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MSQ Installation and Commissioning Guide

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1. L Ara Or ORON EEN O Moreover if an AXP MS pump is to be used for running acceptance tests the backpressure generating restrictor P N 061491 is essential A minimum E of 600 psi is required and the maximum flow rate is 0 25 mL Mmin 1 2 Installation and Commissioning Guide ED N F MSQ EDIONEX Installing the MSQ Site Verification Site Verification Only agree to start the MSQ installation when the user customer returns a completed site installation requirement checklist or pre installation requirements guide checklist The requirements will have been sent to the user when the order confirmation was issued As the Service Representative you are responsible for the installation the user s first impressions of the products and support It is therefore essential that the installation be carried out smoothly You should ensure that you obtain a hard copy of the user order and completed site requirements returned by the user You must also contact the person allocated to the installation at the user s laboratory and establish that they are ready and expecting your arrival If after talking to the user or customer you have any doubts that the installation is going to be ready to start you should take the required action to resolve any issues before you arrive If the installation is attempted without a complete laboratory complete instrument or available trainee it will almost certainly end in re
2. e Red for Vented e Flashing yellow for Pumping down e Yellow for Pumped down Vacuum OK e Green for Pumped down and in Operate AA start D ee c I fF Untitled MSInst Ge i420 Figure 2 2 The taskbar showing Xcalibur Home page and server Starting the Vacuum System Right click the server icon and switch on the vacuum system by clicking Pump in the server window see Figure 2 3 Instrument Tune and Calibration Tune Exit i Kik Figure 2 3 The server window 15 28 The LED display on the front of the instrument should go from vent condition to pumping down condition e the LED should change from red to flashing yellow Upon reaching operational vacuum the sever virtual LED icon should change to steady green and providing that the source door is closed the indicator LED on the front of the MSQ should change to steady green Installation and Commissioning Guide EDI N F A MSQ EDIONEX Mass Spectrometer Functional Verification Powering Up NOTE If the source door is open the indicator LED on the front of the MSQ will remain yellow Initial System Operational Check Operate OFF While waiting for the system to pump down the source should be set up for ESI observation initial checks of gas flow should be made and the gas connections should be checked for leaks e To set up the source for ESI view the relevant animation or the Getting Started manual e Firs
3. o O T O os S bo m i T Ces DD OL is Lo E UO Up E d O l g So 29 00 LD L z eunbig EDIONEX 966p Aus uaut gag Uz g6 g awg uouajay yea aseg H WS She LOO La sO IA Pehla Rlelel ale la 1072 bie s10 OL uf AH SOdI Jd Fy dja ueo ma yo at 2 32 MS Mass Spectrometer Functional Verification Q Instrument Acceptance Negative APCI e Change the mobile phase to 50 50 methanol water and prime the HPLC pump e Open the tune window click on File Open and select A Sensitivity Spec APCI Neg tune e The parameters that differ from the previous test are Probe Temperature Corona uA Mass and Polarity see Figure 2 22 Description Headback Setpoint Tune Control Probe Temperature TL 349 Corona pA UU UU H Mass Polarity Cone l 180 00 ve DU Figure 2 22 Tune parameters that differ from those shown in Fig 2 17 e Click on View Options This opens the Tune Options window Tune Options xX Surveyor MSO Tune Options Configure the tune and display parameters Tune Number of tune masses fi Acquisition filename nstallation tests Sensitivity Spec APC vweraw Tune filename ass ensitivity Spec APC ve tune P Filled traces Show advanced parameters Figure 2 23 Tune Options window APCI ve e Using the button to the right of Acquisition filename browse through to C Xcalibur Installation
4. DIONEX MSQ Installation and Commissioning Guide Document No 031869 Revision 02 October 2003 Now sold under the Thermo Scientific brand Thermo SCIENTIFIC 2003 by Dionex Corporation All rights reserved worldwide Printed in the United States of America This publication is protected by federal copyright law No part of this publication may be copied or distributed transmitted transcribed stored in a retrieval system or transmitted into any human or computer language in any form or by any means electronic mechanical magnetic manual or otherwise or disclosed to third parties without the express written permission of Dionex Corporation 1228 Titan Way Sunnyvale California 94088 3603 U S A DISCLAIMER OF WARRANTY AND LIMITED WARRANTY THIS PUBLICATION IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND DIONEX CORPORATION DOES NOT WARRANT GUARANTEE OR MAKE ANY EXPRESS OR IMPLIED REPRESENTATIONS REGARDING THE USE OR THE RESULTS OF THE USE OF THIS PUBLICATION IN TERMS OF CORRECTNESS ACCURACY RELIABILITY CURRENTNESS OR OTHERWISE FURTHER DIONEX CORPORATION RESERVES THE RIGHT TO REVISE THIS PUBLICATION AND TO MAKE CHANGES FROM TIME TO TIME IN THE CONTENT HEREINOF WITHOUT OBLIGATION OF DIONEX CORPORATION TO NOTIFY ANY PERSON OR ORGANIZATION OF SUCH REVISION OR CHANGES TRADEMARKS Chromeleon and PeakNet are registered trademarks of Dionex Corporation Cone Wash MSQ and Xcalibur are trademarks of The
5. Mass Spectrometer Functional Verification Instrument Autotune and Calibration MSQ 2 10 Full System Autotune Full System Autotune performs the following sequence of actions 1 Resets all parameters to default values including ion energy and Low and High mass resolution controls 2 Deep Tune 3 Resolution Setup 4 Mass Scale Calibration This operation only needs to be performed if the spectrometer has been moved to a different environment as at installation Xcalibur software has been reinstalled updated or if the conformance protocol demands it Deep Tune Deep Tune is an automated operation that adjusts the operating frequency of the RF generator to match the natural resonant frequency of the Quadrupole Analyser This is necessary to ensure that the spectrometer will operate to the maximum value of its range On previous models this was a manual operation Resolution Setup Resolution Setup is an automated operation that electronically adjusts the resolution at high and low mass 1971 6m z and 172 8m z it 1s adjusted to unity Dalton at the baseline of each peak It also performs a linearity adjustment to the same criterion at mid mass 1072 24m z As with Deep Tune this was a manual operation on previous models Mass Scale Calibration This is described in Standard Mass Scale Calibration in the following section Standard Mass Scale Calibration For routine full mass range calibration the end user will norm
6. n a General Control Operate n a On Nitragen Gas n a On lonization Mode n a APC Figure 2 19 Tune parameters that differ from those shown in Fig 2 17 e Click on View Options This opens the Tune Options window Tune Options xj Surveyor MSO Tune Options Configure the tune and display parameters Tune Number of tune masses i Acquisition filename Installation tests Sensitivity Spec SPC vera Tune filename A Sensitivity Spec APC e tune SE Display Filled traces Show advanced parameters Figure 2 20 Tune Options window APCI ve e Using the button to the right of Acquisition filename browse through to C Xcalibur Installation Installation tests and type in Sensitivity Spec APCI ve raw Check that the Tune filename is A Sensitivity Spec APCI ve tune see Figure 2 20 Continue as in Positive ESI but use the 5pg uL erythromycin sample Installation and Commissioning Guide 2 31 MSQ Mass Spectrometer Functional Verification Instrument Acceptance mn FE gE got L t Odd CW 3IL IDG IN sier SES uIDAWOAIYJAIZ N 6dgQ g 10 s insay Auatsueeg OdV IEOIdAL ec L UOleWag PAB_UeLS LD9 asion oL Eug Fed aupen Gugas QOL sapu ze L EE abue asiopy Sanper pape ynaje7y CULL BUU Ce UC GC H C Fg na Jg GL HL FH gH UL GU HU Fu GH 0 TVE 8 DLT ESE LVE yF ELLO ib EPL Of TBO 780 990 OSD DEn LU Ol ZS 3 oz O D E OC S CG SN Ka Op x
7. 2 29 Installation and Commissioning Guide EDIONEX Q a WON OF ior Bre Cc Ke T O Ge D gt bs S SOdIsa S SN OL So EI des LL 2 IN oe S o 2 ZS O 85 N E 4s 2 er DOC GE uer BLE 0E BRT BLE EST DU UJDAWOAYAAA NPAO 10 Susan APAHISUVS SF EVAL St sandy GDL UONEWeg DIEHUEI ZZ Se10N OY Jeug 8285044 3ujaseg SuBIS FOL saynui ggg oz abuey asion sanjeA payejnajep uuu awa Gz o z EZ SOZ le Feli L0Uc SU GE G ESL PST r Da EL auon sayy UE pOO ep Z Ague CLO Seu OL t Aysuaquy GIG UEIS ggg awy uonuayayY yea aseg Ob GU UL Oe S80 790 SEH Z00E FLL pgg OF os 04 asuepungy aajejay SIb d 06 00t Hr WS Hr UU JL oDd IA Bieu lolol ale la daH webojyewos ma p3 a 407 NED ISION 01 peubis mersOdIsape EDIONEX Installation and Commissioning Guide 2 30 MSQ EDIONEX Mass Spectrometer Functional Verification Instrument Acceptance Positive APCI e Configure the source for APCI as shown in the animations e Open the tune window click on FILE Open and select A Sensitivity Spec APCI Pos tune e The parameters that differ from those shown in Figure 2 17 are the Probe Temperature Corona uA and lonization Mode see Figure 2 19 Description Readback Setpoint Tune Control Probe Temperature TL T DU Corona p UU 50 Acquisition Control Retention Time mins 0 0
8. 98 1075 Dn 1074 49 UO A 24 l222 14 l222 38 1226 48 l224 82 0002 6 L372 04 1372 f1 L376 1 1375 05 UO 3 OL 1521 93 1522 95 1526 95 1525 29 UU 3 36 Loyl Hs lors 19 Lory 19 1675 70 D003 H4 1821 72 18523 6 60 1827 D 1526 08 UDOO4 36 1971 61 1973 98 1977 98 19768 41 UDOO4 70 Ret Peak Residual O12 88 UO OU 74 0322 78 0 0095 O472 6 7 0 0528 622 57 OO 1189 Or e2 46 O 0217 0922 36 0 1005 l 72 25 UO 0166 l 22 14 UO 0695 1372 04 UO UL Ap L521 45 O 0587 171l Hs OO 048 L241 72 UO 0203 1971 61 0 0068 MissedRetPeaks S 3 Standard Deyiation 0 0227 Sqr Root of Mean Square Error 3 3067 Max Residual Error gt 0 0530 Number of co efficients 3 Coeffo Oo 000000e 000 Coeffl 1 000000e 000 Coeff2 1 000000e 000 Valid calibration range 172 88 to 1971 61 AMU 3 12 Installation and Commissioning Guide El N I H MSQ Detector Voltage Registry Location a Registry Editor Appendix E Detector Voltage Registry Location Appendices Appendix E Registry Edit view Favorites Help CH Aagilent1100 MWD CC Agilent1100 QuatPump 9 Agilent1100 vWD 9 Gilson215 E Hp1050 AS H E Hp1050 IsoPump o CH Hp1050 MWD H E Hp1050 QuatPump e CC Hp10s0 vwD CO Hp1090 LC H E HP1100 45 H E HP1100 BinPump e HP1100 DAD 9 1 HP1100 Heater H HP1100 IsoPump d r HP1100 MWD J HP1100 QuatPump H 8 HP1100 Mu E 55420 Ee 55420x H E Survey
9. Figure 2 1 Instrument Configuration window Click and drag the icon of the MSQ from the LHS Available Devices panel to the RHS Configured Devices panel and click on Done to exit the Instrument Configuration program There is no need to Configure the MSQ As described later verification should be performed manually using a Rheodyne or similar injector or optionally with an AXP MS pump Installation and Commissioning Guide EDI N f A MSQ Mass Spectrometer Functional Verification Configuring Xcalibur for the Functional Verification NOTE Do not configure any other devices in Xcalibur All configurations of LC devices will be through Chromeleon PeakNet which will be installed later in the commissioning process SI N I Installation and Commissioning Guide 2 3 Mass Spectrometer Functional Verification Powering Up MS Q 2 4 fl Surveyor KSC Tune Powering Up The MSQ should now be ready to have the power supplied Switch on the MSQ at the rear of the instrument Open the Xcalibur Tune window by double clicking the Tune shortcut icon on the Windows desktop The Server The server is the software that handles all communication between the MSQ and its controlling PC When started by running either Xcalibur or Tune the server LED icon is displayed in the System Tray of the Windows taskbar It is shown in Figure 2 1 just to the left of the time This icon mimics a tri state LED display showing
10. The MSQ reference inlet system Click on Valve Control Calibrant Reservoir Pressure as in Figure 2 10 Retention Time mins 0 46 n a General Control Uperate n a Ort Nitrogen Gas n a Off TC lonization Mode n a ESI Valve Control Calibrant Reservow Pressure n a Ort Figure 2 10 Advanced Per Method Parameters Watch the waste line connected to the waste bottle left hand side bottle as soon as a steady stream of drips 5 10 drips sec is observed click the Calibrant Reservoir Pressure to off The system is now primed 8 Tune window parameter display There are two levels of Per Method Parameters available to users in the Tune window The first level Operator level shows only those parameters that need to be accessed for normal use Changing any of these will not produce any irrecoverable errors The Advanced Parameter level should only be accessed when necessary by supervisors or Dionex personnel Following any parameter change the parameter level should be returned to Operator level Installation and Commissioning Guide EDI N f A MSQ Mass Spectrometer Functional Verification Instrument Autotune and Calibration Note Before proceeding it is important to understand that the instrument should now have been under vacuum for a period of 1 2 hours and also have been in operate with its cover in place for at least 1 hour e Return the Per Method Parameters to Operator level by clearing the
11. and transfer 200uUL of the stock solution to the vial Then using the ImL pipettor add another 2mL of mobile phase Shake well This gives a solution of 50ng uL 500pg uL solution e Using the lmL pipettor transfer 2mL of mobile phase to the 500pg pL vial Using the 200uL pipettor remove and dispose of 40uL of mobile phase from this vial e Change the 200uL pipettor tip and transfer 40uL of the 50ng pL solution to the vial Then using the 1mL pipettor add another 2mL of mobile phase Shake well This gives a solution of 500pg nL Spg uL solution e Using the lmL pipettor transfer 2mL of mobile phase to the 5pg nL vial Using the 200uL pipettor remove and dispose of 40uL of mobile phase from this vial 3 4 Installation and Commissioning Guide El N I H MSQ Sample Preparation EDIONEX Appendices Appendix A e Change the 200uL pipettor tip and transfer 40uL of the 500pg pL solution to the vial Then using the I1mL pipettor add another 2mL of mobile phase Shake well This gives the ve APCI test specification solution of 5pg nL 50 50 Acetonitrile Water This mobile phase is unstable and will generate ions overnight thereby producing a noisy background and considerably degrading the sensitivity For good results it is essential to mix this freshly and then degas by ultrasonic bath on the morning of use Similarly the dilute test samples should be disposed of at the end of the working day and the
