or negatively charged ions are transmitted to the mass analyzer You can set up data acquisition methods for the mass spectrometer to analyze positively or negatively charged ions or to switch between these polarity modes during a single run The lenses in the API source and ion optics act as a gate to start and stop the transmission of ions from the API source to the mass analyzer An Automatic Gain Control AGC process controls the function of these lenses and sets them to transmit the optimum number of ions to the mass analyzer The mass analyzer measures the mass to charge ratios of the ions produced in the API source Selected ions are ejected from the mass analyzer and reach the ion detection system where they produce a signal The detection system electronics then amplify this signal for display and analysis by the data system The data system serves as the user interface to the mass spectrometer autosampler LC and syringe pump Refer to the data system Help for more information about the LTQ Series data processing and instrument control software Each sequence of loading the mass analyzer with ions followed by mass analysis
104. leeve Because you must thread the tubing through these small orifices you might find a magnifying device useful Thermo Scientific LTO Series Hardware Manual 63 5 Maintenance lon Source Probe Maintenance To install the new sample tube and PEEK safety sleeve 1 Cut approximately 38 cm 15 in of fused silica tubing by using the fused silica cutting tool and then under magnification check that the end is cut squarely The piece of sample tubing must be long enough to extend through the ESI probe and the natural PEEK safety sleeve 2 Remove the sample inlet adapter from the ESI probe sample inlet 3 Insert the sample tube through the ESI needle that protrudes from the front of the ESI nozzle and then push it through the ESI probe until approximately 3 5 cm 1 5 in protrudes past the front of the probe The remaining length of the sample tube protrudes from the ESI probe sample inlet at the back of the probe Figure 33 Figure 33 Fused silica sample tube inserted through the front of the ESI probe NUR r EN 7 X il u 9 N yt Ss a s z N p e 4 ud 1 J 1 1 1 N N N x N 7 needie b z z ng 5 Fused silica sample tube 4 Slide the safety sleeve over the end of the sample tube that protrudes at the back of the probe sample inlet and then push the safety s
105. leeve into the probe until it meets resistance Figure 34 CAUTION The PEEK safety sleeve acts as a second level of protection against accidental electrical discharge 64 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Probe Maintenance Figure 34 Natural PEEK safety sleeve installed in the sample inlet ESI probe 3 5 cm 7 cm 25 6m 1 5 in 2 7 in 10 in u gt N gt 1 1 l Fused silica Needle seal Natural PEEK sample tube safety sleeve 5 With the external threads facing the ESI probe sample inlet slide the natural PEEK fitting adapter over the safety sleeve and then finger tighten the fitting into the ESI probe sample inlet Figure 35 Figure 35 Natural PEEK adaptor fitting installed to secure the safety sleeve ESI probe Natural PEEK adaptor fitting 6 Slide the other fingertight fittings onto the PEEK sleeve Figure 36 as follows a Slide the natural PEEK ferrule with the tapered end facing the sample inlet onto the safety sleeve b Slide the red one wing fingertight fitting with the threaded end facing the sample inlet onto the safety sleeve c Slide the natural PEEK two wing fingertight fitting with the threaded end facing away from the sample inlet onto the safety sleeve Thermo Scientific LTO Series Hardware Manual 65 5 Maintenance lon Source Probe Maintenance d Slide the natural PEEK ferrule with the taper
106. lica 100 um ID 193 um OD 0 003 in ID 0 008 in OD 00106 10499 Tubing red PEEK 127 um ID 1 16 in OD 0 005 in ID 1 6 mm OD 00301 22912 Vacuum Manifold Parts O ring Viton 3 25 in ID 1 8 in thick between outer cage and vacuum manifold 00107 13000 Split chamber O ring 12 33 x 6 65 x 3 21 in x wx 5 97055 40005 130 LTO Series Hardware Manual Thermo Scientific D Glossary AB CD EF GH JK L MNOP QRS TU VW XY Z A API ion transfer tube A tube assembly that assists in desolvating ions that are produced by the ESI NSI or APCI probe API ion transfer tube offset voltage A dc voltage applied to the ion transfer tube The voltage is positive for positive ions and negative for negative ions API source The sample interface between the LC and the mass spectrometer It consists of the API probe ESI or APCI and API stack API stack Consists of the components of the API source that are held under vacuum and includes the API spray shield API ion transfer tube API tube lens skimmer the ion transfer tube mount and the tube lens and skimmer mount API tube lens A lens in the API source that separates ions from neutral particles as they leave the ion transfer tube A potential applied to the tube lens focuses the ions toward the opening of the skimmer and helps to dissociate adduct ions API tube lens offset voltage A DC voltage ap
107. lotted screwdriver 92 LTO Series Hardware Manual Thermo Scientific 5 Maintenance 000 RF Lens Maintenance Figure 66 000 rf lens assembly 2 731 in ID O ring Ball plungers 6x Q00 rf lens outer cage Contact ring Lens LO Ball plungers 3X Q00 rf lens Threaded guide post 2x Cleaning the Q00 RF Lens Assembly Components To clean the 000 rf lens and lens LO 1 Inspect the components under magnification for any lint particulates and sample buildup or coatings 2 Sonicate the components for 10 15 min in a 50 50 methanol water solution or a 196 solution of Liquinox in water Clean the bore in each lens by using the 6000 grit MICRO MESH polishing swabs N Rinse the components thoroughly with water Rinse the components with methanol 6 Dry the components with a rapid stream of nitrogen gas 7 Inspect the components under magnification for any lint or particulates Note Inspect the orifices to confirm that no lint or particulates are present in the bore of the orifices Use tweezers or a similar tool to remove the lint or particulate Thermo Scientific LTO Series Hardware Manual 93 5 Maintenance 000 RF Lens Maintenance Reassembling the 000 RF Lens Assembly To reassemble the 000 rf lens assembly IMPORTANT When reassembling the Q00 rf lens assembly remember to tighten any ball plungers that you loosened 1 Insert the QOO rf lens through the front of the outer cag
108. lowable operating range Green The vacuum is within the allowable operating range Communication Yellow The mass spectrometer and data system are trying to establish a communication link Green The mass spectrometer and data system are communicating System Yellow The mass spectrometer is in standby mode Green The mass spectrometer is on Off The mass spectrometer is off Scanning Flashing blue The mass spectrometer is on and scanning Off The mass spectrometer is not scanning LTO Series Hardware Manual 13 2 Functional Description Mass Spectrometer Power Panel The power panel is located on the right side of the mass spectrometer Figure 8 and Figure 9 show the power panels for the LXQ LTQ XL and Velos Pro mass spectrometers Figure 8 Power panel for the LXO Reset button Peripheral Control Stat Ready Start n Out peoni ri Ethernet 100 Base T El Reset Power In Main Power m On Mech Pumps Electronics Normal m m Analog Input L A Servic Mode Electronics Main Power switch service switch Figure 9 Power panel for the LTO XL and Velos Pro Reset button Ethernet ununu A Main Power 0 El O Reset i EE L Electronics Normal TV MAX V MAX Analog Input A Servii Mode Peripheral Control 7 oar 23 Mech Pumps Accessory Power In 230 VAC 154 Electronics Main Power switch service switch The mass spectrometer r
109. mo Scientific LTO Series Hardware Manual 51 A Daily Operation After Operating the LTO Series System Emptying the Solvent Waste Container Check the solvent level in the solvent waste container daily If necessary empty the container and dispose of the solvent waste in accordance with local and national regulations Placing the System in Standby Mode After you complete the daily maintenance procedures place the mass spectrometer in standby mode as described in Placing the Mass Spectrometer in Standby Mode on page 35 52 LTO Series Hardware Manual Thermo Scientific MEN ia Maintenance The performance of the LTO Series mass spectrometer depends on the maintenance of all P P P parts of the instrument You are responsible for maintaining the system properly by performing the system maintenance procedures on a regular basis Note Unless otherwise noted For the LTQ mass spectrometer follow the LTQ XL information For the LTQ Velos mass spectrometer follow the Velos Pro information Contents Tools and Supplies Source Probe Maintenance on Source Interface Maintenance e 000 RF Lens Maintenance QO and QI Ion Guides Maintenance Electron Multiplier Replacement Forepump Maintenance Fan Filter Maintenance For optimal results use the following guidelines when performing the procedures in this chapter Proceed methodically e Always wear a new pair of lint and powder free glo
