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MSQ Plus Mass Detector Getting Started Guide

1. AutoTune Report Laboratory Product Evaluation Filename Calibration msqreport Instrument ID MSQ Plus Tune Date 10 27 2004 8 31 28 AM Serial Number 999999 Report Date 10 27 2004 8 45 58 AM Tune Parameters Set Point Actual m z 173 02 m z 107223 mz 1971 54 Pr nei S48 a Width 0 081 Width 0 78 Width 1 22 Needle Voltage kV 30 30 N i Detector Voltage V 988 1023 H i RF Lens Bias V 0 5 0 5 u i lon Energy V 0 5 n a i il j lon Energy Ramp mV amu 0 3 n a i I Low Mass Resolution 12 7 n a High Mass Resolution 12 5 n a i Cone V 75 74 i im I RF Frequency 236755120 n a E Linearity Adjust 0 05 n a I Low Mass Res Mid Point 55 n a i i E High Mass Res Mid Point 14147 n a i I Pa ti fi I i Mass Calibration Results Fast Slow 4 Calibration Type Autotune Autotune Missed Ref Peaks 0 0 Standard Deviationfmax 0 2 0 0509 0 0436 i I I R M S Error 0 0520 0 0446 A Max Residual Error m z max 0 3 0 1328 00778 14 Wa Calib
2. Save as type Tune Parameter Files tune Cancel b Type an appropriate name in the File name box c Click Save to save the tune file with the optimized MS parameters for your compound of interest MSQ Plus Mass Detector Getting Started Guide 47 Manual Tuning in the APCI Mode Before you create an instrument method you must optimize the acquisition parameters of the MSQ Plus Mass Detector for your compound of interest The process of optimizing the acquisition parameters of the mass detector for a particular compound or family of compounds is referred to as manual tuning and is performed from the Tune window This chapter describes how to optimize the tune parameters for a compound of interest Perform the procedures that are provided in this chapter in the following order If your LC devices are controlled by the Xcalibur data system begin with Opening the Instrument Setup Window on page 51 Otherwise begin with Selecting Your Tune Options on page 51 Contents e Opening the Instrument Setup Window e Selecting Your Tune Options e Acquiring and Viewing a Raw Data File In the APCI mode you optimize the parameters listed in Table 6 Table 6 Tune controls in the APCI mode Sheet 1 of 2 Tune window control Description Typical value Corona mA This is the current on the The optimal value depends on the structure of your corona pin analyte Although allowable values range from 2 to 50 uA use the
3. Show mass spectrum for centroid or profile data 5 From the shortcut menu choose the view that you want for this cell Viewing Reports After you open a data file you might want to check the instrument parameters that were used to acquire it To view a report that lists the instrument control parameters used to acquire the data file 1 Open a raw data file in the Qual Browser facility as described in Opening a Raw Data File in Qual Browser on page 92 2 Choose View gt Report gt Instrument Method to display the Instrument Method report The instrument method is displayed in the pinned cell The instrument method is divided by device with the parameters for each device displayed on a separate page Figure 71 shows an Instrument Method report Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 95 9 Using Qual Browser Viewing Reports Figure 71 Report for an instrument method C Xcalibur data data14 06 24 2003 10 30 04 AM datal4 MSO Method Options Analysis Time Raw Display File Tune File Stop After LC Per Method Parameters Ionization Mode Probe Temperature SIM Scan Events Mass amu 346 20 560 10 ee 10 None Specified Using current tune Yes ESI 550 00 Span Time Range amu minutes 1 00 00 00 10 00 1 00 0 00 10 00 Dwell Time seconds 1 00 1 00 Polarity ve ve Cone volts 60 00 60 00 3 Click the Show
4. Getting Started Guide 60111 97044 Revision A September 2013 DOCUMENTATION 2013 Thermo Fisher Scientific Inc All rights reserved Thermo Scientific Xcalibur and Accela are registered trademarks and M Path Fastloc MSQ and MSQ Plus are trademarks of Thermo Fisher Scientific in the United States and other countries Windows is a registered trademark of Microsoft Corporation in the United States and other countries Agilent is a registered trademark of Agilent Technologies Inc in the United States and other countries Edwards is a trademark of Edwards Limited in the United States All other trademarks are the property of Thermo Fisher Scientific Inc and its subsidiaries Thermo Fisher Scientific Inc provides this document to its customers with a product purchase to use in the product operation This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc The contents of this document are subject to change without notice All technical information in this document is for reference purposes only System configurations and specifications in this document supersede all previous information received by the purchaser Thermo Fisher Scientific Inc makes no representations that this document is complete accurate or error free and assumes no responsibility and will not be liable for any errors omissi