12. 50 mg milligram of the Nal and add this to the IPA water in the beaker stirring thoroughly as it is being added Weigh out 250 ug microgram of the desoximetasone and add this to the IPA water in the beaker stirring thoroughly as it is being added Sonicate solution for 1 minute to ensure that both compounds are completely dissolved in the IPA water Pour the solution from the beaker to the plastic bottle screw on the bottle top and seal the top with PTFE tape Installation and Commissioning Guide 3 7 Appendices Appendix B MSQ Signal to Noise Calculator Shortcut to Sighoise exe MSQ Appendix B MSQ Signal to Noise Calculator The MSQ Signal to Noise Calculator application will perform a signal to noise calculation on a specified chromatogram The results can then be printed or copied to the Clipboard as a metafile for inclusion in a report Tutorial Open the Signal to Noise Calculator by either double clicking on the desktop icon or selecting Tools Sig Noise from the Xcalibur Home page 1 Go to the raw file selection dialog box by selecting the File Open menu item or by clicking on the toolbar button 2 Select a raw file on which to perform the signal to noise calculation the specified file must contain MS data 3 Normally signal to noise calculations are performed on mass chromatograms In order to specify a mass chromatogram select the Chromatogram Ranges menu item The Chromatogram Ranges dia
13. Document 25 10 2001 10 22 H system autocall102501111637 log 2KB Text Document 25 10 2001 10 17 E 2 templates 2KB Text Document 25 10 2001 10 04 1 Test Results 60007 1KB Text Document 25 10 2001 10 03 al amp Local Disk D 1KB Text Document 25 10 2001 10 03 zi Compact Disc E 1KB Text Document 25 10 2001 10 03 d EE 1KB Text Document 25 10 2001 10 03 E aiai 1KB Text Document 25 10 2001 10 03 d interme Explorer 1KB Text Document 25 10 2001 10 03 1KB Text Document 25 10 2001 10 03 1KB Text Document 25 10 2001 10 03 1KB Text Document 25 10 2001 10 03 1KB Text Document 25 10 2001 10 03 1KB Text Document 25 10 2001 10 03 1KB Text Document 25 10 2001 10 03 1KB Text Document gier 10 02 Type Text Document Size 1 40 KB EDIONEX Installation and Commissioning Guide 3 11 D 40 KB My Computer Appendices Appendix D MS Q Typical Report of a Calibration Appendix D Typical Report of a Calibration Si autocal102501114248 log Notepad Ioj x File Edit Format Help File created at Thursday October 25 2001 11 42 48 Needle Voltage 7 2 98 Cky3 Source Temprature gt 346 69 CC Der Peak Gear ch window Real Peak Mass Error O12 Hp 0168 88 0176 B88 Ul ZA fa 000 15 Da2 78 0420 63 0324 63 Os2 2 91 OOOO Ls 472 67 470 80 04 74 80 473 16 Oooo 49 0522 97 0621 05 0625 05 0623 67 OOO1 10 D72 Ap OF FL 56 0775 56 Ov Ys 85 OOO1 39 0922 56 0921 75 0925 75 0924 08 OOOL 73 Lore 25 1071
14. FO EEN 2 25 Surveyor MSQ Signal to Noise Calculator cccccccsesessssssssesssesssesssssseeeseeeeeens 2 26 Acquisition of Specification Chromatograms 2 27 POSVETE Tee pean tan cities bate tatouc caus E EEEE E E AE 2 27 Ee te Cl na E E E EE EE E EEEE EE E 2 30 Nea APE E 2 31 EK a O EE 2 32 INS Uy D RE 2 34 EH 2 36 Sen SE EE se sscaceratsanwasiaisea aus E so saciena se sans EE E TS 2 36 Those tasks which must be completed before Sign Off cc cccccccceeeeeeeeeeeees 2 36 Those tasks that must not be performed before Sgpn oft 2 36 PRG OTA OVD Te ned Se srex tue E E EERS EE mec ee EE E 2 37 Surveyor MSQ Connection ks 2 37 er aap E ew yee ce es oe cele cen te oes ce See eee E ese ee eens 2 38 Connecting the MSO to the HPLC System siciccsscseinsssccsacesssesaceaevesedssascaaccasiaiaaseseaasesevaradesasacnceai 2 39 DUD O66 G95 9S be NG sergrein rann AEE NEE REE EAEE EAEN 2 39 rees 2 40 EE 2 40 Completing the EH ee 2 41 EH 3 1 Appendix A Sample Preparation EE 3 2 rte 3 2 EE HEEN 3 2 R guired Samples ee 3 2 Suggested Method for Sample Preparation cccccceeessssssesessssssssssssssseseeseeseseees 3 3 Sample EE TE 3 3 Erythromycin Spo Ui EE 3 3 50 50 Acetonitrile E 3 4 leese 3 5 BEE 3 5 Appendix B Surveyor MSQ Signal to Noise Calculator 3 7 TUDO IA E 3 7 TON ae sates EE E E E 3 8 E N f X Installation and Commissioning Guide jii Contents MSQ FiO Ee 3 9 EEN ege 3 9 Appendi
15. Figure 2 12 Instrument Tuning and Calibration window Failure to Autotune Mass Calibrate If the system fails any part of the Autotune sequence the Instrument Tuning and Calibration window will display suggestions as to the possible cause Throughout the sequence the tune window may be observed While re attempting Autotune the per method parameters should be monitored Basic Instrument Operation Checklist LI A Full System Autotune has been performed successfully Date Completed Service Representative s Initials 2 14 Installation and Commissioning Guide DI N F MSQ EIDIONEX Mass Spectrometer Functional Verification System Training System Training Schedule The user will require basic training on the general operation of the instrument and its maintenance plus training on how to perform simple loop injection MS acquisitions During the installation it is very important that the user designated to be with you for the install is present all the time as this will avoid duplication of your time and effort Most of the training can be completed during the setup and installation of the MSQ The user must be shown how to start up and shut down the complete system This should include hints or tips on determining if the computer and MS system are still communicating and a demonstration of when and how to re boot the MSQ The user should be shown how to put the system into vacuum and how to vent the system A
16. Installation tests and type in Sensitivity Spec APCI ve raw Check that the Tune filename is A Sensitivity Spec APCI ve tune See Figure 2 23 Continue as before but use the 2pg uL p Nitrophenol test sample EI N I A Installation and Commissioning Guide 2 33 MSQ Mass Spectrometer Functional Verification Instrument Acceptance jousydoyN d 7N 6do z 104 s insay APAWISUdS dv IedAL vZ Z aunbi4 me a mas ad Pal _ mm OO WOneWeg PEpueLS 29 asioy OL jeubis Sep Aysuaqu fa cpg auljaseg S00 ues SUBI5 p04 samuiw ggz egz abuey asioy GEE awi UOlUalay Sanjea pajejnajeg yea asp uu aw 0 oF OF GE UE Ti 0z D D GU l 0 Ob 02 2 3 DE D 1 S enn a A denn FLA OF T z EDE gez 78 Set ggZ zz ESI EST wl set O80 wn soc os S pam 5 O ua S S OL i 08 OANIod 06 SH SIL tI9F L i IN ELE BEE ss BL WS GES 6PO JL HE FG GL LOO SD LE JJM da LA Biela Rleleop ale la daH we oyewo5 mal 1073 ag xie H ME EI Ge F510 OF jeubis au HOND N MSQ EDIONEX Mass Spectrometer Functional Verification Instrument Acceptance Negative ESI e Configure the source for ESI as shown in the animations e Open the tune window click on File Open and select A Sensitivity Spec ESI Neg tune e The parameters that differ from the previous test are Probe Temperature C Needle kV Ionization Mode and Cone see Figure 2 25 Description Readback Se
17. O A Nard copy of the Ee EE O A clean 10 uL PEEK or Stainless Steel sample loop E Aclean D gas tight Syringe anatase cent ected seectetoseaedateicictasacieieeeteseeesetetees oO It is highly recommended that a clean and known good injector be taken to carry out the installation many installation problems are due to poor quality and or dirty injectors supplied by CUStOMErS E A quality plastic tube cutter capable of cutting up to 6 mm OD tube O A Junior hacksaw or similar tool for cutting the 25 mm OD Metal reinforced VACUUM ve L A 1 25 A F open ended spanner for the Gas Regulator O A 14 mm A F open ended spanner for the A BSP to 6 mm Legris adapter O A 2 5 mm flat end Allen key for Heater removal replacement O A 3 mm flat bladed screwdriver for Source Block cleaning O A 5 mm flat bladed screwdriver for Heater removal replacement E An 8 mm flat bladed screwdriver for Source Block cleaning O A bottle of 50 50 Propan 2 ol Water for leak checking gas lines It is conceivable that this could be prepared on request on site prior to your SEENEN O A 3 digit DVM Fluke model 77 or equivalent For checking the line voltage 2 1
18. SES Banjo Seal Figure 1 7 Installing the hose adapter c Use the banjo bolt and the two bonded seals to fit the hose adapter to the gas ballast adapter 4 Use the flexible oil return tubing to connect the drain adapter on the oil mist filter to the hose adapter a Cut a suitable length from the flexible oil return tubing Ensure that the ends of the tubing are free of burrs and that they are squarely cut In addition ensure that the tubing is neither taut nor kinked and that the flow path from the drain adapter on the oil mist filter to the hose adapter on the forepump is downhill all the way b Fit the brass restrictor into one end of the tubing 1 18 Installation and Commissioning Guide EN 0 N F MS Installing the MSQ Q Connecting the Vacuum System Exhausts Gas and Power c Attach one end of the tubing to the drain adapter on the oil mist filter and the other end to the hose adapter Use the two hose clips to secure the ends of the tubing see Figure 1 8 Drain Adaptor Flexible Tu bing eum ED NARDS Oil Mist Filter EMF 20 Hose Hose Adaptor Figure 1 8 Connecting the flexible oil return tubing 5 Connect the oil mist filter to the vent using the 26 mm tubing clamp and centering ring Source Exhaust The MSQ source exhaust consists of 3 m of 4 ID 26 mm OD tubing This should be cut to length on site to fit the suitably positioned solvent trap see Figures 1 9 and 1 10 The exhaust fr
19. before beginning the installation Some of its material is repeated here as an aide m moire for experienced Service Representatives however most will need the detail contained within this user manual Animations Service Representatives should also view the animations and video that can be viewed via the Product Portfolio desktop shortcut before beginning the installation This will provide a helpful overview of many of the operations necessary for a successful commissioning Installation and Commissioning Guide 2 1 Mass Spectrometer Functional Verification Configuring Xcalibur for the Functional Verification MSQ 2 2 Instrument Configuration Configuring Xcalibur for the Functional Verification The MSQ is delivered with all necessary Xcalibur software loaded Switch on the PC It is not yet necessary to power up the MSQ After some time a log on window will appear showing Administrator and asking for a password Do not enter anything just press return Configuring the MSQ To configure the MSQ execute the Instrument Configuration program by double clicking the Instrument Configuration desktop icon or selecting Programs Xcalibur Instrument Configuration on the Windows Start menu This will bring up the window shown in Figure 2 1 Instrument Configuration x Device Types All Available Devices Configured Devices Surveyor A P Surveyor MSG E Surveyor PDA TSP Autosampler
20. click this to start the calculator Following the acquisition of each sensitive check chromatogram the calculator should be started and the chromatogram opened A full description of how to use the calculator is provided in Appendix C If the icon is lost e g because Xcalibur is reloaded or updated make a shortcut in the usual way The program is called SigNoise exe and is located in the C Xcalibur system programs folder It is possible to install this Macro as an item on the Tools menu of the Xcalibur Home page Select Tools Add Tools and select Add on the Add Programs to Tool Menu window Click on Browse in Locate Programs to be Added window and select SigNoise exe from the Xcalibur system programs folder Installation and Commissioning Guide 2 2 Mass Spectrometer Functional Verification Instrument Acceptance MS Q Acquisition of Specification Chromatograms The acquisition of Specification Chromatograms should follow the steps outlined in General Method on page 2 25 Positive ESI e Open the tune window click on File Open and select A Sensitivity Spec ESI Pos tune e Check that the parameters are the same as those shown in Fig 2 17 e Click on View Options This opens the Tune Options window e Using the button to the right of Acquisition filename browse through to C Xcalibur Installation Installation tests and type in Sensitivity Spec ESI ve raw Check that the Tune filename is A Sensitivity Sp
21. necessary to acquire and print out test results are l Select the appropriate mobile phase as specified in the tables on pages 2 20 2 23 Note the addition of ammonium hydroxide solution to the mobile phase when running APCI sensitivity tests 10 Il 12 Open the Tune window Open the appropriate tune file e g D Sensitivity Spec ESI ve tune Open the Tune Options Window assign an acquisition file destination directory and enter the appropriate file name Set Nitrogen Gas to On and Operate to On Start the HPLC pump If you are using Xcalibur to control the HPLC pump you will need to open the Xcalibur Home page first Check that there is a stable flow of ImL min Wait for the probe heater to reach the set temperature and then wait for the source enclosure to stabilize 5 minutes Start an acquisition using the Tune window acquisition facility Open the Xcalibur Roadmap Home page and open the Qual Browser Open the current acquisition file and observe the chromatogram In order to view data as it is acquired periodically press F5 Wait for a stable baseline and then make three Blank injections mobile phase at 30 second intervals Wait 1 minute and then make three Sample injections at 30 second intervals Wait 30 seconds Stop the acquisition using the Tune window control Install the Surveyor MSQ Signal to Noise Calculator if necessary and use it to measure sensitivity Save