110. n analysis scan Comprised of one or more microscans Each microscan is one mass analysis ion injection and storage scan out of ions followed by ion detection After the microscans are summed the scan data is sent to the data system for display and or storage The process of ramping the amplitude of the rf and dc voltages on the quadrupole rods in the mass analyzer to transmit ions from the lowest mass to the highest mass of a specified scan range signal to noise ratio S N The ratio of the signal height S to the noise height N The signal height is the baseline corrected peak height The noise height is the peak to peak height of the baseline noise skimmer A vacuum baffle between the higher pressure tube skimmer region and the lower pressure region The aperture of the skimmer is offset with respect to the bore of the ion transfer tube syringe pump A device that delivers a solution from a syringe at a specified rate T turbomolecular pump A vacuum pump that provides a high vacuum for the mass spectrometer and detector system V vacuum manifold A thick walled aluminum chamber with machined flanges on the front and sides and various electrical feedthroughs and gas inlets that encloses the API stack ion optics mass analyzer and ion detection system LTO Series Hardware Manual 133 MEN _ I Index A air leaks checking 47 fixing 47 APCI probe cleaning 73 cleaning flushing 73 maintaining 72 nozzle
111. n the vacuum manifold with the following values TS Convectron gauge reading Condition gaug i g foreline tube skimmer analyzer region region Open ion transfer tube orifice 0 75 x 107 to 1 0 1 5 Torr ion transfer tube at 250 C 1 5x 1072 Torr 482 F Note f the current values are higher than normal there might be an air leak or the helium flow might be insufficient f the pressure is above 5 x 1072 Torr in the analyzer region and the system restarted within the last 30 to 60 minutes wait another 30 minutes and recheck the pressure If the pressure decreases with time check the pressure periodically until it is within the typical range for the mass spectrometer e If the pressure remains high the system might have an air leak To check the system for major air leaks Listen for a rush of air or a hissing sound inside the mass spectrometer Example causes of a major leak might be a loose or disconnected fitting an improperly positioned O ring or an open valve To fix an air leak Shut down the system see Shutting Down the Mass Spectrometer Completely on page 36 Make a visual inspection of the vacuum system and vacuum lines for leaks Check each fitting and flange on the system for tightness and tighten the fittings or flanges that are loose Do not tighten fittings indiscriminately Pay particular attention to fittings that have been changed recently or to fittings that have
112. nce or service You do not need to shut down the system completely if you are not going to use it for a short period of time such as overnight or through the weekend Instead put the system into standby mode as described in Placing the Mass Spectrometer in Standby Mode on page 35 CAUTION HOT SURFACE Allow heated components to cool to room temperature about 20 minutes before servicing them l To shut down the mass spectrometer completely Turn off the flow of sample solution from the LC or other sample introduction device Note For instructions about operating the LC from the front panel refer to the LC manual Follow the procedure Placing the Mass Spectrometer in Standby Mode on page 35 Place the electronics service switch in the Service Mode down position This turns off the power to the nonvacuum system electronics Turn off the Main Power switch The following occurs All power to the mass spectrometer including the turbomolecular pump and forepump or pumps turn off All LEDs on the front panel are off e After approximately 5 seconds power to the vent valve solenoid shuts off the vent valve opens and the vacuum manifold vents to filtered air You can hear a hissing sound as the air passes through the air filter e After about 2 minutes the vacuum manifold is at atmospheric pressure Thermo Scientific 3 System Shutdown Startup and Reset otarting the S
113. ncy 4 23 2003 Positive lon Mode L Transfer Lenses 4 24 2008 Electron Multiplier Gain 4 23 2003 Negative lon Mode L Transfer Lenses 4 24 2009 Electron Multiplier Gain 4 24 2009 Mass Calibration r he lO Ties i72 Fann lili SUMMARY of CALIBRATION Positive lon Transfer Optics Calibration SUCCESSFUL Bil requested calibratian s SUCCESSFULLY completed Saving All Calibrations Calibration is FIMISHED Cancel Print Help Thermo Scientific LTO Series Hardware Manual 117 5 Maintenance Forepump Maintenance 5 Do one of the following a For the LXQ and LTQ XL select both the Positive Ions Electron Multiplier Gain and Negative Ions Electron Multiplier Gain check boxes b For the Velos Pro under both Positive Ion Mode and Negative Ion Mode select Electron Multiplier Gain 6 Click Start 7 After the electron multiplier gain calibrations are complete set up the mass spectrometer for operation as described in the LTQ Series Getting Started Guide Forepump Maintenance Inspecting adding purging and changing the pump oil are all that is required to maintain the forepump or forepumps depending on the mass spectrometer model Check the forepump oil often It is a translucent light amber color During normal operation oil must always be visible in the oil level sight glass between the MIN and MAX marks If the oil level is below the MIN mark add oil If the
114. nd Figure 39 Figure 38 Safety sleeve connection to the grounding union ESI probe Natural PEEK ferrule Grounding union LL Two wing natural PEEK fingertight fitting e Ensure that the sample tube is held tightly in the grounded union by gently pulling it from the exit end of the ESI needle Figure 39 Figure 39 Sample tube securely tightened to the grounding union ESI probe ath gt NY sample tube to verify that it is secured to the grounding union 8 Adjust the position of the sample tube as follows a Cut the sample tube approximately 2 5 cm 1 in past the tip of the ESI needle by using the fused silica cutting tool b From the ESI sample inlet loosen the red PEEK fitting and then pull the safety sleeve backwards so that the sample tube is positioned appropriately within the ESI needle Figure 40 The optimal position of the sample tube depends on the solvent flow rate as follows For flow rates less than or equal to 100 uL min set the sample tube protrusion to mm past the ESI needle tip e For flow rates greater than 100 pL min ensure that the sample tube is flush with the ESI needle tip or recessed inside the ESI needle by less than 1 mm Figure 41 Thermo Scientific LTO Series Hardware Manual 67 5 Maintenance lon Source Probe Maintenance Figure 40 Adjusting the sample tube position ESI probe 2 5 cm 1 in 25 cm 25cm 10 in
115. nd supporting ferrule For part numbers see lon Source Probes and Parts on page 126 LTO Series Hardware Manual 69 5 Maintenance lon Source Probe Maintenance Figure 42 Components of the metal ESI needle insert Metal sample tube ESI needle Needle guide fitting mn ferrule Figure 43 Tip enlarged of the metal ESI needle insert ESI needle Y i 1 1 1 1 1 1 1 1 1 05 mm wi Metal sample tube For Field Service use only Part number HESI II probe 32 gauge and 34 gauge needle inserts See page 126 To replace the metal needle insert 1 Place the mass spectrometer in Standby mode see page 55 and let it cool to room temperature 2 Remove the HESI II probe from the API source housing 3 Unscrew the fingertight fitting from the sample inlet port 4 Remove the metal needle insert from the probe as follows Figure 44 a Remove the two M x 35 mm long hex socket head screws by using the 3 mm hex driver b Pull the end cover off of the probe 10 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Probe Maintenance c Unscrew the metal needle insert and then pull it out of the probe body Figure 44 HESI ll probe disassembled exploded view Metal ESI needle insert End cover Probe body Adjustable union socket head cap screws 5 Insert a new metal needle insert into the probe body 6 Hand tighten the adjust
116. nel above the syringe pump Figure 3 turns the syringe pump on and off The motor has two speeds normal and fast The normal speed produces the flow rate specified in the data system Pressing and releasing the button turns on the syringe pump and sets the motor speed to the normal speed Pressing and holding the button in causes the motor to move the pusher block at the fast speed the motor maintains the fast speed until you release the button or the pusher block reaches the end of its path When you release the button the pusher block slows to normal speed Pushing the button a second time turns off the syringe pump LTO Series Hardware Manual 9 2 Functional Description Divert Inject Valve Figure 3 SV av hs oyringe pump on off button Pump On Syringe Pump LED A light emitting diode LED to the right of the on off button indicates whether the pump is on or off Table 3 lists the states of the syringe pump LED Table 3 Syringe pump LED states State Meaning Not illuminated The syringe pump is off Steady green The syringe pump is on The pusher block is moving at a normal speed that produces the flow rate specified in the data system The allowable flow rate setting depends on the syringe size Flashing green The syringe pump is on and the pusher block is moving at the fast speed Divert Inject Valve The divert inject valve is located on the front of the LTQ Series mass spectrometer to the left of the API source