5. To set up the LC pump 1 For Xcalibur 2 2 SP1 or later choose Start gt Programs gt Thermo Xcalibur gt Xcalibur On the Roadmap view in the Xcalibur data system click the Instrument Setup icon The Instrument Setup window appears with icons for all of the currently configured devices for your LC MS instrument displayed down the left side of the window Instrument Setup pages and dialog boxes for the selected device are displayed on the right side of the view You can access additional dialog boxes for the device by clicking the device listing in the menu bar 2 Open the Direct Control dialog box for your LC pump 3 Leave the Direct Control dialog box open and adjust the size of the Instrument Setup window to half the size of your view screen Checking the Solvent Levels in the Reference Inlet System Thermo Scientific The reference inlet system includes a reference inlet reservoir bottle and a waste bottle To perform a full system autotune or a mass scale calibration the reference inlet reservoir bottle must contain a sufficient level of calibrant solution gt 50 mL and the waste bottle must not be full The factory supplied calibrant compatible with the MSQ 2 0 software contains 1 3 mM sodium iodide Nal 0 05 M potassium iodide KI and 0 02 mM cesium iodide CsI in 50 50 isopropanol water A 250 mL bottle of calibrant is shipped with the MSQ Plus Mass Detector You can purchase refill bottles from Thermo Fisher Sc
6. x a a a w 4 Hide Method Options 2 If you cannot see the browse buttons in the Method Options view click the Hide Per Method Parameters bar to hide the Per Method Parameters table 3 Optional Open a raw file and display its chromatogram a Click the browse button next to the Rawfile box b From the Open dialog box select a raw raw file c Click Open to close the Open dialog box and open the raw file d Click the Hide Method Options bar to display the Chromatogram view You can use the chromatogram to edit the retention times of your scan events as described in Editing the Scan Events on page 69 Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 67 7 Creating Instrument Methods Creating an LC MS Instrument Method e After you finish working the chromatogram click the Show Method Options bar to reopen the Method Option view 4 Select a tune tune file by doing one of the following e Select the Use Current Tune File check box to use the Tune file that is in the current memory of the Xcalibur data system e Clear the Use Current Tune File check box Click the browse button next to the Use Selected Tune file box to display the Open dialog box Select the Tune file that you created for your analyte and then click Open Note For ESI methods the instrument method uses the needle voltage value from the Tune file For APCI methods the instrument method uses the corona current val
7. 2 The extracted ion chromatogram for the mass range 180 to 220 m z 3 Base peak chromatogram for the masses 182 and 213 m z 4 UV chromatogram at 260 nanometers Figure 65 Four traces generated by settings in the Chromatogram Ranges dialog box RT 0 00 8 00 a 352 714 NL 1 67E7 100 6 29 703 W 7 17 TIC MS MixA 10ppm 1 80 6 7 76 1 60 352 NL 6 75E6 m z 180 00 220 00 F 0 0 c ESI Icorona sid 60 00 det 906 00 Full ms 80 00 500 00 MS Mi A 10pprn 1 _ 119 0 03 0 64 1 09 1 71 264 292 380 432 3 52 NL 4 36E6 Base Peak m z 181 50 182 50 212 50 213 50 F 0 0 c ESI corona sid 60 00 det 906 00 Full 3 604 __6 32 ms 80 00 500 00 MS Mix A 10ppm 1 BE 204 3 7 24 7 58 0 068 NL 3 86E4 nm 259 5 260 5 PDA Mix A 10ppm 1 0 p5 PrF TETT ch Fade Lei Te de Bd ee Dr LT Tr Te ak Tl Eo De e 0 1 2 3 4 5 6 7 8 Time min Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 87 Using Qual Browser Cell States Thermo Scientific This chapter provides an introduction to using Qual Browser a facility that you can use to review the MS data contained in your data files Contents Cell States Cursor Actions Opening a Raw Data File in Qual Browser Adding Cells to the Grid Viewing Reports Viewing the Mass Spectrum for a Specific Time Point When you open a raw data file in the Qual Browser window the information within the data file is displayed as a grid of cells