22. of the MSQ see Connection 8 in Figure 1 11 2 Plug the other end into a suitable electrical wall outlet see Connection 9 in Figure 1 13 connections are complete J CAUTION Do not switch on the power until the installation and all ED N f A Installation and Commissioning Guide 1 27 Installing the MSQ Connecting the Vacuum System Exhausts Gas and Power MSQ 0 l fe isi o SOURCE S USERIVO e fe RESET o BACKING meng EXHAUST d A mains onor QO o PUMP OUT GAS IN 6 BARS MAX MAINS IN Figure 1 13 Power connection to the MSQ Note If your local area is subject to power fluctuations or power interruptions a power conditioning device or an uninterruptible power supply UPS should be installed in your laboratory See the topic Power Conditioning Devices in the MSQ System Pre installation Requirements Guide NOTE For European cables if supplied The Brown wire is the Live wire The Blue wire is the Neutral wire The Green Yellow wire is the Earth wire 1 28 Installation and Commissioning Guide E 0 N F Installing the MSQ MSQ Connecting the Vacuum System Exhausts Gas and Power Power Connection Checklist Is the power source correctly rated for the requirements of the MSQ Is the power cord terminated in a suitable plug Is the instrument plugged into the power source ED N f A Insta
23. on will allow the noise range to be specified with the left mouse button D I Invoke the About Box Plot Properties Displayed retention time range The largest peak in this range will be used as the base peak for the signal to noise calculation e E The retention time range to be used for the noise calculation minutes The scan filter describing this chromatogram This field can Scan Filter be left blank to specify a chromatogram that will incorporate all scan filters in the file Time Range minutes Chromatogram type this can be Mass Range TIC or Base Plot Type Peak When Mass Range or Base Peak is specified the Range s edit control will be available The mass or mass ranges to use when retrieving a mass range or base peak chromatogram This can take the form of Range s a single mass e g 272 a range e g 271 8 272 2 a mass sum eo 272 275 or combinations e g 272 274 8 215 2 Smoothing Enable Disable smoothing The type of smoothing to perform Boxcar or Gaussian The number of points to use when smoothing 3 10 Installation and Commissioning Guide ED N I H MS Appendices Appendix C Location of Calibration Reports Appendix C Location of Calibration Reports SN report File Edit View Favorites Tools Help lt Back gt 2 Qsearch G Folders lt Buistory AS OF XxX A S Goes Fe RE Folders Mame Size Type Modified ST Kr Desktop E Detec
24. parameter values in all the tune and calibration procedures will be correct for the supplied sodium iodide calibrant SOng uL Nal in 50 50 Instrument Preparation e Prior to performing either a Full System Autotune or a Standard Mass Scale Calibration the source must be configured for ESI acquisition and the MSQ Reference Inlet System must be prepared and ready For more information about configuring the source for ESI Ionization Mode view the supplied animations and the manual e The 250mL calibrant reservoir right hand side bottle should be filled with at least 200mL of standard calibrant Do not attempt to use with less than SmL of calibrant see Figure 2 9 e The HPLC pump should be set up to give a stable flow of 200uL min While any mobile phase should suffice acetronitrile H 0 is advised Installation and Commissioning Guide 2 11 Mass Spectrometer Functional Verification MSQ Instrument Autotune and Calibration If the calibrant reservoir has been emptied and re filled it will be necessary to prime the MSQ reference inlet system In order to perform a priming operation it is necessary to enter into the Tune window advanced parameter display F a E E SEET To display the advanced parameter set click on View Options in the tune window check the Show advanced parameters box in the Display section of the Tune Options window and click OK Do not change any other parameters Figure 2 9
25. suggested that the customer obtains 50mL of ammonium hydroxide solution SIGMA ref A 6899 prior to commissioning of the MSQ Supplied Samples The installation kit contains the Surveyor MSQ Sensitivity Test Kit this is available as a spare part P N FM104284 This contains two 25mL glass vials one of which contains 10mg of erythromycin and the other 10mg of p Nitrophenol Both samples should each be dissolved in 10 mL of solvent to give Imig or Img L stock solutions When refrigerated these stock solutions are stable for many months Installation and Commissioning Guide El N I H Me Appendices Appendix A Sample Preparation Required Samples 5pg yuL Erythromycin in 50 50 Acetonitrile Water The above are normally prepared from a 1 mg mL solution by successive dilutions of 20 1 100 1 and 100 1 2pg uL p Nitrophenol in 50 50 Methanol Water The above are normally prepared from a 1 mg mL solution by successive dilutions of 50 1 100 1 and 100 1 CAUTION Always wear protective gloves and safety glasses when you use solvents or chemicals Also contain waste streams and use proper ventilation Refer to the Material Safety Sheets MSDS for procedures that describe how to handle a particular solvent and or chemical Suggested Method for Sample Preparation Equipment required 1 x 10 mL graduated pipette 1 pipette filler 10 x 4 mL screw top polypropylene vials 1 x 1 mL fixed or adjustable pipettor 1 x 200uL adjusta
26. visit or very poor user impressions Even if the product is in good order a critical shortage can cause frustration and disappointment Pre Site Arrival Requirements Checklist Ensure that you have the done the following e Obtained a hard copy of the order e Obtained a hard copy of the site installation requirements signed and returned by the customer e Contacted the person who will be the customer representative during the installation e Established that the lab and person are ready to receive you e Established that the supply for the MSQ is 220 240 Vac 50 60 Hz and NOT 207 Vac Phase Phase 120 Vac e Ask customer to measure this voltage and note below e Measured Line Voltage e If the bench is back to the wall ensure that a 100 mm x 200 mm slot is to be cut through the surface at the rear to enable the vacuum hoses to pass through to the floor mounted backing pump e Establish very clearly the LC system with which the MSQ is going to be interfaced Installation and Commissioning Guide 1 3 Installing the MSQ Site Verification MSQ LC Equipment Third Party Accessories Please list the LC equipment and third party accessories below 1 4 Installation and Commissioning Guide ED l N F A Installing the MSQ MSQ Site Verification Post Site Arrival Requirements Checklist e Check with the customer that all items on the installation requirements are in place e The bench space is adequate for the M
27. 50 PM E Figure 2 13 The Xcalibur Home page road map view e Click on the Real Time Plot View button to activate the real time display see Figure 2 14 Figure 2 14 Default Real time Display The default presentation for the real plot gives a display showing a spectra above a chromatogram with an information pane to the left To display only 2 26 Installation and Commissioning Guide B N I A MSQ EDIONEX Mass Spectrometer Functional Verification Instrument Acceptance the chromatogram double click anywhere in the chromatogram display and click the Information Pane Button This gives a far clearer display as shown in Figure 2 15 Do Real Time Plot Home Page l 5 x File Actions View GoTo Help leie el mja AL Sl S odele Alm al el NL 9 29E4 TIC MS esiposO1 i i i i i i i i o o E oa ic 3 2 st o V g o E i i i 219 208 vu 2 34 289 324 378 392 440 4 92 507 5 62 613 6 30 6 58 7 00 7 38 7 66 7 90 4 0 Time min For Help press F1 NUM 27 09 2001 10 18 Figure 2 15 Chromatogram only display You may drag with the left button anywhere across the display to expand that section however the display will lock up and fail to update To release the lock select View Reset Display MSQ Signal to Noise Calculator The MSQ is shipped with the Signal to Noise Calculator installed on the desktop Just double
28. ESI ve specification SIM data acquisition A Sensitivity Spec APCI ve tune C Xcalibur Installation Installation tests Sensitivity Spec APCI ve raw APCI ve specification SIM data acquisition A Sensitivity Spec APCI ve tune C Xcalibur Installation Installation tests Sensitivity Spec APCI ve raw APCI ve specification SIM data acquisition A Sensitivity Spec ESI ve tune C Xcalibur Installation Installation tests Sensitivity Spec ESI ve raw ESI ve specification SIM data acquisition Table 1 Files for performance demonstration and installation acceptance tests The installation sensitivity test specifications are defined in the accompanying MSQ Installation Acceptance Form P N FM103826 2 18 Installation and Commissioning Guide DI N F MSQ Mass Spectrometer Functional Verification SSP formance Demonstration and Installation Acceptance Tests There follows a r sum of the methods and parameters used for the installation sensitivity test specifications Specification Tests This is a r sum of the methods and parameters used Fundamentally the sensitivity test consists of measuring the signal to noise ratio of a series of Loop Injection peaks on a free running chromatogram For an efficient installation it is most important that the loop injections be made by hand with a Rheodyne 7725 or similar injector A manual injection may be repeated at very short intervals thus enabling rapid opt
29. Exhausts Gas and Power MSQ Using suitable adapters connect the MSQ system to the nitrogen supply as follows 1 Cuta suitable length of the supplied 4 mm OD PTFE tubing 2 Screw the 4mm x 1 4 1in BSP half union into the adapter extending from the nitrogen supply source 3 Push one end of the 4mm PTFE tubing into the 4 mm 1 4 in BSP half union 4 Push the other end of the tubing into the inlet of the inline auxiliary pressure regulator NOTE The arrows on the back of the auxiliary pressure regulator indicate the direction of gas flow 5 Cut another suitable length of 4 mm OD PTFE tubing 6 Push one end of the 4mm OD PTFE tubing into the outlet port of the auxiliary pressure regulator 7 Connect the other end of the 4mm OD PTFE tubing to the inlet marked GAS IN on the rear of the MSQ system see Connection 7 in Figure 1 11 C K Ir crs o o o ar a fe uep JO SOURCE o S a o RESET BACKING oD EXHAUST k ft Auxiliary Pressure Regulator 5 MAINS ON OFF PUMP OUT amp GAS IN 6 BARS MAX MAINS IN Hl Je 3 wi f T z Figure 1 11 Source nitrogen connections 1 24 Installation and Commissioning Guide ED 0 N F MSQ Installing the MSQ Con
30. Full System Autotune and a Standard Mass Scale Calibration must be demonstrated along with tuning the instrument The user must also be shown how to change probe inserts and ion mode If the user s other HPLC system modules are to be controlled by Xcalibur the configuration and basic operation of these should be demonstrated Where unsupported equipment is to be used in conjunction with the MSQ the Service Representative must demonstrate the triggering of acquisition via the remote start input An animation of cleaning stripping and re assembling the ion source and hexapole is included with the system software This should be shown and demonstrated to the user together with the extensive Help system The user must be shown how to check the rotary pump oil and must be advised that it may require changing every 3 months Replacement of the oil filter must also be explained The user must be made aware that it may be necessary for Dionex Service personnel to change the turbo pump oil pads at yearly intervals The user should be shown how to set up and perform a basic LC MS acquisition and how to set up Sequence Lists Chromatogram and spectrum manipulation must be demonstrated an autosampler acquisition should be demonstrated if this option is fitted Installation and Commissioning Guide 2 15 Mass Spectrometer Functional Verification System Training MSQ System Training Checklist The following list is a checklist to ensure that t
31. Gas and Power MSQ 7 The design operating pressure is 75 psi although the MSQ may be operated with up to 80 psi in the ESI mode and less about 45 to 55 psi in the APCI mode Nitrogen Supplies Checklist Have the assembled fittings and tubing been checked for leaks L Was the system found to be gas tight Is the regulator set to between 75 and 80 psi 1 26 Installation and Commissioning Guide EN 0 N F MS Installing the MSQ Q Connecting the Vacuum System Exhausts Gas and Power Connecting Power Refer to the MSQ Pre installation Requirements Guide for information on power supply requirements The MSQ is delivered with four 2m IEC power leads Depending upon the country to which the instrument is to be shipped the free ends will be fitted with appropriate plugs or left with free wires that must be fitted with appropriate plugs As requested in the installation requirements 230 Vac and the PC and monitor cables are usually 115 Vac Make sure the N CAUTION For North American installations the MSQ and pump cables are 230Vac cables are well marked The supply requirements are 230 Vac regulated to 10 at 50 or 60 Hz Phase are NOT suitable If this is the situation contact the Dionex N CAUTION 207 Vac supplies i e 120 Vac 3 phase connected Phase Regional Office for information To connect the MSQ to a power supply 1 Plug the 3 pin IEC socket into the MSQ port marked MAINS IN on the rear
32. Guide 2 21 Mass Spectrometer Functional Verification Performance Demonstration and Installation Acceptance Tests MSQ Negative lon APCI Sensitivity Ionization Mode APCI ve Inlet Method Manual loop injection 50 50 methanol water fresh degassed Mobile Phase Optional containing 0 1 of 30 ammonium hydroxide solution Acquisition Parameters Negative Ion APCI Sensitivity Given in A Sensitivity Spec APCI ve tune S RT Probe Temperature 550 C Acquisition Time 0 to 20 min Peak Format Corona Current 30uA Acquisition Mode SIM 0 09 0 1 Span Ss Cone Voltage 2 22 Installation and Commissioning Guide el N F MSQ Mass Spectrometer Functional Verification Performance Demonstration and Installation Acceptance Tests Negative lon ESI Sensitivity Acquisition Parameters Negative Ion ESI Sensitivity Given in A Sensitivity Spec ESI ve tune S RT Probe Temperature 550 C Acquisition Time 0 to 20 min Peak Format none Sos Acquisition Mode si SIM 70V 0 09 0 1 B N I Installation and Commissioning Guide 2 23 Mass Spectrometer Functional Verification Performance Demonstration and Installation Acceptance Tests MSQ Preparation for Sensitivity Tests For an efficient installation it is most important that the HPLC pump should be primed and ready to run at 1mL min using the appropriate mobile phase NOTE Some HPLC pumps require a backpressure generator to be fitted to their out