117. netic Transmissions Your instrument is designed to work in a controlled electromagnetic environment Do not use radio frequency transmitters such as mobile phones in close proximity to the instrument For manufacturing location see the label on the instrument WEEE Compliance This product is required to comply with the European Union s Waste Electrical amp Electronic Equipment WEEE Directive 2002 96 EC It is marked with the following symbol Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union EU Member State and these companies should dispose of or recycle this product See www thermo com WEEEROHS for further information on Thermo Fisher Scientifics compliance with these Directives and the recyclers in your country WEEE Konformitat Dieses Produkt muss die EU Waste Electrical amp Electronic Equipment WEEE Richtlinie 2002 96 EC erf llen Das Produkt ist durch folgendes Symbol gekennzeichnet Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs Entsorgungsfirmen in allen EU Mitgliedsstaaten getroffen damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann Mehr Information ber die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific ber die Verwerter und weitere Hinweise die n tzlich sind um die Produkte zu identifizieren die unter diese RoHS Anweisung fallen finden sie unter www thermo com WEEERoHS Conform
118. ng additional LTE features salation Reagent lon Sou lon Trap HC D Full FA MS Analog Inputs Ethernet License Instrument WW arnir license 5 Reboot the data system and then the Velos Pro mass spectrometer XXIV LTO Series Hardware Manual Thermo Scientific Preface Safety and Special Notices Ensure that you follow the precautionary statements presented in this guide The safety and other special notices appear in boxes Safety and special notices include the following CAUTION Highlights hazards to humans property or the environment Each CAUTION notice is accompanied by an appropriate CAUTION symbol IMPORTANT Highlights information necessary to prevent damage to software loss of data or invalid test results or might contain information that is critical for optimal performance of the system Note Highlights information of general interest Tip Highlights helpful information that can make a task easier Table 1 lists additional caution specific symbols that appear in the LTQ Series Hardware Manual Table 1 Caution specific symbols and their meanings Symbol Meaning Electric Shock An electric shock hazard is present in the instrument Proceed with caution Hot Surface Allow heated components to cool before touching or servicing the instrument Chemical Hazardous chemicals might be present in the instrument Wear gloves when handling carcinogenic corrosive irrit
119. ng for the Convectron Gauge Pressure If the reading is considerably below 1 Torr clean the ion transfer tube 84 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Interface Maintenance To remove the ion transfer tube 1 Turn off the flovv of liquid from the LC or other sample introduction device to the API source as follovvs a Open the Tune Plus window see page 24 b Choose Setup gt Inlet Direct Control to open the Inlet Direct Control dialog box Figure 59 Figure 59 Inlet Direct Control dialog box for an Accela 1250 Pump Inlet Direct Control Accela 1250 Pump Accela AS Pump 1 Flow Time A Inlet A Inlet B Inlet C Inlet D Pressure NA imi c Click the Pump Off or Stop Pump button 2 Place the mass spectrometers electronics service switch in the Service Mode down position to turn off the nonvacuum system voltages CAUTION Ensure that the electronics service switch is in the Service Mode down position before proceeding CAUTION HOT SURFACE The ion transfer tube operates above 250 C 482 F Allow the ion sweep cone and ion transfer tube to cool to room temperature approximately 20 minutes before touching them 3 After cooling to room temperature remove the API ion source housing from the front of the mass spectrometer Thermo Scientific LTO Series Hardware Manual 85 5 Maintenance lon Source Interface Maintenance 4 Grasp the o
120. nject valve positions From LC From LC ee To API source To API source To waste To waste Load position Inject position Mass Spectrometer The LTQ Series mass spectrometer provides sample ionization and mass analysis of injected samples or samples eluted from a liquid chromatograph The mass spectrometer uses a linear ion trap mass analyzer with an ion source external to the mass analyzer The LTQ Series mass spectrometer includes the following components e LEDs on page 13 Povver Panel on page 14 e API Source on page 15 Ion Optics on page 20 Mass Analyzer on page 23 12 LTO Series Hardware Manual Thermo Scientific LEDs Thermo Scientific 2 Functional Description Mass Spectrometer Ion Detection Systems on page 26 e Vacuum System on page 28 Inlet Gases Hardware on page 31 Cooling Fans on page 32 Figure 7 shows the LEDs on the front panel of the LIQ Series mass spectrometer with their descriptions listed in Table 4 Figure 7 LTO Series front panel LEDs Power Vacuum Communication System Scanning Table 4 LIQ Series front panel LEDs LED State Meaning Power Green Power is being supplied to the mass spectrometer The electronics service switch is in the Electronics Normal position Off Power is not being supplied to the mass spectrometer The electronics service switch is in the Service Mode position Vacuum Yellow The vacuum is outside the al
121. nnector install the new electron multiplier assembly on the top cover plate Ensure that the high voltage connector is properly inserted into the high voltage feedthrough and that the electron multipliers screw holes align with the holes in the top cover plate Reinstall the two hex socket head screws that secure the electron multiplier support to the top cover plate by using the 5 64 in hex driver Repeat step 2 and step 4 with the second electron multiplier Reinstall the top cover plate over the vacuum manifold s opening see page 110 Thermo Scientific 5 Maintenance Electron Multiplier Replacement 7 Reinstall the top cover of the mass spectrometer see page 110 8 Start up the system as described in Starting the System after a Complete Shutdown on page 37 After replacing the electron multipliers reset and save the initial voltage settings to the appropriate values for new multipliers and then calibrate the electron multipliers voltages Tosetthe electron multiplier voltages 1 Open the Tune Plus window see page 34 2 Choose Diagnostics Diagnostics to open the Diagnostics dialog box Figure 80 3 In the Tools list select Set Device Figure 80 Diagnostics dialog box showing the Set Device list Diagnostics Plot readback 1 ion current LA r Detector settings API 1 needle voltage kV PE tune API 2 ton current ps Loop AFI 2 needle voltage D librat evice calib
122. o cool to room temperature approximately 20 minutes before touching it e f the mass spectrometer connects to an LC system leave the solvent flow from the LC pump on while the probe cools to room temperature To maintain the HESI II probe follow these procedures Flushing the Sample Transfer Line and Sample Tube Replacing the Needle Insert Flushing the Sample Transfer Line and Sample Tube You can minimize cleaning of the probe components by flushing the sample transfer line sample tube and probe at the end of each work day or more often if you suspect they are contaminated To remove contamination use a 50 50 methanol water solution flushing for approximately 15 minutes from the LC system through the API source For instructions see Flushing the Sample Transfer Line Sample Tube and API Probe on page 49 Replacing the Needle Insert Thermo Scientific If the metal sample tube is plugged you can replace the needle insert The needle insert is assembled at the factory and consists of an adjustable union needle guide fitting ferrule O ring ESI needle and metal sample tube Figure 42 The ferrule is swaged onto the ESI needle Factory adjusted the metal sample tube protrudes 0 5 mm from the end of the ESI needle Figure 43 To support flow rates of 5 2000 pL min Thermo Fisher Scientific provides two metal needle inserts for the HESI II probe The difference between the two inserts is the size of the metal needle a
123. o use in the product operation This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc The contents of this document are subject to change without notice All technical information in this document is for reference purposes only System configurations and specifications in this document supersede all previous information received by the purchaser Thermo Fisher Scientific Inc makes no representations that this document is complete accurate or error free and assumes no responsibility and will not be liable for any errors omissions damage or loss that might result from any use of this document even if the information in the document is followed properly This document is not part of any sales contract between Thermo Fisher Scientific Inc and a purchaser This document shall in no way govern or modify any Terms and Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents Release history Revision A April 2009 Revision B May 2011 Software version Thermo LTQ Tune Plus version 2 7 0 or later Microsoft Windows 7 Professional SP1 Thermo Foundation version 2 0 or later and Thermo Xcalibur version 2 2 or later Windows XP Workstation SP3 Foundation version 1 0 2 SP2 or earlier and Xcalibur version 2 1 SP1 or earlier For Research Use Onl