8. Inactive ells een een een 90 Active but Unpinned Cells ie vee ie ee Bu 90 Activeand Pinned Cell nn eu 90 VEST PTO id eee e eee hh ee ead hn tea dal aM ed stg he each 92 Opening a Raw Data File in Qual Browser 0 0 eee ce eee 92 Adding Cells to the Grid sea a He d wees eh wa 94 Viewing Reports ageres me mare es bear 95 Viewing the Mass Spectrum for a Specific Time Point 00 98 Sample Formulations 0 0 cee eee ee eee eee eee eee eee 101 Sensitivity Test Solutions REN 102 Preparing the Stock Solutions for the Sensitivity Tests 102 Preparing the Working Solutions for the Sensitivity Tests 103 Preparing the MSQ Plus Mass Detector Calibration Solution 105 Kir Contents nes rare 105 Preparing the Calibration Solution sure seta 105 Cali Dnt Solutions suis Rare 106 Preparing a Concentrated Stock Solution of the Calibration Mixture 107 Preparing the Working Calibration Solution 0004 107 Nexus eisen 109 MSQ Plus Mass Detector Getting Started Guide ix Preface This MSQ Plus Mass Detector Getting Started Guide explains how to set up calibrate and tune the Thermo Scientific MSQ Plus Mass Detector and how to acquire LC MS data This manual supports the release of the Thermo MSQ 2 0 instrument software shipped with the Thermo Xcalibur data system version 2 2 SP1 or later Contents e Related Documentation e
9. There are three hierarchical states which are described in this topic for a cell within the grid e Inactive Cells e Active but Unpinned Cells e Active and Pinned Cells The grid always contains either one active but unpinned cell or one pinned cell If the grid contains more than one cell only one cell can be active and the rest of the cells are inactive An unpinned cell has a gray pin icon in its upper right corner A pinned cell has a green pin icon gy in its upper right corner MSQ Plus Mass Detector Getting Started Guide 89 9 Using Qual Browser Cell States Inactive Cells Inactive cells are not highlighted with a gray border and the pin icon in their upper right corners are gray The cell in the lower portion of Figure 66 is inactive as indicated by the absence of a gray border Menu commands toolbar buttons and cursor actions do not affect inactive cells If you want to zoom the contents of a cell or access its shortcut menu you must make it an active cell Active but Unpinned Cells An active but unpinned cell is highlighted with a gray border and the pin icon in its upper right corner is gray The cell in the upper portion of Figure 66 is active but unpinned Menu commands toolbar buttons and cursor actions affect the active cell If no cell in the grid is pinned clicking an inactive cell in the grid makes it the active cell Active and Pinned Cells Clicking a pin in the upper right corner of a c
10. lowest value that gives adequate sensitivity Corona readbacks might vary depending on the eluent composition and conductivity Typical values range from 3 to 5 kV Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 49 6 Manual Tuning in the APCI Mode Table 6 Tune controls in the APCI mode Sheet 2 of 2 Tune window control Description Typical value Probe Temperature This is the temperature The optimal value depends on the flow rate of the mobile setting of the probe heater phase In general you need to increase the probe temperature as you increase the flow rate of the mobile phase See Table 1 on page 7 Cone V This is the voltage that is The optimal value depends on the structure of your placed on the source block analyte and the entrance cone Increasing the cone voltage can decrease adduct formation common to ESI and give rise to fragmentation which provides structural information about your analyte Increasing the cone voltage to reduce adduct formation is useful in the presence of interfering compounds Typical cone voltage values range from 75 to 150 V Note To enter the optimal corona current for your sample into an instrument method you must determine its value from the Tune window save the value in a tune file and then import the Tune file into an instrument method The MSQ Plus Mass Detector is shipped with the ESI probe installed Install the APCI probe and the APCI corona pin b
11. 25 MSQ Plus Mass Detector Getting Started Guide 41 5 Manual Tuning in ESI Mode Selecting Your Tune Options Figure 25 Tune Options dialog box Tune Options MSQ Plus Tune Options Configure the tune and display parameters Number of tune masses a Acquisition filename E Thermo Instruments MSQ data default raw o Raw data file button Tune filename C Thermo Instruments MSQ methods defaul a Tune file button Display I Filled traces IV Automatic intensity ranging Show advanced parameters 3 Enter an acquisition file name for the raw data file that the data system creates after you start data acquisition in the Tune window a Click the button to the right of the Acquisition Filename box to open the Select Tune Raw File Name dialog box shown in Figure 26 Figure 26 Select Tune Raw File Name dialog box Select Tune Raw File Name Look in ER El a Files of type Raw Files raw x Cancel 42 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Thermo Scientific 5 Manual Tuning in ESI Mode Selecting Your Tune Options b Browse to the directory where you want to store your raw data Then type an appropriate file name in the Filename box c Click Open to create the file name for the raw file and close the Select Tune Raw File Name dialog box Note The Xcalibur data system does not check your directory for the reserved file name If you reuse a