33. OS PG O SE H LS Al Edwards Forepump Figure 1 4 Rotary vacuum pump connections Edwards 4 Connect the power cord of the Edwards rotary vane pump to the PUMP OUT receptacle in the lower right portion of the rear panel of the MSQ see Connection 3 in Figure 1 4 1 14 Installation and Commissioning Guide EN 0 N F MSQ a Installing the MSQ Connecting the Vacuum System Exhausts Gas and Power provided with the pump fill 1t up to the top mark on the inspection port on CAUTION The rotary pump is shipped with no oil in it Using the oil J the rotary pump Remember to check that none of the O ring seals have any small particles or dust on them as you assemble the rotary connections J WARNING Do not fail to fit some exhaust device the fumes emitted from the rotary pump are harmful Rotary Pump Connection Checklist Has the rotary pump been filled to the correct level with oil and the oil filler cap securely fitted Is the T piece fitted to the rotary pump inlet Have connections been made between the T piece and the backing hose and between the T piece and the source hose Has the rotary pump documentation been passed to the customer Have the rotary pump and source exhausts been connected ED N f A Installation and Commissioning Guide 1 15 Installing the MSQ Connecting the Vacuum System Exhausts Gas and Power MSQ Rotary Pump Exhaust The pump exhaust outlet w
34. SQ and peripheral equipment If the bench is back to the wall ensure that a 100 mm x 200 mm slot is cut through the surface at the rear to enable the vacuum hoses to pass through to the floor mounted backing pump e All gas supply regulators and gas lines are suitable and terminated in the correct clean tubing e The power supplies have been checked and measured as Vac Note this value in the Engineers Log e The exhausts are suitable e The air flow around the bench and instrument will be suitable e If any problems were encountered they have been reported to the factory and local office Unpacking and Initial Inspection Damage to Packaging Ask the user to show you all the boxes that were shipped with the instrument and then check all the external packaging for damage e g check the Tip and Tell indicators on the crates for evidence of rough handling or any obvious impact Check that none of the boxes have been opened or tampered with If external damage is apparent or there is evidence of tampering ensure that the user agrees and then mark this down on the installation report and ask the user to sign or initial next to your comments Where possible photographs should be taken of the damaged crate If the customer has not already contacted the appropriate Dionex office to report the damage do so immediately Note these on the Installation Report and notify Product Support in Sunnyvale ED N F A Installa
35. Show advanced parameters box in the Display section of the Tune Options window Close the MSQ doors and set the following parameters e Probe Temperature to 350 C e Nitrogen Gas to On e Operate to On e Allow the probe temperature to stabilize and then start the HPLC pump e Open the Tuning and Calibration Wizard by right clicking the server icon and clicking on Instrument Tune and Calibration see Figure 2 11 Instrument Tune and Calibration Tune Vert Exit ki 5 15 28 Figure 2 11 The server window e Select Full System Autotune and click on Next see Figure 2 8 page 2 9 The tune calibrate sequence will start and its progress will be displayed in the Instrument Tuning and Calibration window see Figure 2 12 e When you see the message Autotune has finished Successfully click on Finish and stop the HPLC pump flow e This mass calibration will become the Current Mass Calibration and will be used for all future acquisitions that is until the next successful calibration SI N I Installation and Commissioning Guide 2 13 Mass Spectrometer Functional Verification Instrument Autotune and Calibration MSQ Instrument Tuning and Calibration Full System Autotune Performance optimization and mass scale calibration Status Calibration In Progress Calibration Successty Autotune has finished Successtully Task Progress E Total Progress AeA Back Cancel
36. ally select the Standard Mass Scale Calibration option This achieves the specified accuracy over the range 172 9 m z to 1971 6 m z and approaching that over the range 60 m z to 2000m z Mass calibration is performed to improve the intrinsic accuracy and linearity of the Analyser from intrinsic errors of anything up to 8 m z to a Standard Deviation of lt 0 035 m z Maximum Deviation lt 0 065 m z Installation and Commissioning Guide EDI N F A MSQ EIDIONEX Mass Spectrometer Functional Verification Instrument Autotune and Calibration Mass calibration is achieved by acquiring a mass spectrum of known masses and comparing the measured masses with the known values This comparison generates a series of mass measurement errors which are then plotted against mass A curve is fitted to this plot from which a third order polynomial is generated This polynomial is saved and used by the mass scan generating circuitry to modify the otherwise linear ramp generating the mass scan Be aware that LM amp HM Resolution and Ion energy and RF lens Bias settings all influence the mass calibration greatly therefore it is essential that the user re calibrate if these settings are adjusted advanced tune only This does not apply if a Full System Autotune is being performed as this resets all parameters to default values including ion energy and Low and High mass resolution controls Performing a Full System Autotune The default
37. an installations where there will be two marked 230 Vac cords for the MSQ and two standard 115 Vac cords for use on the PC data system Shipment Verification Checklist Ensure that the following checks are carried out with the customer Damage to any of the boxes Any evidence of tampering or opening of the boxes Delivered items match the order L The MSQ is placed on the bench ready for installation with no evidence of tampering or damage L The data system is placed on the bench ready for installation with no evidence of tampering or damage rg CAUTION Any third party or customer software should not under any circumstances be loaded until the acceptance document is signed ED N f A Installation and Commissioning Guide 1 9 Installing the MSQ IQ OQ Test Optional Equipment and Software Data MSQ IQ OQ Test Optional Equipment and Software Data Where the optional System Validation Package is to be applied model numbers serial numbers and license numbers need to be recorded Some of these items can only be obtained from the operating system therefore the data system should now be plugged in to the line and switched on The following should enable the less obvious items of information to be located The references in parentheses refer to the IQ OQ Hardware IQ ref 4 1 PCs e Hard Disk Size Click on My Computer Local Disk C File Properties e Microprocessor Usually Pentiu
38. and so that you can access the drain plug to drain the filter o Fit the clamp over the flange and hand tighten 1 16 Installation and Commissioning Guide EN 0 N F MS Installing the MSQ Q Connecting the Vacuum System Exhausts Gas and Power Bonded Seal SCH Oil Mist Filter 1 T c Centring Ring Clamp a Adaptor O Ring Gas Ballast e M e Sp Exhaust Port Figure 1 5 Connecting the oil mist filter to the exhaust port 2 Connect the drain plug to the oil mist filter a Remove the drain plug and the bonded seal from the oil mist filter Gas Ballast Knob lt lt r Ws Gas Ballast Filters Port Circlip Figure 1 6 Removing the circlip wire mesh and filters ED N f A Installation and Commissioning Guide 1 17 Installing the MSQ Connecting the Vacuum System Exhausts Gas and Power MSQ b Place the bonded seal onto the drain adapter and then screw the drain adapter into the oil mist filter 3 Connect the hose adapter to the forepump a Remove the circlip wire mesh and filters from the gas ballast inlet on the forepump see Figure 1 6 Retain these parts for future use b Fit the O ring to the gas ballast adapter Then screw the gas ballast adapter into the gas ballast port on the forepump see Figure 1 7 Gas Ballast Knob a Bieser GEES Gas Ballast ITT Port DE Hose Adaptor d Ze O Ring Gas Ballast Adaptor Bonded l Bonded
39. as a bitmap and plot the results if possible Enter the results on the Installation Acceptance Form Real time display Xcalibur Road Map Home Page To start Xcalibur either Double click on the Xcalibur shortcut icon shown on the Windows desktop or Installation and Commissioning Guide 2 25 Mass Spectrometer Functional Verification Instrument Acceptance MS Q e Click on the Start button on the Taskbar and choose Programs Xcalibur Xcalibur Xcalibur displays the Home page with the road map view as shown in Figure 2 13 fe Hoad Map Home Page Mil E3 File Actons View Tools Golo Help JEE GA cessing P Setup Sequence K Real Time Plot Home Page of x File Actions View GoTo Help wae vlelml ws adeslczl vale a al Status Acquisition Queue Le Nk V 9 2364 Run Manager wl MV TIC Ms Check Devices hecht Sequence Sample Name Working On Position Raw File Inst Method TRACE GC 2000 Initializing moo osom aget agis tay 208 Rasan 2e fisar mmm ug agal 480505 51 She 561 gy ea Ip 100105 138 mm a Tit eee pee ee pete ep ee ee ee Pee ee ee ee ee ge ee Pd ep ee ed a pe ae ee ee et et rp esipos0l 2240 RT 009751 WU NESTED 8 WD ESI sid SM ms 734 46 734 55 30 00 gt 4 I i 4 LA Relative Abundance nm I i LA 7341 734 2 7343 7344 7345 734 6 1347 734 8 134 9 miz For Help press F1 NUM 10 10 01 5
40. ation will be the highest peak currently visible in the display In order to specify a different peak use the left mouse to zoom in on an area as described in Step 4 and make sure that the desired peak is the largest in the display The display range can be restored to show the full chromatogram at any time simply select the Chromatogram Zoom Reset menu item or its equivalent toolbar button NOTE The noise range can be re specified and the display range updated with the mouse until the desired results are obtained by repeating Steps 4 and 5 Each time a new noise range or display range 1s selected the signal to noise values will be updated accordingly 7 To print the results select the File Print menu item or click on the toolbar button Toolbar Invoke the Raw File Open dialog box Print the currently displayed chromatogram and calculation results Copy the current chromatogram and calculation results to the Clipboard as a metafile Zoom the chromatogram display in Zoom the chromatogram display out Installation and Commissioning Guide 3 9 Appendices Appendix B MS Q MSQ Signal to Noise Calculator Kad Reset the chromatogram to show the full range on the x axis Reset the chromatogram to show the full range on all axes std Invoke the Chromatogram Ranges dialog box ff ts a Toggle the noise range selection As an alternative to using the right mouse button toggling this button
41. ble pipettor 100mL beaker Sample Preparation Erythromycin 5pg uL Note The first dilution of this sample is made with 100 acetonitrile This is to avoid the rapid deterioration of your base solution which then should be stable under refrigeration for several months e Add 10 mL acetonitrile to the supplied erythromycin sample vial El N I H Installation and Commissioning Guide 3 3 Appendices Appendix A MS Q Sample Preparation e Close cap and shake until the sample has completely dissolved This gives a stock solution of Img mL or Ipg Jul Prepare your mobile phase by mixing 400mL acetonitrile with 400mL of HPLC water in the pump mobile phase bottle and sonicating for 10 minutes Decant 100ml of this to the beaker for use in the following dilutions e Decant from this 4ml of mobile phase to each of two of the 4 mL screw top polypropylene vials Label one Blanks and the other Wash e Label three of the remaining vials Note There is a Word document on the Engineers disk called sample labels This will print S0ng uL Erythromycin S00pg uL Erythromycin all the required labels on to a 8 Sen sheet of Avery 35mm slide Spg HL Erythromycin labels L7656 50ng uL solution e Using the ImL pipettor transfer 2mL of mobile phase to the 50ng nL vial e Using the 200uL pipettor remove and dispose of 200uL of mobile phase from this vial e Change the 200uL pipettor tip
42. bration This section describes the procedures that must be performed prior to running the Sign off sensitivity tests There are no manual adjustments available on the MSQ all setting up is done via the Xcalibur user interface 1 e no pre sets Overview The MSQ 1s provided with a comprehensive Autotune system that offers two levels of fully automatic system tuning and mass calibration namely Full System Autotune and Standard Mass Scale Calibration as shown in the Tuning and Calibration Wizard Figure 2 8 At installation the Full System Autotune should be made and demonstrated to the end user Once set up the MSQ is extremely stable in the region of 0 05 m z C In a normal air conditioned laboratory it will rarely if ever need re calibration the rational criterion for re calibration is a noticeable small drift in mass accuracy In spite of this however recognized practice frequently demands system calibration prior to batch processing Instrument Tuning and Calibration Welcome to the Instrument Tuning and Calibration Wizard This wizard guides you through the steps required to gain maximum performance from your instrument Full System Autotune Standard Mass Scale Calibration Acoess to instrument tune allowing you to manually optimize or modify the system settings for your samples Back Cancel Figure 2 8 Tuning and Calibration Wizard SI N I Installation and Commissioning Guide 2 9
43. e 2 Remove the pump access plate securing screws using a No 1 point Posidrive screwdriver 3 Remove the access plate 3 14 Installation and Commissioning Guide El N I MSQ Appendices Appendix F Pfeiffer Pump Oil Reservoir Change 4 Unscrew the locking cap using the supplied locking cap removal tool turn counterclockwise 5 Remove the cap including the O ring and wipe with a clean lint free cloth Place somewhere secure SI N k Installation and Commissioning Guide 3 15 Appendices Appendix F MSQ Pfeiffer Pump Oil Reservoir Change 6 Using a small flat bladed screwdriver gently prise out the lubricant reservoir including the O ring and dispose of safely 7 Using a clean lint free cloth remove any dirt 3 16 Installation and Commissioning Guide El N I H MSQ Appendices Appendix F Pfeiffer Pump Oil Reservoir Change EDIONEX Replacement Procedure The replacement procedure is essentially the reverse of the removal Tools amp parts Locking Cap Removal tool Thermo Finnigan P N FM104442 Pfeiffer P N SUMP LEVER TOOL Pfeiffer replacement oil wick Thermo Finnigan P N FM104398 Pfeiffer P N PM 063 265 T Installation and Commissioning Guide 3 17 Appendices Appendix G MSQ MSQ Service Tools Bill of Materials P N FM103865 Appendix G MSQ Service Tools Bill of Materials P N FM103865 Supplier Description Description Part Nu