124. oard E EE 70005 20606 5706772763 0 000 her 70005 60182 LTO Series Hardware Manual 127 7 Replaceable Parts Q00 Lens Parts Q00 Lens Parts All Models O ring 2 005 Viton 0 101 in ID 0 070 in zz 00107 02456 O ring 2 148 Viton 884 2 737 in ID 0 103 in zz 00107 15542 LXO Outer cage assembly ya mass EE n dique saa Pese pee RE 97055 60180 LTO XL Outer case assembly a e soa oyanan Rss TIN ayy sonlu 97055 60036 LTO Velos and Velos Pro Outer case assembly uos tone wet 97055 60036 00 and 01 lon Guide Parts LXO EL Vasa o m so bo ml on 97055 20022 DEJC e guage Spar et 97055 20054 Sua 7 eR ee ee 97055 60035 SIUE 97055 60034 SPIEL SU et ERPD ERES qudd n RES 97055 20482 Thumbserews 10 22 4 21a O56 5 ea su S d Ee Boa Ed eS ace 97000 20235 LTO XL 97055 20022 Mul pole bracket 97055 20054 per ae pre dus 97055 60035 DE ee te E 97055 60034 ETATE re peated sete EM EE 97055 20023 Thumbscrews 10 32 97000 20235 LTO Velos lenS aed eee he bee wee 97055 20022 Multipole bracket ONG 7708000000 97055 20570 CEdundulclu s a s oya suda suni 70005 60200 777 97055 60207 Quadrupole bracket 1s acia eie tries
125. oil is cloudy or discolored purge the oil to decontaminate dissolved solvents If the pump oil is still discolored change it Plan to change the pump oil every 3000 hours or about every four months of operation Refer to the manufacturer s documentation for procedures to purge add and change the forepump oil CAUTION To minimize the risk of oil contamination in the vacuum system ensure that the purging ballast is closed when venting the system to atmosphere For Field Service use only Part number Forepump oil 1 L 00301 15101 See the MSDS cautionary statement on page page 56 118 LTO Series Hardware Manual Thermo Scientific 5 Maintenance Fan Filter Maintenance Fan Filter Maintenance Clean the fan filter every four months or sooner if it is dirty The fan filter is located on the back of the mass spectrometer on the left side when facing the back To clean the fan filters 1 Remove the fan filter by pulling it up and out of the fan filter bracket 2 Wash the filter in a solution of soap and water 3 Rinse the filter with tap water 4 Squeeze the water from the filter and allow it to air dry 5 Reinstall the fan filter in the fan filter bracket Thermo Scientific LTO Series Hardware Manual 119 Diagnostics The diagnostics test the major electronic circuits within the mass spectrometer and indicate whether the circuits pass or fail the tests If there is a problem with the instrument electronics the dia
126. on Sweep Cone Spray Cone and lon Transfer Tube Clean the ion sweep cone spray cone and the ion transfer tube on a regular basis to prevent corrosion and to maintain optimum performance of the API source A good practice is to wash or flush the ion sweep cone and ion transfer tube at the end of each operating day after you pump a solution of 50 50 methanol water from the LC system through the sample transfer line sample tube and API probe see Flushing the Sample Transfer Line Sample Tube and API Probe on page 49 If you use a mobile phase that contains a nonvolatile buffer or inject high concentrations of sample you might need to clean these parts more often It is not necessary to vent the system to flush the ion sweep cone and ion transfer tube CAUTION When the ion transfer tube is installed do not flush it with cleaning solution which flushes the residue into the mass spectrometer For detailed instructions refer to Chapter 8 in the LTQ Series Getting Started Guide Purging the Oil in the Forepump Purge decontaminate the oil in the forepump daily to remove water and other dissolved chemicals which can cause corrosion and decrease the lifetime of the forepump The best time to purge the oil is at the end of the working day after you flush the API probe ion sweep cone and ion transfer tube For instructions refer to the forepumps documentation Remember to close the purge valve before continuing normal operation Ther
127. ormal position all components of the mass spectrometer have power en you brie ress the reset button the embedded processing system and digital circuitr When you briefly press th t button the embedded p g syst d digital try reset and the system software reloads from the data system For information about resetting the mass spectrometer see Resetting the Mass Spectrometer on page 39 The API source forms gas phase sample ions from sample molecules that are contained in solution Ihe API source also serves as the interface between the LC and the mass spectrometer You can operate the API source in the ESI H ESI NSI APPI or APCI mode For more information about the API source refer to Chapter 2 Setting Up the API Source in the LTQ Series Getting Started Guide lon Source Interface Thermo Scientific The ion source interface for the LIQ Series mass spectrometer consists of the components of the API source that are held under vacuum except for the atmospheric pressure side of the ion sweep cone in a vacuum chamber that the one or two forepumps evacuate The ion sweep cone is a metal cone over the API ion transfer tube The ion sweep cone acts as a physical barrier that protects the entrance of the ion transfer tube and increases source robustness The ion transfer tube is a metal cylindrical tube that assists in desolvating ions produced by the API probe while transferring them into the vacuum system LTO Series Har
128. ove the ion source probe or API source housing after it has cooled to room temperature CAUTION If you are using APPI do not leave the LC or other liquid delivery device on while the mass spectrometer is in standby mode The absence of sheath and auxiliary gas can cause the hot VUV vacuum lamp to break upon contact with liquids The mass spectrometer turns off the electron multipliers conversion dynodes 8 kV power to the API source main rf voltage and ion optic rf voltages The mass spectrometer also turns off the auxiliary and sheath gas flows See Table 5 on page 42 for the On Off status of the mass spectrometer components when the mass spectrometer is in standby mode The System LED on the front panel Figure 7 on page 13 turns yellow when the system is in standby mode Thermo Scientific LTO Series Hardware Manual 35 3 System Shutdown Startup and Reset Turning On the Mass Spectrometer Turning On the Mass Spectrometer A ul n Standby l 2 To turn on the mass spectrometer Open the Tune Plus vvindovv see page 34 Click the On Standby button to select the On mode The System LED on the front panel turns green The high voltage to the electron multipliers turns on Shutting Down the Mass Spectrometer Completely 36 LTO Series Hardware Manual Shut down the LIC Series mass spectrometer completely only if it is not in use for an extended period of time or if it must be shut down for maintena
129. passes A potential is applied to lens LO to aid in ion transmission Lens LO also acts as a vacuum baffle between the Q00 and QO ion optics chambers The QO ion optics transmit ions from the Q00 ion optics to the mass analyzer The QO ion optics include the QO quadrupole and the lens L1 The QO quadrupole is a quadrupole array of square profile rods that acts as an ion transmission device Figure 16 and Figure 17 An rf voltage applied to the rods creates an electric field that guides the ions along the axis of the quadrupole The QO offset voltage increases the translational kinetic energy of ions emerging from C00 20 LTO Series Hardware Manual Thermo Scientific Thermo Scientific 2 Functional Description Mass Spectrometer The QO quadrupole for the Velos Pro is curved along the central axis Figure 18 This feature removes the line of sight of neutrals from entering the mass analyzer chamber Figure 16 00 quadrupole for the LXO and LTO XL LTO Series Hardware Manual 21 2 Functional Description Mass Spectrometer The lens L1 is a metal plate with a circular hole in the center through which the ion beam passes An electrical potential applied to the lens accelerates or decelerates ions as they approach the lens This electrical potential focuses the ion beam as it passes through the lens Lens L1 also acts as a vacuum baffle between the QO ion optics chamber and the mass analyzer chamber 01 lon Optics The Q1 ion op
130. pectrometer that includes a syringe pump a divert inject valve and an Ion Max S ion source LTO Series Hardware Manual 3 1 Introduction Overview of an LC MS Analysis Overview of an LC MS Analysis In a typical LC MS analysis the liquid chromatograph LC portion of the system separates a mixture into its chemical components The LC pump produces a solvent stream the mobile phase that passes through an LC column containing the stationary phase under high pressure An autosampler introduces a measured quantity of sample into this solvent stream As the solvent stream passes through the LC column the sample separates into its chemical components The rate at which the components of the sample elute from the column depends on their relative affinities to the mobile phase and the solid particles that make up the column packing As the separated chemical components exit the LC column they pass through a transfer line and enter the L TC Series mass spectrometer where they are ionized and analyzed As the mass spectrometer analyzes the ionized components and determines their mass to charge m z ratios it sends a data stream to the data system computer In addition to supplying information about the mass to charge ratios of ionized compounds the mass spectrometer can also supply structural and quantitative information by performing MS experiments Because the mass spectrometer has a built in syringe pump and divert inject valve it pro