12. 3 Choose Left Right Above or Below 4 Right click the cell that you just inserted into the grid to access a shortcut menu as shown in Figure 70 94 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 9 Using Qual Browser Viewing Reports Figure 70 View of Qual Browser window with the shortcut menus for selecting the options for a cell M Qual Browser ForDerek ForDerek RAW File Edit Yiew Display Grid Actions Tools Window Help ses a Belo I Rl elslefe E ale lm S RE i x EJ 10 2 2001 2 01 32 PM Herbicides WUssjo pe hughxealsharet 5 UV Channels PDA 5 SIMs 2 Full scans gt EER li X X X X X X X RT 0 00 10 00 100 so so Relative Abundance a t 0 2 24 4 28 8 13 659 728 73 3 54 5 6 7 Time min 1 2 3 24 0 26 0 74 172240 3 25 T j 1 ad pin 4 NL n 2 52E5 TIC F MS Data1 8 63 8 79 9 00 Wi 9 89 8 9 100 90 80 70 50 50 40 30 Relative Abundance Data 1 RT 0 00 AV 4 NL 6 442 1 wu ESI corona sid 50 00 det 1200 00 Full ms 100 00 300 00 170 85 183 35 ven 19727 Plot gt 148 37 198 83 Subtract Spectra Library gt Export gt Elemental Comp Ranges Display Options Chromatogram Map Ton Map Spectrum List Scan Header Scan Filters Report p 285 78 100 120 140 160 180 200 220 240 260 280 300 miz
13. After Sequence Set System On C Standby C Off OK Cancel Help The User box contains your login name and the Run Rows box contains the number of the row that you selected in the sequence spreadsheet 2 In the Acquisition Options area confirm the following e The mass detector and LC components are configured for operation as Xcalibur devices in the Instrument list e The autosampler is configured as the start instrument After the injection valve of the autosampler switches to the inject position the autosampler sends a signal to the detector to begin data collection 3 To change the components of your LC system or change the device that starts the run do the following a Click Change Instruments to open the Change Instruments In Use dialog box shown in Figure 63 Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 83 8 Creating and Running Sequences Starting Data Acquisition Figure 63 Change Instruments In Use dialog box Change Instruments In Use Start Instrument MSO Plus Accela AS Accela Pump A list of components that have been configured for operation as Xcalibur devices appears The autosampler is typically selected as the start instrument Add or remove components as appropriate To select a start instrument in the Instrument list click the Start Instrument list in the row of the instrument of choice The blank space changes to display Yes 4 To start
14. Browse Calibration File ne Bromse m Samples Number of Samples f Iray Type Injections per Sample f Initial Vial Position amp 1 V Re Use Vial Positions Base Sample ID Select Vials sncel Select Bracket Type None Open Non Overlapped Overlapped Calibration Ic Add Standards Add GCs T After meperLevel fT J W Fillin OK Cancel Save As Default Help __Caneel_ Saves Defaut Help 76 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 8 Creating and Running Sequences Creating a Single Sample Sequence Creating the Sequence Follow these steps to create a new sequence To create a new sequence 1 Set the parameters in the General area a Type a name for the raw data file into the Base File Name box b Browse to the data file directory where you want to store your raw data files The data system adds the raw file extension to the data files that contain the chromatographic and spectral data c Browse to the instrument method that you want to use to acquire your raw data files Instrument methods have a meth file extension For information on creating an instrument method see the Help For more detailed information on controlling the Accela LC system refer to your manual d Ifyou have not yet created a processing method that contains the information needed to quantify your unknowns leave the Processing Method box blank You can cre