44. e ratio of the analyte peak height to the RMS noise from a continuous section of the chromatogram after the application of appropriate smoothing In each case the peak width should be less than 0 15 minutes wide at half height and the solvent blank less than 20 of the sample peak Electrospray ve ion sensitivity Loop injection of 10ul of a 5pg ul solution of Erythromycin in 50 50 acetonitrile water into an LC flow of 1 ml min of 50 50 acetonitrile water will give a signal noise ratio of gt 1000 1 monitoring m z 734 5 in SIM mode after appropriate smoothing m z 734 5 from Erythromycin gt 1000 1 Demonstrated Result include screen capture of results Electrospray ve ion sensitivity Loop injection of 10ul of a 2pg ul solution of p Nitrophenol in 50 50 acetonitrile water into an LC flow of 1 ml min of 50 50 methanol water will give a signal noise ratio of gt 500 1 monitoring m z 138 in SIM mode after appropriate smoothing m z 138 from p Nitrophenol gt 500 1 Demonstrated Result include screen capture of results APCI ve ion sensitivity Loop injection of 10ul of a 5pg ul solution of Erythromycin in 50 50 acetonitrile water into an LC flow of 1 ml min of 50 50 acetonitrile water will give a signal noise ratio of gt 200 1 monitoring m z 734 5 in SIM mode after appropriate smoothing m z 734 5 from Erythromycin gt 200 1 Demonstrated Result include screen capture of results APCI ve ion sensitivity Loop injec
45. eanbi4 CAFC Ausuaqyy Lop up CR L au uouajay yea asp 80 90 ro 0 00 igo NI Sen ern SLO son 690 SPO ar 0S 09 SIUVEPUNGY saAyejay OL 08 06 Oot Bl WS 906 000 La gJNISZ a Mole ene S dja pDOeuouUD mak 07 op 4072 NIE asiON O1 jeUBIS AWUOINISAa E EDIONEX Installation and Commissioning Guide 2 36 MS Mass Spectrometer Functional Verification Q Instrument Acceptance Instrument Acceptance Sign off Liability This topic has two clear areas that is unless the customer has contractualised otherwise 1 Those tasks which must be completed and those functions that must be demonstrated before the Service Representative should reasonably request signing of the acceptance form 2 Those tasks that must not be performed before sign off this includes the installation of third party software Those tasks which must be completed before Sign off In addition to proving the sensitivity of the spectrometer and the tasks outlined in Section 2 5 System Training it 1s requisite of the Service Representative to install and verify all connections for supported HPLC systems when supplied as accessories They must establish communication with the customer s HPLC system and at least three samples should be run if an autosampler is being controlled If the customer s HPLC is not supported the Service Representative must demonstrate how an acquisition on the MSQ may be triggered by
46. ec ESI ve tune see Figure 2 16 and that the check boxes in Display are selected as shown Click OK Tune Options q Surveyor MSQ Tune Options Configure the tune and display parameters Tune Number of tune masses Acquisition filename Installation tests Sensitivity Spec ESI verany Tune filename A MSensitivity Spec ESI Ave tune m Filed traces Show advanced parameters Cancel Help Figure 2 16 Tune Options window e Using a lm flow of 50 50 acetonitrile H O continue with the steps outlined from the general method Step 3 page 2 25 Typical results are shown in Figure 2 18 2 28 Installation and Commissioning Guide B N I A z S S ID om O F oO SO Gel cc oo Sa E d 5 ce 5 uge o re D bna D 5 K O S Go Lo gt sJajawesed uolisinboe out SF Uu MOPUIM OUNL Z Z anbi4 WH 295753449 000000 Apeay quiodjas 0 08 aa 020 MIS 00 02 600 DSPE E KE EES joun wooy 9PH auo eyo uy ueos yeunogyeag 1H uede sW awe N ppo OEGHEZ OcGHEZ OLlStEL OOS ree Obr Pee Otte Oe Pes OOF Fee T co D 000S a ef apo IW UOUS ZOO ng epp USGOn ajyeado 6 jonu je12u32 5 Lu aui Hondaa 01u07 uoisinbay AM abaan Cl am adup 20017 OO D Wd 000 800 0 IdE deiere IOIIOT aun j L LUU0DO 2 1 yseqpeay uonduasaq NI Oeng 4040 ele Ciel daH weih ally EG UE KE ACEN J
47. eck that the Needle kV Readback matches the set value 10 Check at e Using the Tune Window Scan Event Editor Figure 2 7 check the following Scan Time Polarnty Cone Rdbk l oom On Off 1 00 e 100 0 Woo Figure 2 7 Part of the tune window Scan Event Editor e The Cone Voltage readback follows the set value 10 Check at and 200V 180V 220V e Open the source door and check that the indicator LED on the front of the MSQ changes to steady yellow e Close the source enclosure again Once the above checks have been completed set the cone voltage to 25V the probe temperature to 20 C and then switch both operate and API gas off Installation and Commissioning Guide 2 Mass Spectrometer Functional Verification Powering Up MSQ Mass Spectrometer Functional Verification Checklist E The instrument is correctly configured for ESI E The instrument has been powered up successfully with the expected initial status 1 e read backs and front panel LED display E The system has achieved vacuum and the front panel LED display indicates the status of the system The system has passed the basic operate off tests D D The system has passed the basic operate on tests Date Completed Service Representative s Initials 2 8 Installation and Commissioning Guide DI N F MSQ Mass Spectrometer Functional Verification Instrument Autotune and Calibration Instrument Autotune and Cali
48. eeees 2 10 Performing a Full System Autotune ccccccccccccccececceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee es 2 11 Instrument Preparation cc ccccccccccssssseeeeeseeeeeeeeeeeeeeeeeeaaeseeeeeesseeeseeeeeeeeeeeeeeeeeeaaaags 2 11 Failure to Autotune Mass Calbrate 2 14 Basic Instrument Operation Checker 2 14 DY SECM a a eege 2 15 BG CG ara A E E 2 15 SS NERT E E EE 2 16 ROUGNS Maintenant ss sswscis2rccverinesmveususostorrenseanteduceussdcaeasnswebedandecteatneaetatsteddseaenenwteds 2 16 purveyor MSO Flow Syste egene ege 2 16 EE 2 16 SI OPE e 2 17 Performance Demonstration and Installation Acceptance Tests 2 18 Eet CC te 5 oe PE E P E N E AN A T TE ET T aes 2 18 DP Cll CAMO TA EE 2 19 Tune Window Acquisition Facility oo cccccccscscccccceceeceeeceeeeeeeeeceeceeeeeeeeeeeeeeeess 2 19 Method for all ionization modes ccccceececccccccceeeeeeeseaeeeseeeeeeeececcceeeeeeeeeeaaaaas 2 20 Settings and Parameters for Qualification ccecssesssseseeceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeess 2 20 Positive lon ESI Sensitivity eege 2 20 I Installation and Commissioning Guide El N I H MSQ Contents Positive Ion AP CLS Sms 0 EE 2 21 Negative om APCI Sensitivity cc cccsssncnnonsarraxesannnenornadnsnadaaqsbnerdavbasehsaustnoneadhanenenuseandees 2 22 Negative lon Blende 2 23 Preparation for Sensitivity KE 2 24 Seting up an X calbur ACO UISIUl ON osre riseire riina ione N EE EEEE EEEE 2 24 TARO e E 2 24 TMC UA VIC
49. en using the ImL pipettor add another 2mL of mobile phase Shake well This gives a solution of 20ng uL 200pg uL solution e Using the ImL pipettor transfer 2mL of mobile phase to the 200pg pL vial Using the 200uL pipettor remove and dispose of 40uL of mobile phase from this vial e Change the 200uL pipettor tip and transfer 40uL of the 20ng pL solution to the vial Then using the 1mL pipettor add another 2mL of mobile phase Shake well This gives a solution of 200pg nL 2pg uL solution e Using the lmL pipettor transfer 2mL of mobile phase to the 2pg uL vial Using the 200uL pipettor remove and dispose of 40uL of mobile phase from this vial e Change the 200uL pipettor tip and transfer 40uL of the 200pg pL solution to the vial Then using the 1mL pipettor add another 2mL of mobile phase Shake well This gives the ve APCI test specification solution of 2pg nL 3 6 Installation and Commissioning Guide El N I H MSQ Sample Preparation EDIONEX Appendices Appendix A Calibration Solution The Surveyor MSQ Sensitivity Calibration Solution P N FM104285 is composed of 50 mg sodium iodide resulting in 200 ng uL 0 25 mg desoximetasone a corticosteroid Sigma D6038 resulting in 1 ng uL 250 mL of 50 50 isopropyl alcohol water Instructions Wash the plastic bottle thoroughly with boiling water Add 250 ml of the 50 50 by volume IPA water solution to a clean glass beaker Weigh out
50. he customer receives adequate training Please complete this checklist and the list on the Installation Acceptance report Routine Maintenance E Rotary pump oil inspection and changing E Changing the oil filter Busch pump only E Frequency of these operations MSQ Flow System E Using the MSQ cone wash system during LC acquisitions E Sample infusion from a syringe pump on request Instrument Operation Start up and shutdown of the system Configuration of the system Starting Xcalibur software Starting the vacuum system and venting the vacuum system Operating the animation software Removing and swapping probes Replacing the probe capillary including use of the protrusion gauge to reset capillary protrusion Removing and cleaning the source Removing and cleaning the hexapole Connecting the source to an LC pump Tuning the ion source in ESI and APCI LU UUUU UUU OODD LU Performing a Full System Autotune 2 16 Installation and Commissioning Guide DI N F MSQ EIDIONEX Q Q Mass Spectrometer Functional Verification System Training Performing a Standard Mass Scale Calibration Using the Product Portfolio and Xcalibur manuals Software Operation Q Q Date Completed The use of Xcalibur Tune to optimize instrument parameters Using the Tune Window or Instrument Setup method editor together with Sequence Setup to acquire data in Centroid Profile MCA and SIM formats Using Sequence Se
51. ill preferably be at atmospheric pressure Connection to a direct extraction system with too great a negative relative pressure will result in excessive oil consumption CAUTION The rotary pump exhaust should NEVER be connected to the source exhaust To do so could possibly result in SEVERE DAMAGE which would not be covered by any warranty in place at the time CAUTION Damage can be caused to the rotary pump or the exhaust plumbing by the initial surge of exhaust if the line is blocked or shut off Busch Pump The Busch pump is supplied with 3 m of 3 8 OD tubing for the rotary pump exhaust The exhaust from the rotary pump should be directed out of the room to atmosphere or into a fume hood Edwards Pump 1 The Edwards venting system is more complex than the Busch system It consists of an oil mist filter kit connected to the exhaust port of the Edwards pump a Turn off the power to the Edwards pump Disconnect the power cable b Use pliers or a wrench to remove the brass pipe fitting extending from the exhaust port of the pump Clean the area around the exhaust outlet d Fit the O ring to the adapter into the exhaust port outlet and hand tighten Do not over tighten the adapter or you will damage the O ring seal e Fit a centering ring to the adapter as shown in Figure 1 5 f Position the flange of the oil mist filter on the centering ring Rotate the filter assembly so that the oil level sight panel is visible
52. imization of the acquisition parameters The above does not preclude the use of an autosampler indeed this may be required to finalize the acceptance However the lack of a manual injector may delay installation considerably if there are problems Finally in all cases the Service Representative should use a known good 10uL loop NOTE As yet no specification exists for the chromatographic performance of an MSQ combined with an HPLC column Tune Window Acquisition Facility While it is assumed that the Service Representative will be sufficiently familiar with Xcalibur to use the sequence editor to set up and obtain an acquisition for the sake of simplicity all acquisitions for the specification tests will be made using the Tune window acquisition facility The Xcalibur Real Time Display should be used to observe the chromatogram Following acquisition the signal to noise ratio sensitivity will be determined using the MSQ Signal to Noise Calculator SigNoise exe Signal to noise given here is the ratio of Peak Signal to RMS Noise where signal is the average intensity of three peaks and noise is the RMS value of 100 scans Method for All lonization Modes Acquisition should be made from the Tune window Using the manual injector make three Blank injections followed by three Sample injections SI N I Installation and Commissioning Guide 2 19 Mass Spectrometer Functional Verification Performance Demonstrat
53. ion and Installation Acceptance Tests MSQ Stop the acquisition manually Using appropriate data processing measure the signal to noise ratio e The area of each of the three sample peaks should be within 10 of the value of the greatest of the three e No Blank should exceed 20 of the height of the Sample peaks e Plot where possible and save results to the C Xcalibur installation Installation tests folder Settings and Parameters for Qualification Positive lon ESI Sensitivity Ionization Mode ESI ve ive SS Acquisition Parameters Positive Ion ESI Sensitivity Given in A Sensitivity Spec ESI ve tune N RT 0 to 20 Probe Temperature 550 C WEE Tine Peak Format Needle 1 5kV Acquisition SIM Mode 0090 1 le Cone Vas 2 20 Installation and Commissioning Guide DI N F MSQ Mass Spectrometer Functional Verification Performance Demonstration and Installation Acceptance Tests Positive lon APCI Sensitivity Ionization Mode APCI ve Inlet Method Manual loop injection 50 50 acetonitrile water fresh degassed Mobile Phase Optional containing 0 1 of 30 ammonium hydroxide solution Acquisition Parameters Positive Ion APCI Sensitivity Given in A Sensitivity Spec APCI ve tune o e to de Probe Temperature 550 C ite Time Corona Current Peak Format Ee Mode Ionization Ionization Mode Ap Sean me Time 02s 2s 0 09 0 1 wl Cone aa SI N I H Installation and Commissioning
54. level with the factory supplied oil PN 062746 or P N 062747 For more detailed information on these procedures refer to the manual that comes with the forepump or the MSQ Hardware Manual The rotary pump KF25 T piece and all the fittings for connecting the rotary will be in the rotary pump box Place the pump in a location with reasonable ventilation Installation and Commissioning Guide 1 13 Installing the MSQ Connecting the Vacuum System Exhausts Gas and Power MSQ Refer to the topic Connecting Exhaust Lines for information on connecting the rotary pump exhaust 1 Connect the T piece to the rotary pump with a KF25 centering ring and clamp 2 The backing lines labelled SOURCE and BACKING should then be connected to the T piece on the rotary pump using KF25 centering rings and clamps see Connections 1 and 2 in Figure 1 4 3 Ifnot already fitted a suitable 230V power connector for the locale should be fitted to the mains lead to the MSQ The MSQ connection will be used to connect the pump to the mains supply Connection 1 Source to Forepump Connection 2 Backing to Forepump Connection 3 Forepump power plug to PUMP OUT receptacle SOURCE G7 Start In Start In USER UO doi Ready Out RESET E H olo MAINS ON OFF QO 3 elle PUMP OUT Power Supply GAS IN to RotaryPump o 6 BAR MAX MAINS wl Je Surveyor MSQ System Exhaust Port E ij P