131. plied to the tube lens The value is normally tuned for a specific compound API tube skimmer region The area between the tube and the skimmer which is surrounded by the tube lens It is also the area of first stage evacuation in the API source Thermo Scientific atmospheric pressure chemical ionization APCI A soft ionization technique done in an ion source operating at atmospheric pressure Electrons from a corona discharge initiate the process by ionizing the mobile phase vapor molecules A reagent gas forms which efficiently produces positive and negative ions of the analyte through a complex series of chemical reactions atmospheric pressure ionization API Ionization performed at atmospheric pressure by using atmospheric pressure chemical ionization APCT electrospray ionization ESI or nanospray ionization INSI atmospheric pressure photoionization APPI A soft ionization technique that shows an ion generated from a molecule when it interacts with a photon from a light source Automatic Gain Control AGC Sets the ion injection time to maintain the optimum quantity of ions for each scan With AGC on the scan function consists of a prescan and an analytical scan autosampler The device used to inject samples automatically into the inlet of a chromatograph LTO Series Hardware Manual 131 Glossary C collision induced dissociation CID A method of fragmentation where molecular ions are accelerated
132. pole DO Offset V s lens fl V For Help press F1 NUM 6 9 2008 10 34 AM Z 34 LTO Series Hardware Manual Thermo Scientific 3 System Shutdown Startup and Reset Placing the Mass Spectrometer in Standby Mode Placing the Mass Spectrometer in Standby Mode You do not need to shut down the LTQ Series mass spectrometer completely if you are not P P yuy going to use it for 12 hours or more Instead place the mass spectrometer in standby mode To place the mass spectrometer in Standby mode 1 Complete all data acquisition if any 2 Open the Tune Plus window see page 34 3 If an LC pump is provided turn off the solvent flow to the API source When controlling the LC pump through the Xcalibur data system you can turn off the solvent flow from the Inlet Direct Control dialog box For example to turn off the solvent flow from a Surveyor MS Pump Plus or an Accela Pump do the following a ChooseSetup Inlet Direct Control and then click the tab for the LC pump m b Select the Take Pump Under Control check box and then click the Stop button 4 In the Tune Plus window do one of the following f the mass spectrometer is off choose Control gt Standby Al m f the mass spectrometer is on click the On Standby button to select the Standby On Standby mode When clicked this button cycles through the power modes shown in the left margin The LC MS system is now in standby mode and you can safely rem
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134. procedure after cleaning or replacing ESI probe components To assemble the ESI probe 1 Insert the resistor and battery contact subassembly into the ESI manifold Figure 32 Front end of the ESI probe exploded view Needle seal ESI nozzle with ESI manifold 0 676 in O ring rd Resistor Battery contact 26 gauge needle 2 Insert the entrance end of the ESI needle into the needle seal 3 Position the ESI needle and needle seal in the ESI manifold 4 Ensure that the 0 676 in ID O ring is in the precut groove on the ESI nozzle Figure 31 on page 61 5 Thread the ESI nozzle over the needle and into the ESI manifold Slightly wet the nozzle threads with LCMS grade methanol for lubrication 6 Tighten the ESI nozzle until it is a little more than fingertight by using the 5 16 in open end vvrench do not overtighten the nozzle 7 Insert the high voltage socket into the back of the ESI manifold and use the 1 2 in open end wrench to tighten the socket 8 Reconnect the sheath liquid inlet fitting 9 Install a new sample tube see page 64 62 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Probe Maintenance Installing a Fused Silica Sample Tube and PEEK Safety Sleeve When you use a fused silica sample tube with the ESI or HESI II probe cover the exposed portion of the sample tube with a PEEK safety sleeve CAUTION AVOID ELECT
135. r supply V Pi 1 ian current pA l 150 power supply V Display settings 1 00 000 Set 180 jon gauge Toggles 24 V power supply v Triggers 24 V turba Mass calibration 28 V supply current A System evaluation 20 W supply voltage v 300 power supply V 36 V top cover Y R UV power supply V Testing 3 Click Tests to display the list of tests Figure 87 Figure 87 Diagnostic tests list Diagnostics EF General O All tests A diu L Status can device RF E Fieadbacks Ft fies Power supplies API and temperatures LI lon detection API source Lenses RF DAL L 1 0 part requires test loop Analog board Top cover board Cancel Erint Help 122 LTO Series Hardware Manual Thermo Scientific 6 Diagnostics 4 Select one of the following options To test all of the electronic subsystems that is the vacuum system power supplies lenses ion detection system and rf voltage electronics under General select All and under What to Test select the All Tests check box To test an individual subsystem click the item corresponding to that subsystem and select the appropriate check boxes 5 Click Start Testing starts and the Testing text box displays a chronological log of all diagnostic tests After completing the tests for a specific subsystem the Result column displays either Pass or Fail If the diagnostics ind
136. r user interface Functional block diagram of an LTO Series system Talet Divert valve poo Mass spectrometer API 07 lon lon nstrument detection control system electronic assemblies Mass optics analyzer Vacuum system 8 Series Hardware Manual Data system Printer Personal computer Video monitor Thermo Scientific Syringe Pump 2 Functional Description oyringe Pump The LTQ Series mass spectrometer includes an electronically controlled integrated syringe pump see Figure 2 The syringe pump delivers sample solution from the syringe into the API source Figure 2 yringe pump LC Needle oyringe oyringe Pusher union holder block TS R a F E m Me ac M L e bA x T vi Pars of m dpi mi E b b E Werks a REMO ol 4 Mim When the syringe pump is operating a motor drives the pusher block that depresses the plunger of the syringe at a user selectable rate Liquid flows out of the syringe needle and into the sample transfer line as the plunger is depressed A syringe holder holds the syringe in place For instructions about setting up the syringe pump refer to the LTQ Series Getting Started Guide Syringe Pump On Off Button Thermo Scientific The blue button located on the front pa
137. ramp of the main rf voltage to a new storage voltage to eject all ions except those of the selected mass to charge ratio For SRM CRM or MS n gt 1 full scan analyses the resonance excitation ac voltage is applied to the exit rods to cause CID Product ions with a mass to charge ratio of less than the minimum storage mass to charge ratio are not stored Finally the sample ions or product ions are scanned out The main rf voltage ramps up from low voltage to high voltage and simultaneously the resonance ejection ac voltage is applied to the exit rods to facilitate ejection As the main rf voltage increases ions of greater and greater mass to charge ratios become unstable and eject through the slots in the exit rods Most of these ions are focused toward the ion detection system where they are detected Figure 21 illustrates this process Thermo Scientific LTO Series Hardware Manual 25 2 Functional Description Mass Spectrometer Figure 21 Visual representation of mass analyzer operation Dynode in the lon detection system The Velos Pro mass spectrometer operates in a slightly different manner The LXQ and LTQ XL mass spectrometers perform all four steps in one trap but the Velos Pro does not In the Velos Pro the scan out step can only occur in the trap with the electron multipliers which is the low pressure trap while initial trapping isolation and dissociation of the ions occur in the high pressure trap
138. rap mass spectrometers are part of the Thermo Scientific family of mass spectrometers Note The Glossary on page 131 defines some of the terms used in this manual Contents LIQ Series Mass Spectrometers Overview of an LC MS Analysis LTO Series Mass Spectrometers The LTQ Series mass spectrometers includes the models listed in this section Descriptions of the various hardware components are in Chapter 2 Functional Description Velos Pro e ITQ Velos LTQ XL LXQ Thermo Scientific LTO Series Hardware Manual 1 1 Introduction LTO Series Mass Spectrometers Velos Pro Model Velos Pro is a dual cell 2D linear ion trap mass spectrometer that includes a syringe pump a divert inject valve and an Ion ion source This instrument has an improved ion detection system and other added features Thermo VELOS PRO LTO Velos Model LTQ Velos is a dual cell 2D linear ion trap mass spectrometer that includes a syringe pump a divert inject valve and an Ion Max ion source Ri E m 7 LNG L 2 Thermo LTQ VELOS 2 LTO Series Hardware Manual Thermo Scientific Thermo Scientific 1 Introduction LTO Series Mass Spectrometers LTO XL Model LTQ XL is a three segment 2D linear ion trap mass spectrometer that includes a syringe pump a divert inject valve and an Ion Max ion source LXQ Model LXQ is a single segment 2D linear ion trap mass s