15. Documentation a ach invade pet saree deiae enano xi Safety and Special Notices sinc cos ie nie Kehoe erie kee kee Ae eS xii S fety Pressullons sanieren xiii Contacting US so Yan ae neh Sh doa lee ee xiv Chapter Introduction u 1 Why Use the MSQ Plus Mass Detector 2 0 eee eee eee 1 Is ESI or APCI Better for Analyzing My Samples see aaa 3 Electrospray ESD ae aan k kier wee eee eee eee R 4 Atmospheric Pressure Chemical Ionization APCH 2222 5 How Do I Introduce My Samples into the Mass Detector 2 2 20 5 What Types of Buffers Can I Use sau ee ee 6 How Do I Set Up the Mass Detector for Various LC Flow Rates 6 How Do I Calibrate the MSQ Plus Mass Detector 00 00 ce eee T How Do I Optimize the Mass Detector Parameters for My Analytes 8 How Do I Create Instrument Control Methods 2 2 22cn22 200 9 Chapter2 Configuring Your LC MS Instrument ccc cece eee eee eee 11 Configuring the Mass Detector 20sdc4 ced dedisan ae lan 11 Configuring the LG System a2 era 13 Chapter3 Preparing Your LC MS for Operation 0ccc cece eee eee eens 15 Checking the Hardware ass 15 Checking the Status of the LC MS Instrument 00 00000 ee ee 16 Checking the Oil Level in the Oil Mist Filter and the Forepump 18 Preparing the LC for Operation ae aus aaa ae lee 21 Thermo Scientific MSQ Plus Mass Detector Getting Starte
16. Getting Started Guide Thermo Scientific A Sample Formulations Sensitivity Test Solutions 5 Store the p nitrophenol stock solution 1 mg mL in a refrigerator until it is needed When refrigerated this stock solution is stable for several months Preparing the Working Solutions for the Sensitivity Tests A working solution of 5 pg uL erythromycin in 50 50 acetonitrile water and a working solution of 2 pg uL p nitrophenol in 50 50 methanol water are required to perform the sensitivity tests Prepare these working solutions daily as needed from the refrigerated stock solutions The following procedures require the materials listed in Table 11 or their equivalents Table 11 Required materials Item Quantity 200 uL adjustable mechanical pipette calibrated or equivalent 1 1 mL adjustable mechanical pipette calibrated or equivalent 1 10 mL adjustable mechanical pipette calibrated or equivalent 1 25 mL glass vials with caps or equivalent 6 50 50 acetonitrile water v v premixed 30 mL 50 50 methanol water v v premixed siti mM Note The following procedures result in a 200000 fold dilution of the erythromycin stock solution and a 500000 fold dilution of the p nitrophenol stock solution Alternative dilution procedures that result in a 5 pg uL solution of erythromycin and a 2 pg uL solution of p nitrophenol with a reasonable level of accuracy are acceptable Preparing the Erythromycin Sensitivity Test Solutio
17. MSQ Plus Mass Detector and your LC devices during a sequence run This chapter describes the features of the method editing windows for the MSQ Plus Mass Detector and how to create an LC MS instrument method that controls both your MSQ Plus Mass Detector and your LC devices Contents e Welcome Page e Method Editor e Creating an LC MS Instrument Method Welcome Page From the Welcome page for the MSQ Plus Mass Detector shown in Figure 40 you can choose from a list of method templates open existing method files and access to the Tune window Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 57 7 Creating Instrument Methods Method Editor Figure 40 MSQ Plus Mass Detector Welcome page in the Instrument Setup window 9 Untitled Thermo Xcalibur Instrument Setup Eile Help Del S x 2 MSQ Pius Welcome Create a new instrument method using an existing template Open an existing file Tune B ESI Full Scan Negative Ion C ESI SIM Positive Ion Access to tune allawing you to optimize ESI SIM Negative Ion or modify the system settings Accela AS Accela 1250 Pump D E ESI Positive Negative Switching F APCI Full Scan Positive Ion l s G APCI Full Scan Negative Ion H APCI SIM Positive Ion i I APCI SIM Negative Ion MSO Plus A J APCI Positive Negative Switching Method Editor The MSQ Plus Mass Detector Method Editor contains the following views tables and menus which are d
18. Opening a Raw Data File in Qual Browser Figure 68 The empty Qual Browser window in the Xcalibur data system ER Qual Browser File View Tools Help sls a Hel gt eles ele FE les SISO S SI Br Allee ei m aal 3 B del tila 2 Choose File gt Open to display the Open Raw File dialog box shown in Figure 69 Figure 69 Open Raw File dialog box Open Raw File Look in data e Erythromycin_1 File name raw Files of type Raw Files raw Cancel Header Information Replace Window f Cell Plot Add Window Plot Default Layout v 3 Select the raw data file that contains the data for the sample that you want to work on Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 93 9 Using Qual Browser Adding Cells to the Grid 4 Select the window layout from the list at the bottom of the dialog box e Select Current Layout if the current layout for the Qual Browser window is different from the default layout and you want to apply it to your data file e Otherwise leave the window layout selection at its default of Default Layout 5 Click Open to open the raw data file into the Qual Browser window Adding Cells to the Grid You can add cells to the grid in Qual Browser To add cells to the grid in Qual Browser 1 Open a raw data file in Qual Browser 2 From the Qual Browser menu bar choose Grid gt Insert Cells