55. llation and Commissioning Guide 1 29 Installing the MSQ LC MS Interconnections MSQ LC MS Interconnections Connections to the Data System The MSQ is connected to the data system using a USB cable This is connected between the USB connector at the rear of the MSQ and one of the ports at the rear of the PC see Figure 1 14 j j E Ell d o SOURCE o USER I O O RESET m O MAINS ON OFF QO o PUMP OUT GAS IN 6 BARS MAX e MAINS IN Data System Computer Dell Model Surveyor MSQ System Figure 1 14 Data system connection the MSQ requires the full capacity of their hub for these two ports Any user supplied devices requiring USB should be fed from a separate hub Note Only one of the two USB ports at the rear of the PC must be used 1 30 Installation and Commissioning Guide DI 0 N F MSQ EDIONEN Installing the MSQ LC MS Interconnections Series A Socket Series B Socket Series A Plug Series B Plug Connections to the LC IC Equipment The connection to the Dionex LC IC equipment will be through either the Chromeleon or PeakNet interface Make sure that Chromeleon PeakNet
56. log box will appear as shown in Figure 3 1 Chromatogram Ranges Plat Properties Time Range minutes baus OOOO Noise Range minutes om rr Scan Filter Fe Plot Type TIC hd Aangel m Smoothing PR Enable pe Figure 3 1 Chromatogram Ranges dialog box 4 Change the Plot Type to read Mass Range and type the required mass in the Range s edit control For example in order to display a mass chromatogram over a short span around mass 272 enter 271 8 272 2 Installation and Commissioning Guide El N I H MSQ Appendices Appendix B MSQ Signal to Noise Calculator EDIONEX Click the OK button to close this dialog box and wait a moment while the mass chromatogram is generated The noise range must now be specified in order for the signal to noise calculation to be performed By clicking on the trace with the left mouse button dragging the mouse left and right over the required time range and then releasing the button it is possible to zoom the display to a specified region Performing the same action with the right mouse button will specify a region to use for the noise calculation Once a noise range has been specified and provided that there are sufficient scans in the range for the calculation to take place the signal to noise calculation will be performed and the results shown at the bottom of the main window The base peak used for the calcul
57. m III as shown on the front panel is sufficient although more details are available from the same page as the next item e Memory Size Click on Windows Explorer My Computer File Properties The size will be found on the General tab listed as RAM e BIOS Date and Revision Start Programs Accessories System Tools System Information The date and revision will be found in the System Summary folder PC Monitors There is so little information on the exterior of the monitor that reference should be made to the accompanying handbook Note The normal default size is 17 inches 1 10 Installation and Commissioning Guide EN 0 N F MSQ EDIONEN Installing the MSQ IQ OQ Test Optional Equipment and Software Data Software IQ ref 4 2 Xcalibur Core The serial number is in reality a license number To find this Start Xcalibur core and click on Tools Configuration choose the Customer Info tab and click on the License Button The Version number may be found in the usual location i e Help About Home Page Microsoft Office Click on Start Settings Control Panel double click on Add Remove Programs click on Microsoft Office 2000 Premium and then on support information The Version and Serial No will be found here Installation and Commissioning Guide 1 11 Installing the MSQ Connecting the Vacuum System Exhausts Gas and Power MSQ Connecting the Vacuum System Exhausts Gas and Powe
58. mber Tool Kit case RS Small tool case SR RS 647 053 Hand Farnell Xcelite 99 1V SH Farnell 441 521 Farnell Xcelite 99 5 5mm 5 5mm Nutdriver blade Farnell 442 161 Farnell Xcelite 99 7mm Nutdriver blade 7mm Farnell 442 185 Farnell Wiha Handle Driver Handle Farnell 109 205 Farnell Wiha 2 5mm hex ball hex driver 2 5mm hex driver ball hex driver Farnell 109 183 S Wiha Farnell 109 187 Farnell Wiha 3mm hex ball hex driver 3mm hex driver ball hex driver Farnell 109 184 S Wiha Farnell 109 187 Farnell Wiha 5mm hex ball hex driver 5mm hex driver ball hex driver Farnell 109 186 S Wiha Farnell 109 187 Farnell Wiha 6mm hex ball hex driver 6mm hex driver ball hex driver Farnell 109 187 S Wiha Farnell 109 187 Farnell Wiha No 1 Pozidriv No 2 Pozidriv Double Ended driver blade Farnell 109 180 S Wiha Farnell 109 187 Farnell Wiha 6mm slot 6mm Flat bladed amp 4mm slot Double Ended 4mm Flat bladed Screwdrivers driver blade Farnell 109 174 5 No 1 Pozidriv No 2 Pozidriv Screwdrivers 3 18 Installation and Commissioning Guide ED N I H MSQ Appendices Appendix G MSQ Service Tools Bill of Materials P N FM103865 Wiha Farnell 109 187 10 ded aner Farnell BACHO 111M 10 mm open ended spanne 707 6447 Farnell Ergo 2 5x50 slot 2mm FB Screwdriver head 723 7777 HPLC Spanner Ya AF x 5 16 AF SI N k Installatio
59. means of an external contact closure Those tasks that must not be performed before Sign off These include connecting to a LAN installing additional hardware PC drives etc and especially the customer s own or third party software EI N I A Installation and Commissioning Guide 2 3 Mass Spectrometer Functional Verification Additional Options MSQ Additional Options Chromeleon or PeakNet Any additional options ordered with the system should be installed and verified Refer to the instructions for the various types of options 2 38 Installation and Commissioning Guide B N I A Me Mass Spectrometer Functional Verification Q Connecting the MSQ to the HPLC System Connecting the MSQ to the HPLC System Supported Systems Following commissioning the customer may reasonably expect you to demonstrate the acquisition of a few loop injection chromatograms For those not familiar with this first review the appropriate sections in the MSQ Getting Started manual viewable via the Xcalibur Documentation desktop shortcut and the appropriate sections in the Chromeleon or PeakNet manuals EI N I A Installation and Commissioning Guide 2 39 Mass Spectrometer Functional Verification Connecting the MSQ to the HPLC System MSQ 2 40 Injection Contact Closure Provided that the injector on the system can provide a contact closure of gt 100 ms and less than the acquisition time there is no reason why an MSQ acqui
60. n and Commissioning Guide 3 19 Lech Ss Dsg tte me weg r Les DIONEX MSQ Installation Acceptance Form Purpose This document is an acknowledgement by the customer that all of the following tests or items have been successfully demonstrated during the period of the installation MSQ Acceptance Form FM103826D System Training Hardware The engineer installing the MSQ will demonstrate the following Completed Start up and venting the vacuum system long term Start up and shutdown of the system short term Rotary Pump maintenance Setting up flow Starting the software Xcalibur Server Running the MSQ in both modes ESI and APCl Use of Xcalibur Tune to optimize instrument parameters Removing and swapping probe inserts Connection of LC IC to the MSQ Setup of Cone Wash Optional How to run the animations How to perform a mass calibration Automated Tuning and Mass calibration completed The engineer installing the MSQ will demonstrate the following Completed Setting up Instrument Configuration Using CHROMELEON to setup Timebase Using CHROMELEON to setup acquisition sequence Using CHROMELEON to setup a program file Using CHROMELEON MS to acquire data Full Scan and SIM Using CHROMELEON MS to display data Making a Report Form Libraries and Library Search Optional Introduction to CHROMELEON Help Screens Acceptance Signal to Noise Sensitivity Th
61. necting the Vacuum System Exhausts Gas and Power Checking for Air Leaks Check the gas supply system for leaks as follows l Zz Prepare a test solution of 50 50 isopropanol water v v Set the pressure to 10 psi by pulling out the regulator adjuster on the auxiliary pressure regulator and then turning clockwise see Figure 1 9 a When the regulator reads approximately 10 psi push the adjuster into its locked position b Apply the test solution to all the joints between the regulator and the MSQ Ensure that no test solution enters the MSQ via the gas inlets The test solution will indicate a leak by foaming If any foaming of the test solution is observed tighten the connection until the foaming stops or replace the connection Increase the pressure to 50 psi Then check for leaks a Ifthe system is airtight go to Step 5 b Ifyou find a leak return to Step 3 Increase the pressure to 100 psi Then check for leaks a Ifthe system is airtight go to Step 6 b Ifyou find a leak return to Step 3 After you have determined that the system 1s airtight reduce the pressure of the nitrogen gas supply line to 75 psi The recommended Operating pressure required for the gas inlet on the rear of the MSQ is 75 to 80 psi as shown in Figure 1 12 Figure 1 12 Auxiliary pressure regulator set to 80 psi EDIONEN Installation and Commissioning Guide 1 25 Installing the MSQ Connecting the Vacuum System Exhausts
62. nfirms that all checklists have been fully verified and that the MSQ is installed and now ready for commissioning Date Completed Service Representative s Name Service Representative s Signature ED N f A Installation and Commissioning Guide 1 33 Installing the MSQ LC MS Interconnections MSQ 1 34 Installation and Commissioning Guide EN 0 N F sw Te Xcalibur Documentation Product Portfolio EDIONEN Section 2 Mass Spectrometer Functional Verification Introduction This section describes the procedures necessary to fully commission an MSQ Mass Spectrometer Detector It should be noted that the format of this manual assumes a basic prior knowledge of Xcalibur software The sequence of actions is as follows e Configuring Xcalibur for the MSQ and if necessary the HPLC pump e Switching on powering up the MSQ and pumping down e Preparing for and executing a full system auto tune e Running the acceptance sign off tests e Training the operator on the basic operation of the MSQ e Training the operator on the basic operation of Chromeleon PeakNet Throughout the entire sequence the principal operator who will be responsible for the day to day running of the MSQ should be present as these procedures represent a significant part of the basic training schedule Getting Started Service Representatives should view the Getting Started manual via the Xcalibur Documentation desktop shortcut
63. om one of the following sources e A large nitrogen gas cylinder size 1A 250 ft 3 Replacement frequency Approximately every two days e A large sealed thermally insulated cylinder containing liquid nitrogen from which the nitrogen is boiled off The 230 psi model is recommended A typical cylinder of size 240 L yields 143 850 L 5 080 ft 3 of gas Replacement frequency Approximately every month e A nitrogen generator with minimum capacity of 5 560 L 200 ft per day at 99 purity with 100 psi at the side panel Worst case consumption of nitrogen gas is 10 L min Replacement frequency Continuous source with no replacement required To make an airtight connection to the nitrogen gas supply perform the procedures that are found in this section e Connecting the Nitrogen Supply to the MSQ System e Checking for Air Leaks Connecting the Nitrogen Supply to the MSQ System Nitrogen enters the MSQ system by way of an inlet labeled GAS IN on its rear The MSQ system is supplied with the following gas line connections e 3mof4mm OD PTFE tubing e Auxiliary pressure regulator e 4mm x 1 4 in BSP half union e You will need to supply suitable adapters to connect your gas line to the 4 mm x 1 4 in BSP half union Note Liquid nitrogen conversion factors e 1 0 lb of liquid nitrogen 0 5612 L e 1 0 kg of liquid nitrogen 1 237 L Installation and Commissioning Guide 1 23 Installing the MSQ Connecting the Vacuum System
64. om the solvent trap should be directed out of the room to atmosphere or into a fume hood The source exhaust solvent trap outlet must be at atmospheric pressure Ombar 100mbar Connection to a direct extraction system with negative relative pressure will reduce sensitivity considerably ED N f A Installation and Commissioning Guide 1 19 Installing the MSQ Connecting the Vacuum System Exhausts Gas and Power MSQ CAUTION It is absolutely essential that the outlet of this exhaust be well separated from the rotary pump exhaust outlet The two exhausts should NEVER be connected together as this could possibly cause SEVERE DAMAGE This damage would not be covered by any warranty in place at the time Connection 4 Connection 5 Connection 6 Figure 1 9 Connecting exhaust lines from the source and rotary pump correct setup EDIONEX 1 20 Installation and Commissioning Guide MS Installing the MSQ Q Connecting the Vacuum System Exhausts Gas and Power Incorrect Setup USB D If the tubing is above the exhaust outlet o SOURCE o the solvent condensing from the exhaust AAN usero F gases can flow back into the instrument GC EXF AUST PUMP OUT GAS IN 6 BARS MAX o ven HK Surveyor MSQ System Solvent Trap xX x Solvent can collect here 77 gt Solvent Trap Solvent Trap Figure 1 10 Connecting exhaust lines from the source and