139. ration Aux Rod Hi Voltage V Pulse Counting Threshold E Display settings Aux Rod Low Voltage V Sel Toggles Ausiliany amplitude v Triggers Auxiliary frequency KHz Mass calibration Ausiliary gas How arb System evaluation Back lens V r zero the electrometer Back Multipole Offset V Back Section Offset v Capillary heater C Execute Capillary voltage V Center Section Offset TV Front lens V Front Section Offset v Fate lans Value 100 000 Set Thermo Scientific LTO Series Hardware Manual 113 5 Maintenance Electron Multiplier Replacement 4 Scroll down the Device list to display the electron multiplier voltages Figure 81 Figure 81 Diagnostics dialog box showing the electron multiplier voltage parameters Diagnostics Multiplier 1 high gain V Detector settings Multiplier 1 norm gain V PF tune Multiplier 2 high gain TV rz Multiplier 2 norm gain V 5 L Multiple offset IV Pulse Counting Threshold 6 Multipole 00 offset VJ Em Toggles Multipole 1 offset V Triggers Multipole frequency kHz Mass calibration Multipale AF BAL v y System evaluation Reagent Cl gas pressure psi i r zero the electrometer Reagent EIS filament bias V Reagent electron lens V Reagent emission current us Execute Reagent ian gate lens V Reagent ian lens 1 V Reagent ian lens 2 V Reagent ian lens 3 V Fesnent inn lens aranlit ide DU og Cancel Pri Help
140. ressure levels checking 46 138 LTO Series Hardware Manual vent valve description 31 voltages line power specifications 14 resonance excitation rf voltage 24 W WEEE compliance ix wiring diagrams QO and QI ion guides LTQ XL 107 QO and Q1 ion guides LXQ 106 QO and Q1 ion guides Velos Pro 108 Thermo Scientific
141. rface 82 LTO Series Hardware Manual Thermo Scientific Thermo Scientific HS O 5 Maintenance lon Source Interface Maintenance To clean the exit lens and S lens CAUTION Do not clean the exit lens or S lens with abrasives acidic or caustic substances or detergents not stated in this chapter Inspect the components under magnification for any lint particulates and sample buildup or coatings Sonicate the components for 10 15 min in a 50 50 methanol water solution or a 196 solution of Liquinox in water If a sonicator is not available do the following a To clean the exit lens use a soft toothbrush with a 196 solution of Liquinox in water b To clean the S lens use a chamois tip swab with a 196 solution of Liquinox in water and use the 6000 grit MICRO MESH polishing swabs to clean the areas that are inaccessible to the chamois tip swab For the exit lens clean the bore by using the 6000 grit MICRO MESH polishing swabs Rinse the components thoroughly with water 5 Rinse the components with methanol Dry the components with a rapid stream of oil free nitrogen gas Inspect the components under magnification for any lint or particulates Note Inspect the orifices to confirm that no lint or particulates are present in the bore of the orifices Use tweezers or a similar tool to remove the lint or particulate To reinstall the S lens and exit lens Slide the S lens into the ion so
142. rometer If you purchased this option you must obtain a new license from Thermo Fisher Scientific and install it in your system before you can use this feature Getting a New License Code You can request a license code through e mail or fax see page xxvi These instructions cover e mail requests only that you send to a specific Thermo Fisher Scientific e mail address To geta Trap HCD license code 1 Choose Start Programs Thermo Foundation Instrument Configuration to open the Thermo Foundation Instrument Configuration window 2 Under Available Devices select the Velos Pro MS icon and click Add 3 Under Configured Devices select the Velos Pro MS icon and click Configure to open the Velos Pro Configuration dialog box xxil LTO Series Hardware Manual Thermo Scientific Preface 4 Select License and click Change License to open the LTQ License dialog box Velos Pro Configuration lon Source Display Tune Plus salation Reagent lan Sour FA MS Analog Inputs rau are licensed for all standard LTO features Ethernet i EZ License Instrument SV arnir o Service Change license 5 Highlight the license key in the License box LTO License rau are licensed for all standard LTO features License ER 6 Press CTRL C to copy the license key to the Windows Clipboard 7 Send an e mail message to ThermoMSLicensing thermofisher com In the Subject line type License Request
143. rs The Velos Pro uses two discrete dynode electron multipliers that provide a higher linear dynamic range The one or two electron multipliers mount on the top cover plate of the vacuum manifold next to the mass analyzer The electron multiplier amplifies the signal and includes a single or common anode that collects the electrons produced by the cathode The data system records the combined current that leaves the one or two electron multipliers as applicable through a common anode Because of the off axis orientation of the ion detection system relative to the mass analyzer neutral molecules from the mass analyzer tend not to strike the conversion dynode or electron multiplier As a result the noise from neutral molecules is reduced LTO Series Hardware Manual 27 2 Functional Description Mass Spectrometer Vacuum System The vacuum system evacuates the region around the API stack ion optics mass analyzer and ion detection system The vacuum system includes the following components Figure 22 Vacuum Manifold Turbomolecular Pump Forepumps Convectron Gauge on Gauge Figure 22 Functional block diagram of the vacuum system Nitrogen gas port sweep gas valve eS eat gas valve Aux gas valve Atmospheric source pressure region DOOR paren NDS region l sample j inlet device l Convectron gauge Exhaust Forepump Foreline 28 LTO Series Hardware Manual Helium gas port
144. s esn 19 opuenb IUoIzne28Jd a1n op 9 orpuaau QUOIZUSINUCW Ip o1u9AJ9jul 8Jenj9jJ8 Ip PW ouippa4IeJ IS Nepjeasul Inueuoduioo auo l pu ny e40 e9 OI O Ip InpisaJ t p ojuauinjeuis o Jad ejes pul ej suinBas 1011 1 9JezzI Df nue1tl IAISOJ09 1uabeynw iuaDoJa2ueo 3ISS0 1210 1 9 nyopoud ipibb upul Jad nuenD a1essopu olysdasedde au SOl021 d 1 ezuejsos Ip ezuasaJd al q ssog IDIWIYD njyopo4d 424 oyedwe s 03In2JI9 IP 9pauos ajjep auoiza10Jd e 149J8doo 8191160 UoN eJouadns OWJAYIS 0 ezuas OJUBWINJJS Ol UON amp 21319 8 eaui ejjep or299Jedde 091 pa alaubads 3110990 euoizua nueuJ Ip o u m u seisjenb 3Jenj13jJ8 Ip ewig 942191 IUOIS9 91e20A0Jd ond aya 9UOISUS e3 e pe 91u9J109 ep 0jejuauii e 9 o1299Jedde 1 euoirze108 0J ep 2oous VZN31d3AAV 8sop ues 9141 U319 JAYSI4 04 sojonpoJd so esed 990 e31U29 B OU TS SV 9p 6121 e uoo 019e U0I ug eseDuod ilnB sold ap sajue esopnp eas ojualulipeo2oJd un ap e2182e aiquinpiyas e opuen enueuJ 1S sepiug1uoo SYUOIIIN ANSUI SP e ouensn e 1113431 Jed ojuauinJjsur ezi n es ugiquie ojoquiis 91S saJolig ue SELOD TB sej ua opinjour ou oubijad un six anb eaiubis yesauab oilbil q O UBWINIISUI e ojuarulu9 u eu 0I9IAJ8S je o soaiunb sojon
145. s divert inject valve 11 mass spectrometer front panel 13 Pump On 9 lens LO cleaning 93 description 20 lens L1 cleaning 104 description 22 line power specification 14 liquid chromatograph solvent flow turning off 35 starting up 37 loop injection 10 LTQ Velos description 2 Thermo Scientific Main Power circuit breaker 15 maintenance APCI probe 72 ESI probe 57 fan filters cleaning 119 forepump oil purging 51 schedule 54 skimmer cleaning 80 supplies 55 tools 55 tube lens cleaning 80 mass analyzer description 23 helium damping gas 25 operation 25 mass spectrometers components turning off 41 description 12 functional block diagram 8 functional description 12 ion detection system 26 LTQ Velos note xxi 7 53 LTQ note xxi 7 53 photos 1 power panel 14 resetting 39 shutting down 36 Standby mode 35 starting up 28 turning on 26 vacuum manifold 29 vacuum system 28 metal needle insert for the HESI II probe 70 nitrogen pressure 48 P power LED 13 panel 14 specifications 14 pressure levels checking 46 pump down time 39 45 Thermo Scientific Index M 0 QO ion guide cleaning 95 104 reinstalling 105 removing 99 QO ion optics See QO ion guide QO quadrupole See QO ion guide QO0 ion optics See QO0 rf lens QOC rf lens assembly disassembling 92 reassembling 94 reinstalling 94 removing 90 cleaning 93 description 20 QI ion guide cleaning 95 104 description 22 reinstalling 105 removin
146. s Hardware Manual 39 3 System Shutdown Startup and Reset Resetting Tune and Calibration Parameters e After several more seconds the Communication LED turns green to indicate that the data system and the mass spectrometer have established a communication link The data system transfers operational software to the mass spectrometer After three minutes the System LED turns yellow to indicate that the software transfer from the data system to the mass spectrometer is complete and that the mass spectrometer is in standby mode Or the System LED turns green to indicate that the mass spectrometer is functional and the high voltages are on Resetting Tune and Calibration Parameters You can reset the LTQ Series mass spectrometer tune and calibration parameters to their default values at any time This feature is useful if you have manually set some parameters that resulted in less than optimum performance However Thermo Fisher Scientific recommends that only Thermo Fisher Scientific field service engineers reset your system s parameters IMPORTANT Ensure that the system problems you are experiencing are not due to improper API source settings such as spray voltage sheath and auxiliary gas flow or ion transfer tube temperature before resetting the instrument parameters to their default values f you reset the instrument calibration file always repeat the calibration of the internal electronic devices Otherwise all instrument
147. tabilize completely which takes approximately 15 24 hours of continuous pumping to ensure that the calibrations are correct Starting the Autosampler Turn on the autosampler by using its on off power switch If necessary configure the autosampler For procedures for placing sample vials preparing solvent and waste containers installing syringes and so on refer to the autosampler manual The LTQ Series Getting Connected Guide provides autosampler connection procedures Resetting the Mass Spectrometer Thermo Scientific If communication is lost between the mass spectrometer and data system computer you might need to reset the mass spectrometer by using the reset button on the right side power panel shown in Figure 8 and Figure 9 on page 14 The following procedure assumes that the mass spectrometer and data system computer are both powered on and operational If the mass spectrometer data system computer or both are off see Starting the System after a Complete Shutdown on page 37 To reset mass spectrometer after communication is lost 1 Ensure that the Communication LED is off 2 Press the Reset button on the power panel The following occurs The embedded computer reboots All LEDs on the front panel turn off except the Power LED After several seconds the Communication LED turns yellow to indicate that the data system and the mass spectrometer are starting to establish a communication link LTO Serie
148. the APCI nozzle head with the retention flanges on the probe body unlocked nozzle in Figure 48 on page 74 3 Rotate the head of the nozzle 90 degrees clockwise to secure the rounded sides of the nozzle head under the retention flanges locked nozzle in Figure 48 on page 74 lon Source Interface Maintenance To maintain the ion source interface follow these procedures Removing the Ion Source Interface Cleaning the Skimmer and Tube Lens on the LXQ and LTQ XL Mass Spectrometers on page 79 e Cleaning the Exit Lens and S Lens on the Velos Pro on page 82 e Reinstalling the Ion Source Interface on page 89 You need the following tools and supplies from Table 7 on page 55 Tools Supplies Ion transfer tube removal tool Chamois tip swabs Magnification device Detergent for example Liquinox Thermo Scientific LTO Series Hardware Manual 77 5 Maintenance lon Source Interface Maintenance Tools Supplies Slotted screwdriver small Gloves lint and power free Sonicator Kimvvipes or lint free industrial tissues Optional Soft toothbrush or similar tool Methanol LCMS grade Optional Wrenches open ended large Nitric acid diluted Nitrogen gas clean dry and compressed Water LCMS grade IMPORTANT e Prepare a clean work surface by covering the area with lint free paper e Put on a new pair of lint and powder free gloves before starting each of these removal cleaning and reinstallation procedures
149. those of a selected mass to charge ratio or narrow ranges of mass to charge ratios During the CID step of SRM CRM or MS 7 1 full scan applications a resonance excitation ac voltage is applied to the exit rods to fragment parent ions into product ions Ion motion is enhanced and the ion gains kinetic energy After many energetic collisions with the helium damping gas which is present in the mass analyzer the ion gains enough internal energy to cause it to dissociate into product ions The product ions are then mass analyzed During ion scan out the resonance ejection ac voltage facilitates the ejection of ions from the mass analyzer which improves mass resolution and sensitivity The resonance ejection ac voltage is applied during the ramp of the main rf voltage Ions consecutively move into resonance with the resonance ejection ac voltage When an ion approaches resonance it moves farther away from the center of the mass analyzer and is subsequently ejected 24 LTO Series Hardware Manual Thermo Scientific 2 Functional Description Mass Spectrometer Helium Damping Gas The mass analyzer cavity contains helium that is used as a damping gas and a collision activation partner The collisions of the ions entering the mass analyzer with the helium slow the ions so that the rf field in the mass analyzer can more efficiently trap them The presence of helium in the mass analyzer cavity significantly enhances sensitivity and mass spectral
150. tics transmit ions from the QO ion guide to the mass analyzer The Q1 ion optics include the Q1 octapole and the split gate lens Figure 19 The QI octapole is an octagonal array of circular rods that act as an ion transmission device similar to QO An rf voltage applied to the rods creates an electric field that guides the ions along the axis of the octapole The Q1 offset voltage increases the translational kinetic energy of ions emerging from QO A split gate lens starts and stops the injection of ions into the mass analyzer by deflecting the beam at high speeds at the appropriate times For positive beams the split gate lens opens at 72 V and closes at 100 V Figure 19 01 ion optics oplit gate lens LXO and LTO XL EE 22 LTO Series Hardware Manual Thermo Scientific 2 Functional Description Mass Spectrometer Mass Analyzer The mass analyzer is the site where ion manipulation and mass analysis occur which includes ion storage ion isolation CID and ion ejection This section describes the components of the mass analyzer voltages applied to the mass analyzer electrodes presence of helium damping gas in the mass analyzer cavity and mass analyzer operation during mass analysis Components The LXQ and LTQ XL mass spectrometers contain a single two dimensional linear ion trap The Velos Pro mass spectrometer contains a dual cell two dimensional linear ion trap The linear ion traps are square arrays of precision machined
151. to high kinetic energy and then allowed to collide with neutral gas molecules such as helium or nitrogen The collisions break the bonds and fragment the ions into smaller pieces conversion dynode A highly polished metal surface that converts ions from the mass analyzer into secondary particles which enter the electron multiplier D divert inject valve A valve on the mass spectrometer that can be plumbed as a divert valve or as a loop injector E electron multiplier A device used for current amplification through the secondary emission of electrons Electron multipliers can have a discrete dynode or a continuous dynode electrospray ionization ESI A type of atmospheric pressure ionization that is currently the softest ionization technique available to transform ions in solution into ions in the gas phase H heated electrospray ionization H ESI Converts ions in solution into ions in the gas phase by using electrospray ionization ESI in combination with heated auxiliary gas high performance liquid chromatography HPLC Liquid chromatography where the liquid is driven through the column at high pressure Also known as high pressure liquid chromatography 132 LTO Series Hardware Manual higher energy collision induced dissociation HCD Collision induced dissociation that occurs in the HCD collision cell of the orbitrap mass analyzer The HCD collision cell consists of a straight multipole mounted inside a coll
152. tting a Irap HCD License e Safety and Special Notices Contacting Us To suggest changes to documentation or to Help Complete a brief survey about this document by clicking the button below Thank you in advance for your help SURVEY Thermo Scientific LTO Series Hardware Manual xxi Preface Related Documentation In addition to this guide Thermo Fisher Scientific provides the following documents accessible from the data system computer for the ETQ Series mass spectrometers LTQ Series Preinstallation Requirements Guide LTQ Series Getting Connected Guide e LIQ Series Getting Started Guide e ETD Module Getting Started Guide with MS ETD system e ETD Module Hardware Manual with MS ETD system MALDI Source Getting Started Guide with MALDI MS system MALDI Source Hardware Manual with MALDI MS system To access the manuals for the mass spectrometer from the Microsoft Windows taskbar choose Start gt Programs gt Thermo Instruments gt Manuals gt model where model is your specific model and then click the PDF file you want to view Note For Xcalibur version 2 0 7 or earlier the path is Start gt Programs gt Xcalibur gt Manuals gt LTQ gt model The software also provides Help To access the Help choose Help from the menu bar Getting a Trap HCD License Ion trap higher energy collision induced dissociation Irap HCD fragmentation is an optional feature for the Velos Pro mass spect