65. onal Check Operate ON While under normal conditions the system will pump down and give a solid green light in a few minutes the Initial Pump Down following shipment or following a prolonged period out of vacuum must be allowed to continue for at least 1 hrs before switching the instrument to Operate In some circumstances especially when the instrument has been stored in a high humidity environment it is strongly advised that the system be left to pump down overnight in order to remove all moisture CAUTION Due to the very high voltages present moisture in the instrument will cause breakdown and serious damage to the MSQ If the preceding advice is kept in mind when the installation is planned it should not prove difficult to schedule an overnight pump down Once you are satisfied with the vacuum proceed with the following e Switch on the API gas using the Nitrogen Gas button on the tune window parameter table see Figure 2 6 e Click the Operate button in the tune window parameter table e Check that the indicator LED on the MSQ door and the server icon both turn green Installation and Commissioning Guide EDI N f A MSQ EIDIONEX Mass Spectrometer Functional Verification Powering Up e Set the Probe Temperature to 250 C and check that the Readback is correct e Set the Probe Temperature to 550 C and check that the Readback is correct e Return the probe heater to 20 C e Ch
66. or 45 CC Surveyor LC Pump I Surveyor MS Pump Surveyor MSQ CH Autotune G Calibration w Settings e Surveyor Sample Pump EI TSP Surveyor PDA H TSP Uwe 3 T5PA53000 H B Waters2690 E Global H A Isotope Viewer Cl Target vin a ee ten e CC Agilent1 100 IsoPump ab Default ab DetectorID ab Detector voltage lab DetectorVoltageStatus ab HMResMidPoint ab Linearity Adjust ab LMResMidPoint lab MinUSBReadTicks ab MinUSBWriteTicks lab OsBuild ab OSMajorVver ab OSMinorver ab RFFrequency ab RFLensRamp lab SourceID ab SystemID ab TuneFileName ab TuneRawFileName value not set 0 0 000000000000000e 000 NOT FACTORY SET 1 450000000000000e 004 5 000000000000000e 002 1 280000000000000e 002 20 20 4 1 3 2 499670960000000e 008 9 900000000000000e 001 2 13 C Xcalibur methods default tune C Xcalibur default raw Change voltage of detector in scientific notation format 1 00e 003 1000 Change NOT FACTORY SET to OK My Computer HKEY_LOCAL_MACHINE SOFTWARE Finnigan xcalibur Devices Surveyor MSQ Settings EDIONEX Installation and Commissioning Guide 3 13 Appendices Appendix F MSQ Pfeiffer Pump Oil Reservoir Change Appendix F Pfeiffer Pump Oil Reservoir Change Removal Procedure Always use protective gloves contaminants in the oil are extremely hazardous 1 First vent the MSQ and then remove the codpiec
67. pump control cable connection 3 to the PUMP RELAY connector at the rear of the MSQ 1 12 Installation and Commissioning Guide Ey N H MSQ Installing the MSQ Connecting the Vacuum System Exhausts Gas and Power II CAUTION These two lines may be reversed some met ay i depending on the revision level of the system Check C Wil labeling of fittings not their relative positions SOURCE Connection 1 USER I O RESET O SE CH oO oOo CH CH CH CH CH AAA ANANANA VVVVVVVVY V Connection 2 QO a l Ane feoi MAINS ON OFF 1000 VA Connection 3 N A GAS IN MAINS IN Figure 1 3 Rotary vacuum pump connections CAUTION The rotary pump 1s shipped with no oil in it Using the oil provided with the pump fill 1t up to the top mark on the inspection port on the rotary pump Ah EDIONEN As you assemble the rotary connections remember to check that none of the O ring seals have any small particles or dust on them WARNING Do not fail to fit some exhaust device the fumes emitted from the rotary pump are harmful Connecting the Rotary Pump Edwards Follow these instructions if the MSQ system is shipped with an Edwards forepump Before connecting the forepump ensure that it is filled to the correct
68. put when running without a column Test specs are all run with Loop Injections The manual injector should be set up together with its 10uL loop and red PEEK tubing on a stable stand a laboratory retort stand 1s ideal Standards for carrying out the installation specification tests are supplied with the instrument The samples should be prepared using the appropriate mobile phase as the solvent For more information see Page 3 1 Appendix A Both positive ionization specification tests are run using pre mixed degassed 50 50 acetonitrile water mobile phase Both negative ionization specification tests are run using pre mixed degassed 50 50 methanol water mobile phase The Service Representative should be aware that the 50 50 acetonitrile water mobile phase is unstable and should always be prepared fresh on the day of testing Similarly the dilute erythromycin should not be stored overnight The floppy disk CD with the files shown in Table 1 should be close at hand Setting Up an Xcalibur Acquisition Introduction What follows in part is a simplified quick start version of the instructions in the MSQ Getting Started manual starting at page 1 9 2 24 Installation and Commissioning Guide DI N F MSQ K Surveyor MSG Tune File wiew Help Eire iew Help EDIONEX x calibur Mass Spectrometer Functional Verification Instrument Acceptance General Method The minimum steps
69. r Note The MSQ configuration that you are installing may have a mechanical pump manufactured by Busch or a pump manufactured by Edwards These two pumps are installed in a similar manner but use different venting and a different type of oil Please note which brand you are working with and perform the necessary changes Connecting the Rotary Pump Busch Type Before connecting the rotary pump ensure that it is filled to the correct level with the factory supplied oil This oil is synthetic pump oil similar to Anderol type 555 oil For more detailed information on these procedures refer to the manual that comes with the pump or the MSQ Hardware Manual The rotary pump KF25 T piece and all the fittings for connecting the rotary will be in the rotary pump box Place the pump in a location with reasonable ventilation Refer to the topic Connecting Exhaust Lines for information on connecting the rotary pump exhaust 1 Connect the T piece to the rotary pump with a KF25 centering ring and clamp 2 The backing lines labelled SOURCE and BACKING should then be connected to the T piece on the rotary pump using KF25 centering rings and clamps see Connections 1 and 2 Figure 1 3 3 Ifnot already fitted a suitable 230V power connector for the locale should be fitted to the mains lead The lead should then be used to connect the pump to the mains supply 4 Finally couple the 9 pin D connector backing
70. r floppy disk A copy of the shipping checklist A copy of the Factory Order Installation and Commissioning Guide Installing the MSQ Complete Delivery ONOOOOVOOO OF OOOOOOOOOOR Installing the MSQ Complete Delivery MSQ Figure 1 1 Unpacking the Spectrometer Shipping Box 1 Figure 1 2 Unpacking the Spectrometer Shipping Box 2 With the user s order at hand open and carefully remove all items from their shipping containers Locate the installation box and get the packing list Check that all items on the order match the items delivered and that the packing list ties up with all items delivered Place the instrument on the bench as per the diagram in the MSQ Pre installation Requirements Document Do not install any of the accessories at this time e g autosamplers Check all the opened boxes for any additional items and then return the empty boxes and packing materials back into the shipping crates At this point if there are any short shipments or discrepancies between the user s order and the delivery note the items on the installation 1 8 Installation and Commissioning Guide Ey 0 N F Installing the MSQ MSQ Complete Delivery report and notify Product Support immediately Configuration of Mains Leads for Country of Use The power cords will be terminated in a plug configuration compatible with the country of installation Generally this will be four cords for 230 Vac operation except for North Americ
71. r signing off the instrument When this form is completed a copy should be retained for your local office A second copy of the installation checklist should be made and then faxed or sent to Dionex Sunnyvale This should be posted immediately to enable Dionex to monitor its product quality and warranty In order to monitor our quality we would ask you and the user to take the time independently and in confidence to fill out the following two hard copies of Feedback Pages and fax them to Dionex Sunnyvale to the attention of the Mass Spectrometer Marketing Manager Fax Number 408 992 0973 Please encourage the customer to complete their copy in confidence if necessary And please complete the Service Representative s copy Completion of both these documents will help us improve our product and our service Installation and Commissioning Guide 2 41 Mass Spectrometer Functional Verification Completing the Installation MSQ To Be Completed by Customer Instrument Serial Number Service Representative s Name Positive Feedback Negative Feedback 2 42 Installation and Commissioning Guide B N I A MSQ Mass Spectrometer Functional Verification Completing the Installation EI N I A Installation and Commissioning Guide 2 43 Mass Spectrometer Functional Verification M Completing the Installation SQ To be completed by installing Service Representative Instrument Serial Number Service Repre
72. rmo Electron Corporation Microsoft is a registered trademark of Microsoft Corporation PRINTING HISTORY Revision 01 July 2002 Revision 02 October 2003 EDIONEX The products of Dionex Corporation are produced under ISO 9001 accredited quality management systems Published by Technical Publications Dionex Corporation Sunnyvale CA 94086 Contents VO e te Mr E V PUDO EE V TEE v Installation amp Commissioning Schedule cccccceeeeeeeeeeseeseeeseeeeeeeesesseeeeeeeeeeeeeeeeegs V Installing the Survey OF Nees 1 1 Required KE 1 3 SE et LEE 1 5 Pre SiteArrival Requirements CMe EE 1 5 Post Sue Arrival Requirements Checker 1 7 Unpacking and mitial Tree 1 8 Damaee tOsPACk agi Oyster eit ae adic oer aaa a cas aot eae eae 1 8 Complete Dele eere RE Re eR eRe Rn PR 1 8 Wine Data Sy Ste EE 1 8 Rotary Vacum Pump BOX eege e 1 9 EE REES 1 9 Configuration of Mains Leads for Country Of Use ccccccccccccccccececeeeeeeeeeeeeeeeeees 1 11 Shipment Vernication Checklist EE 1 11 IQ OQ Optional Test Equipment and Software Daa 1 12 Hardware LEE REN 1 12 EE WEE 1 12 PC MONTOS enoni ene 1 12 SOLCWale TQ TA 2 EE 1 13 Connecting the Vacuum System Exhausts Gas and Power 1 14 Connectime the Rotary Pup E 1 14 Rotary Pump Connection E EE 1 15 Connecting the Rotary Pump and Source Exhausts 1 16 eer EE 1 16 Source E XNA E 1 17 Source and Pump Exhaust Connections Checker 1 19 Connecting the Nit
73. rogen e TEE 1 20 INTMO SEM Supplies CMe Cl LS EE 1 2 Connec ino POW eer ieee ase a 1 2 Power Connection EE 1 21 TG IVES Tine COMING EIDEN 1 22 Connections 10 Te Data Syste E 1 22 Connections tothe LO Egui un EE 1 23 LAC MS Interconnections e EE 1 23 al N I A Installation and Commissioning Guide Contents MSQ Ee EE gege ege 1 24 Mass Spectrometer Functional Verification sccccccsssssssscccsssssssscccssssssscccsscssssssccssesesees 2 1 DAA CC NO EE 2 1 OTC TASC ST AIC VE 2 1 EE eebe 2 1 Configuring Xcalibur for the Functional Vertftcatnon 2 2 Configuring the Surveyor MSC 2 2 Configuring the HPLC Pump Only where essental 2 3 ET UD cones msc ease ene sensaac pateooeate E A 2 4 EE 2 4 ENEE Tae VACUUM SysteN eege 2 4 Initial System Operational Check Operate OFT 2 5 Initial System Operational Check Operate ONT 2 6 Mass Spectrometer Functional Verification Checklist ccccccccccsccccceeceeeeeeeeeeeeees 2 8 Instrument Autotune and Calibration cccc cc ccccccccccc ccc cc cece ee eeeeeeeeeeeeeeeeeeeeeeeeeEEEEEEEEEEEEEEEEEEE EERE EERE EEE 2 9 OV CIN Wi eege 2 9 Full Se Td PUL INS 22 ccc ccactensacoenesspsecosinsecnivancacenasecesmerspieaaieiete eisepsecuayieuraeseemane 2 10 Boon Ta aa E E E E E E 2 10 ee EE 2 10 ISS CAC AMO AE NOI auc caren ceapnenmnnscsscearigeacuwasiaauaue NE 2 10 Standard Mass Scale Calibration cccccsssssssccccceeesecccessseeessnsnnaeeeeeeeeeeeeeeeesse
74. rotary pump incorrect setup CAUTION Care should be taken that the source exhaust tubing does not rise above the level of the point at which the tubing leaves the rear of the MSQ If it does it is possible for mobile phase to collect and flood the source causing severe damage This damage would not be covered by any warranty in place at the time ED N f A Installation and Commissioning Guide 1 21 Installing the MSQ Connecting the Vacuum System Exhausts Gas and Power MSQ CAUTION Care should be taken to avoid loops forming in the run of pipe A to the solvent trap Solvent could collect here and prevent the free exhaust of vapors from the source Source and Pump Exhaust Connections Checklist Is the source exhaust separate from the rotary pump exhaust Is an adequate exhaust system connected to the rotary pump exhaust port and is the line open Are the pipe runs as shown in Figure 1 9 Is the source exhaust at atmospheric pressure 1 22 Installation and Commissioning Guide Ey N H MSQ EDIONEX Installing the MSQ Connecting the Vacuum System Exhausts Gas and Power Connecting the Nitrogen Supply The MSQ system requires a nitrogen gas supply for the source The nitrogen must be high purity 99 The required gas pressure is 520 kPa 5 2 bar 75 psi Maximum nitrogen gas consumption is 10 L min the typical use is 8 L min Therefore it is recommended that nitrogen be supplied fr
75. sentative s Name Positive Feedback Negative Feedback 2 44 Installation and Commissioning Guide B N I A MSQ Mass Spectrometer Functional Verification Completing the Installation EI N I A Installation and Commissioning Guide 2 45 EDIONEX Section 3 Appendices Installation and Commissioning Guide 3 1 Appendices Appendix A Sample Preparation MSQ Appendix A Sample Preparation Introduction The following is only one of many possible ways of making up the solid test samples It is however designed to be relatively easy for somebody with little or no knowledge of sample preparation to prepare sufficiently accurate samples Variances may include e Reducing the volumes all round Write down each stage dilution e Asking the customer what equipment they have which is most suited for the task Please be sure you understand the process and observe the customer if they offer to do it as there is only one test kit and anyone can make a mistake Mobile Phase Positive ESI tests require pre mixed 50 50 acetonitrile water Negative ESI tests require pre mixed 50 50 methanol water Positive APCI tests require the addition of sufficient ammonium hydroxide solution 30 NH 3 to the Positive ESI mobile phase to give a 0 1 solution Negative APCI tests require the addition of sufficient ammonium hydroxide solution 30 NH3 to the Negative ESI mobile phase to give a 0 1 solution It is
76. sition may not be run synchronously with the chromatography The scheme for this is shown in Figure 2 28 To Relay Screen contacts When fitted Figure 2 28 USER I O connector terminal wiring The MSQ has at its rear an eight pole Phoenix connector labelled USER I O This should normally be fitted with a shrouded mating receptacle with screw connectors Remove the shroud from the eight pole Phoenix mating receptacle and wire the pins as in Figure 2 28 and Table 3 Re fit the shroud to the Phoenix mating receptacle and clamp to the cable Connect wire MSQ USER I O input Input Wire i SC to pin definition Floating relay contact TTL with 2k2 pull up Floating relay contact PSU Ground Screen when fitted PSU Ground Table 3 USER UO connector terminal wiring Timing The MSQ acquisition time should be set to be less than the cycle time between samples on the unsupported system as the MSQ has to wait for the second and subsequent injections not the other way around Installation and Commissioning Guide B N I A MSQ EDIONEX Mass Spectrometer Functional Verification Completing the Installation Completing the Installation When all the requirements of the installation are completed it is vital that the paperwork is also completed Complete the acceptance form together with the customer The test results training requirements and customer details should now all be completed prior to the custome
77. software is loaded it should be loaded after the installation of Xcalibur Follow the installation instructions on the CD ROM MSQ Remote Start Contact Closure Regardless of the front end hardware installed pumps autosamplers etc there must be a contact closure signal pulse to synchronize the start of acquisition with the timebase This is performed by connecting a two wire cable to pins 7 and 8 top of the I O Users Interface connector on the rear of the MSQ The connector shell and hood is supplied with the MSQ Connect the other end of the cable to a relay contact closure not a TTL signal from a relay controlled by Chromeleon PeakNet autosampler pump relay or other User I O Relay Remember to add a program line after the Inject command at time 0 00 instructing the relay to close for 1 to 2 seconds this will enable the synchronization pulse Installation and Commissioning Guide 1 31 Installing the MSQ LC MS Interconnections MSQ LC MS Interconnections Checklist Is the cable from the MSQ to the data system connected to one of the USB ports at the rear of the PC L Is the second USB port at the rear of the PC unused Are the correct interconnect cables available for the customer s configuration L Is the system set up with all connections correctly made 1 32 Installation and Commissioning Guide EN 0 N F Installing the MSQ MSQ LC MS Interconnections Installation Sign off This co
78. stock solution stored in a refrigerator overnight Hazard Information Please note that local safety practices in preparing samples must be strictly followed These compounds are hazardous and should be handled with care p Nitrophenol 2pg uL Prepare your mobile phase by mixing 400mL methanol with 400mL of HPLC water in the pump mobile phase bottle Sonicate for 10 minutes Decant 100ml of this to the beaker for use in the following dilutions e Decant from this 4ml of mobile phase to each of two of the 4 mL screw top polypropylene vials Label one Blanks and the other Wash e Add 10 mL of mobile phase to the supplied p Nitrophenol sample vial e Close cap and shake until the sample has completely dissolved This gives a stock solution of Img mL or Ipg Jul e Label three of the remaining vials Note There is a Word document on the Engineers disk called sample labels This will print 20ng uL P Nitrophenol 200pg uL P Nitrophenol all the required labels on toa 66 8 sheet of Avery 35mm slide 2pg uL P Nitrophenol E E 1 666 Installation and Commissioning Guide 3 5 Appendices Appendix A MS Q Sample Preparation 20ng uL solution e Using the ImL pipettor transfer 2mL of mobile phase to the 20ng nL vial e Using the 200uL pipettor remove and dispose of 80uL of mobile phase from this vial e Change the 200uL pipettor tip and transfer 80uL of the stock solution to the vial Th
79. t click on the server icon and then Tune as in Figure 2 4 Instrument Tune and Calibration Tune Vent h Exit et 15 28 Figure 2 4 Server window e This will open the tune window shown in Figure 2 5 5 Zu amp J Man 4 Dipef D A e H e f p D D etn 7 0 ae mig Finnigan Pash Pomme Scan Taaa We Polny Care Adik Detects Adibi dm rein LI aeg 1506 D i Hi SOOT iay tte Figure 2 5 Tune Window Per Method Parameters Slide Bar Ft Eryt mihin MP e Click on the Per Method Parameters Slide Bar as shown in the detail in Figure 2 5 e This will reveal a parameter table as shown partially in Figure 2 6 Installation and Commissioning Guide 2 5 Mass Spectrometer Functional Verification MSQ Powering Up 2 6 Figure 2 6 Tune Window Per Method Parameter Table Description Readback Setpoint Tune Control Probe Temperature LI 0 100 l 3 0 Needle ky UU Acquisition Control Retention Time mins 0 00 n a General Control Operate n a Ott Nitrogen Das n a Un Jonization Mode inva ESI e First note the Probe Temperature Readback This should indicate ambient temperature or slightly above e Click the Nitrogen Gas Button On and open the source cover e Place your hand across the right hand side of the source and check that a good flow of gas can be felt e Switch the gas off e Close the source enclosure Initial System Operati
80. t may be required if additional options are on the order Options of third party equipment and additional application software may take several additional days to set up demonstrate Time should be allowed for installing these and for the successful interfacing of all of the system components Installation and Commissioning Guide V Introduction vi Installation and Commissioning Guide MSQ EDIONEX Section 1 Installing the MSQ This section describes the correct procedures for unpacking the MSQ system and installing it ready and in position for commissioning The following topics and procedures are described in this section Required Tools Site Verification Unpacking and Initial Inspection IQ OQ Optional Equipment and Software Data Connecting the Vacuum System Exhausts Gas and Power LC System MS Instrument Interconnections Throughout this guide the installation and commissioning Service Representative will often be asked to record values screen dumps and spectra chromatograms in the Engineers Log The log may be accessed via an icon on the desktop Installing the MSQ Required Tools eee MR Required Tools Although some of the following tools are shipped with the instrument it is mandatory that you have the required tools in your own toolbox The tools and spares shipped with the instrument are the customer s Do not remove them EN MSQ Installation Acceptance form DIN FM103826D ss LL
81. tion and Commissioning Guide 1 5 Installing the MSQ Complete Delivery Complete Delivery MSQ For North American sites the basic MSQ system will be delivered in three boxes on a pallet A box containing the data system including monitor A box containing the rotary backing vacuum pump A box containing the spectrometer and the remainder of the system For sites in Europe these boxes will be packed into a crate Use the following check boxes to verify the shipment The Data System Mini Tower Monitor Mouse Keyboard Mains Leads 2 off for country of use Software System MS Office 2000 Rotary Vacuum Pump Box Rotary vacuum pump 1 off 1L vacuum pump oil Tools and manual Mains Lead for country of use Installation and Commissioning Guide UU UU g O O UOdO SA EDIONEX MSQ EDIONEX Spectrometer Box MSQ Instrument Installation Kit including Tool Kit Solvent Trap USB lead 3 M Mains Lead for country of use KF25 mm T piece 3 off KF25 mm centering ring and clamp sets Backing Pump Control Cable Nitrogen supply tubing 4 mm PTFE TUBE x 3MP Nitrogen regulator adapter Half Union 4 mm 1 4 BSP Rotary vacuum pump exhaust hose PVC hose 3 8 ID x 3 M for Busch Pump or PVC hose 26 mm x 3 M for Edwards Pump PEEK tube red 1 16 x 0 13 mm ID Test sample kit MSQ Installation amp Commissioning Guide MSQ Media Kit Media kit manual Installation and test files CD ROM o
82. tion of 10ul of a 2pg ul solution of p Nitrophenol in 50 50 acetonitrile water into an LC flow of 1 ml min of 50 50 methanol water will give a signal noise ratio of gt 50 1 monitoring m z 138 in SIM mode after appropriate smoothing m z 138 from p Nitrophenol 50 1 Demonstrated Result include screen capture of results Acceptance Customer Acceptance This is to confirm that the MSQ Installation has been completed and that all the items on this acceptance form have been achieved and demonstrated Serial Number of MSQ Serial Number of Edwards Busch ____ Customer Name Company Institution Customer Address Telephone Number Fax Number e mail Address Application IC LC Type Other Hardware Customer s Signature Engineer s Signature Date Start of Warranty End of Warranty When this form has been completed make a copy for the customer Send the original along with all screen captures of the sensitivity specification runs to the Dionex Regional Office DIONEX Acceptance
83. tor102501145600 log 1KB Text Document 25 10 2001 13 56 a My Documents S Detector102501145557 log 1KB Text Document 25 10 2001 13 56 0 My eBooks E Detector102501145554 log 1KB Text Document 25 10 2001 13 55 i Lal zl My Pictures E Detector102501145550 log 1KB Text Document 25 10 2001 13 55 I g My Computer Detector102501145548 l0g 1KB Text Document 25 10 2001 13 55 il 3 Floppy 4 E Detector102501145544 log 1KB Text Document 25 10 2001 13 55 T Local Disk C Detector 102501145541 log 1KB Text Document 25 10 2001 13 55 SC Program Files 2 Detector102501145538 log 1KB Text Document 25 10 2001 13 55 a SS TEMP 2 Detector 102501145535 log 1KB Text Document 25 10 2001 13 55 te ae Detector102501145532 log 1KB Text Document 25 10 2001 13 55 J Me Activex Sl Detector102501145529 log 1KB Text Document 25 10 2001 13 55 a a cal E Detector102501145526 log 1KB Text Document 25 10 2001 13 55 gt data 2 Detector102501145523 log 1KB Text Document 25 10 2001 13 55 i de methods Sl Detector102501145520 l0g 1KB Text Document 25 10 2001 13 55 a ref Si Detector102501145517 log 1KB Text Document 25 10 2001 13 55 z 2 report Detector 102501145444109 1KB Text Document 25 10 2001 13 55 fy data SI autocal102501114248 log 2KB Text Document 25 10 2001 10 44 i Il examples autocall102501113819 log 2KB Text Document 25 10 2001 10 39 C Help autocall102501113510 log 2KB Text Document 25 10 2001 10 36 o 1 methods autocal102501112125 log 2KB Text
84. tpoint Tune Control Probe Temperature TC 0 AUT Needle kv UU 1 0 Acquisition Control Retention Time mins 0 00 n a General Control Operate n a On Nitragen Gas n a On lonization Mode n a ESI l Cone l 100 Figure 2 25 Tune parameters that change for this test e Click on View Options This opens the Tune Options window Tune Number of tune masses li Acquisition filename Installation tests Sensitivity Spec ESI ve raw e Tune filename Ja Sensitivity Spec ESI e tune a Filled traces Show advanced parameters Figure 2 26 Tune Options window APCI ve e Using the button to the right of Acquisition filename browse through to C Xcalibur Installation Installation tests and type in Sensitivity Spec ESI ve raw and check that the Tune filename is A Sensitivity Spec ESI ve tune see Figure 2 26 Continue as before but use the 0 2pg uL p Nitrophenol test sample Installation and Commissioning Guide MSQ Mass Spectrometer Functional Verification Instrument Acceptance _ _ won Ur BE ODC OBZ BLZ MI SW DLL FAIRE IN CN gz FC aer grz SEZ IoueudomN d qri 6dz 0 10 eunsax A IAIIsUaS Sy 1e91dA L 80 uoenag pIepuels ZZ SION oL BUBIS LECHL suljaseg Sueds 001 Samu Liz gez aBuey asion SanjeA payeynayje WLU awu ad Oz SL OU th CL DL grz 907 OBL ggi oo Hri POL igo 2 L DI oU L SU GG EL LOUSO LE 1
85. tup to set up experiments to run several samples using an autosampler Using the basic functions of the Qual Browser to view manipulate and print chromatograms and spectra Service Representative s Initials Installation and Commissioning Guide Mass Spectrometer Functional Verification S Performance Demonstration and Installation Acceptance Tests M Q Performance Demonstration and Installation Acceptance Tests Introduction At the time of delivery all the files required to carry out the installation performance tests should be available on an Engineers CD floppy disk While it may seem more convenient to copy these to the C Xcalibur methods folder be aware that if a parameter changes for example during tuning the source file will be automatically overwritten with the new values when you leave tune or load a new file You cannot avoid this by making the files read only as the system refuses to load such files If however the files are run from the CD or write protected floppy disk the system will accept them Therefore it 1s recommended that you do so Before proceeding create a folder directory within the C Xcalibur folder and call it Installation Then create a folder within this folder called Installation tests This is where the test results will be stored Test to Be Carried out Associated Files A Sensitivity Spec ESI ve tune C Xcalibur Installation Installation tests Sensitivity Spec ESI ve raw
86. x C Location of Calibration Renate 3 10 Appendix D Typical Report of a Calibraton cccccccccccssccesscccsssecessecesseecesecessecesseceessesenseens 3 11 Appendix E Detector Voltage Registry Locapon 3 12 Appendix F Pfeiffer Pamp Oil Change eege 3 13 EEN wee 3 13 eege 3 16 dee 3 16 Appendix G MSQ Service Tools Bill of Materials 0 0 0 cccccccccscscceeceeeeeeeeeceeeeeceeeeeeeeseeeeeees 3 17 Installation and Commissioning Guide El N I H EDIONEX Introduction Purpose This procedure has been written to give the Dionex Service Representative a comprehensive guide and checklist for installing and commissioning an MSQ in two days The installation setup and system training required for options and the travel time to and from the user s laboratory are not included in these two days Audience Service Managers and Service Representatives One copy to be sent to the Service Manager of the concerned office agency upon receipt of order this individual should hand it to the installing Service Representative when the customer returns the completed pre installation checklist Installation amp Commissioning Schedule Day 1 From Section 1 3 up to and including Section 2 3 Initial system operational check Operate OFF Day 2 From Section 2 2 Initial system operational check Operate ON up to and including Section 2 7 and Section 2 10 Day 3 Sections 2 8 and 2 9 This is an additional day tha

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