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154. up and Reset Many maintenance procedures for the LTQ Series mass spectrometer require that the system be shut down completely If the system is not used for 12 hours or more you can place the mass spectrometer in standby mode If the system is not used for two or more months you can shut down the mass spectrometer completely Contents e Shutting Down the System in an Emergency Opening the Tune Plus Window Placing the Mass Spectrometer in Standby Mode e Turning On the Mass Spectrometer e Shutting Down the Mass Spectrometer Completely e Starting the System after a Complete Shutdown Resetting the Mass Spectrometer Resetting Tune and Calibration Parameters Restarting the Data System Turning Off Selected Mass Spectrometer Components Shutting Down the System in an Emergency CAUTION If you need to turn off the mass spectrometer in an emergency turn off the main power switch located on the right side power panel Figure 8 and Figure 9 on page 14 This switch turns off all power to the mass spectrometer including the vacuum pump or pumps Although removing power abruptly does not harm components within the system this is not the recommended shutdown procedure to follow See Shutting Down the Mass Spectrometer Completely on page 36 To turn off the LC data system computer and autosampler in an emergency use their respective on off switch or button Thermo Scientific LTO Series Hardware Manual 33 3 Syst
155. urce interface cage and align the thumbscrews with the screw holes Figure 57 on page 82 Align the exit lens lead pin with the lead pin socket on the S lens and firmly press it until it snaps into place Hand tighten the thumbscrews LTO Series Hardware Manual 83 5 Maintenance lon Source Interface Maintenance Cleaning the API lon Transfer Tube Buffer salts or high concentrations of sample can block the bore of the ion transfer tube and must be cleaned If the pressure in the ion transfer tube skimmer region as measured by the Convectron gauge drops considerably below 1 Torr you should suspect a blocked ion transfer tube Note You do not have to vent the system to remove the ion transfer tube To clean the ion transfer tube follow these procedures 1 To check the Convectron gauge pressure 2 To remove the ion transfer tube 3 To clean the ion sweep cone optional spray cone and ion transfer tube on page 88 4 To reinstall the ion source interface on page 89 For Field Service use only Part number O ring Vespel 0 325 in ID 97055 20442 Ion transfer tube See page 127 To check the Convectron gauge pressure 1 Open the Tune Plus window see page 34 2 Choose Setup gt Vacuum to open the Vacuum dialog box Figure 58 Figure 58 Vacuum dialog box Vacuum lon Trap lan Gauge On C Off lan Gauge Pressure E 5 Tor 0 73 Convectron Gauge Pressure Torr 0 32 3 Check the readi
156. uter ridges of the ion sweep cone and pull it off of the API cone seal If necessary first loosen the ball plungers by using a small slotted screwdriver Figure 60 shows the two types of ion sweep cones available on the LTQ Series mass spectrometers The ion sweep cone shown on the bottom has an offset orifice Figure 60 lon sweep cones Gas inlets Offset orifice 86 LTO Series Hardware Manual Thermo Scientific 5 Maintenance lon Source Interface Maintenance 5 Remove the ion transfer tube as follows a Turn its exposed spray cone counterclockwise with the custom removal tool provided in the MS Accessory Kit Figure 61 b When the tube is free of the spray cone pull it straight out of the ion source interface Figure 61 lon transfer tube removal tool Custom removal opray cone tool of the ion transfer tube Thermo Scientific LTO Series Hardware Manual 87 5 Maintenance lon Source Interface Maintenance To clean the ion sweep cone optional spray cone and ion transfer tube 1 Soak the ion transfer tube in a 50 50 methanol water solution for 5 10 min to remove contaminants 2 Sonicate the ion transfer tube in LCMS grade water for 15 min 3 Clean the ion sweep cone and optional spray cone by wiping the interior and exterior surfaces with Kimwipe tissues soaked in methanol 4 Remove and inspect the O ring that is in the spray cone under the entrance end of the ion transfer tube Figure 62 and Figur
157. ves when handling the components of the API source ion guides mass analyzer and ion detection system Always place the components on a clean lint free work surface e Never overtighten a screw or use excessive force Thermo Scientific LTO Series Hardware Manual 53 5 Maintenance Table 6 lists the maintenance procedures and their recommended frequency Table 6 LIU Series mass spectrometer maintenance procedures and frequency Component API source Cooling fans Forepump Procedure Flush clean the sample transfer line sample tube and API probe Trim the sample tube Replace the sample tube and safety sleeve Clean the fan filters Frequency Daily end of the sample tube is elongated obstructed Every 4 months Daily Location page 49 page 57 page 69 If the polyimide coating on the page 58 If the sample tube is broken or page 63 page 119 Manufacturer s Purge decontaminate the oil and Ion source interface check for leaks Change the oil Add oil Every 3 months or if the oil is cloudy or discolored As needed based on oil level documentation Flush clean the ion sweep cone QO and Q1 ion guides lens L1 and split gate lens optional spray cone and ion transfer tube Remove and clean the ion transfer tube Replace the ion transfer tube Clean the skimmer and tube lens Clean the exit lens or S lens Clean the QO and Q1 ion guides l
158. vides four additional ways to introduce a sample into the mass spectrometer described in Table 2 Table 2 Introducing samples into the mass spectrometer Method to introduce sample Description Automated loop Connect a sample loop an LC pump and the syringe pump injection to the divert inject valve After you connect the plumbing specify the flow rate at which the syringe pump fills the sample loop After the loop is filled the data system triggers an injection High flow infusion Use a union tee to combine the flow from the syringe pump with the flow from an LC pump Infusion Connect the built in syringe pump directly to the atmospheric pressure ionization API source of the mass spectrometer Manual loop injection Connect a sample loop a needle port fitting and an LC pump to the divert inject valve After you fill the sample loop with sample switch the position of the divert inject valve which places the contents of the sample loop in the path of the solvent flow produced by the LC pump The mass spectrometer consists of an API source ion Optics a mass analyzer and an ion detection system The ion optics mass analyzer ion detection system and part of the API source are enclosed in a vacuum manifold 4 LTO Series Hardware Manual Thermo Scientific Thermo Scientific 1 Introduction Overview of an LC MS Analysis Ionization of the sample takes place in the API source The specific method used to ionize the samp
159. y Not for use in diagnostic procedures Thermo SCIENTIFIC Regulatory Compliance Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with applicable domestic and international regulations When the system is delivered to you it meets all pertinent electromagnetic compatibility EMC and safety standards as described in the next section or sections by product name Changes that you make to your system may void compliance with one or more of these EMC and safety standards Changes to your system include replacing a part or adding components options or peripherals not specifically authorized and qualified by Thermo Fisher Scientific To ensure continued compliance with EMC and safety standards replacement parts and additional components options and peripherals must be ordered from Thermo Fisher Scientific or one of its authorized representatives Regulatory compliance results for the following Thermo Scientific products XQ Mass Spectrometer February 2005 e LIQ XL Mass Spectrometer September 2006 LIQ XL ETD System January 2007 e MALDI LTQ XL System August 2007 LIQ Velos Mass Spectrometer August 2008 LTQ Velos ETD System November 2008 Velos Pro Mass Spectrometer April 2011 e Velos Pro ETD System April 2011 LXQ Mass Spectrometer February 2005 EMC Directive 89 336 EEC as amended by 92 31 EEC and 93 68 EEC EMC compliance has been evaluated
160. ystem after a Complete Shutdown 5 Unplug the power supply cord for the mass spectrometer from the electrical outlet CAUTION Do not disconnect the power supply cord at the mass spectrometer while the other end is still plugged into the electrical outlet 6 Optional Follow the next procedure To turn off the LC gases data system and autosampler Tip If you only plan to perform routine or preventive system maintenance on the mass spectrometer you do not need to turn off the LC gases data system and autosampler In this case the shutdown procedure is complete However if you plan to have the system off for an extended period of time Thermo Fisher Scientific recommends that you also turn off these other parts 9 To turn off the LC gases data system and autosampler 1 If provided turn off the LC system as described in the LC manual 2 Turn off the helium and nitrogen gas supplies at their tanks 3 Shut down the data system computer and turn off the monitor and printer if provided 4 f provided turn off the autosampler by using its On Off switch Starting the System after a Complete Shutdown To power up the LTQ Series mass spectrometer after it has been shut down completely follow these procedures Starting the LC System e Starting the Data System Starting the Mass Spectrometer Starting the Autosampler on page 39 if this is a part of the system Starting the LC System To start up

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