19. Previous and Show Next buttons Ki gt to move through the pages of your acquisition method 4 Choose View gt Report gt Status Log to display the Status Log report The status log displays the settings that were imported from the tune file as shown in Figure 72 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Thermo Scientific CAMy Documentsi 20ppm_caf_sim1 MSQ Plus 20612 Scan Time Source Mode Negative Polarity Peak Format Profile Resolution Source Temperature Needle Voltage Detector Voltage Ion Energy RF Lens Bias Ion Energy ramp Cone Ramp DAC Scan Time Rdback Profile Res Rdback Det Voltage Rdback DC Gen 1 Rdback DC Gen 2 Rdback Pos 15v Rdback Neg 15v Rdback Rectified RF Rdback Vacuum Gauge Rdback RF Drive Rdback Dynode Rdback PreFilter Rdback RF Lens Bias Rdback Pos 5v Rdback Pos 24v Rdback Exit Cone Rdback Cone Rdback Source Temp Rdback Needle Rdback ESP Current Rdback Source Vec Rdback Source 15v Rdback Source Energy Rdback 5v Ref Rdback CBO Ref Rdback RF Lens Ramp Rdback RF Lens Gain Rdback 13 Status Log Time 0 04 RF Lens Output Rdback Figure 72 Status log showing needle voltage 11 11 2008 3 49 20 PM 0 20000000 0 off 2 64 550 00000000 3 00000000 953 00000000 0 80000000 1 00000000 0 30000000 0 00000000 0 20000000 64 982 01660156 47 57812500 42 36718750 14 93164063 15 38085938 53 95507813 19 14062500 2 17529
20. Thermo Scientific MSQ Plus Mass Detector Getting Started Guide xiii Preface Contacting Us CAUTION Contain waste streams Because the API source can accommodate high solvent flow rates you must make provisions to collect the waste solvent CAUTION Provide adequate fume exhaust systems for the API source solvent waste container and the forepump Your laboratory must be equipped with at least two fume exhaust systems one to vent the waste container connected to the exhaust port API solvent drain on the back of the mass detector and the other to vent the forepump exhaust As described in the MSQ Plus Mass Detector Getting Connected Guide route the blue forepump exhaust hose to a dedicated fume exhaust system Because the exhaust hose acts as a trap for exhaust fumes that would otherwise recondense in the forepump oil the hose should travel at floor level for a minimum of two meters 78 5 in before it reaches the external exhaust system Route tubing from the waste container connected to the exhaust port on the back of the mass detector to a second dedicated fume exhaust system Consult local regulations for the proper method of exhausting the fumes from your system Do not vent the PVC drain tube or any vent tubing connected to the waste container to the same fume exhaust system that is connected to the forepump The forepump exhaust contains pump oil which can seriously contaminate the analyzer optics of the mass spectrometer Contact
21. Time s Polarity Cone SIM 1 564 00 0 50 0 00 5 00 0 20 ye 75 00 1971 00 0 50 4 00 9 00 0 20 ve u iy u o a Rn w Menus The Method Editor view has two menus the Preview menu and the Scan menu as shown in Figure 47 Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 63 1 Creating Instrument Methods Method Editor Figure 47 Method Editor menus Preview All Scans Full Scans SIM Scans Parameters Scans Preview Menu Add Full Add SIM Create Group Delete The Preview menu contains the following commands All Scans Full Scans SIM Scans and Parameters With these commands you can do the following Scan Menu View scan events defined in the Full Scan Events and SIM Scan Events tables in the Chromatogram view View and print a report of the method parameters To use the commands in the Preview menu Choose All Scans to display scan events defined in both the Full Scan Events table and the SIM Scan Events table in the Chromatogram view A colored bar appears for each scan event a full scan event is orange and a SIM scan event is green If you hover the cursor over a bar a tooltip showing the event name start time and end time appears Choose Full Scans to display scan events defined in the Full Scan Events table in the Chromatogram view Each scan event is displayed as an orange bar If you hover the cursor over a bar a tooltip showing the event name
22. by turning it six rotations counterclockwise 20 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 3 Preparing Your LC MS for Operation Preparing the LC for Operation 4 Operate the Edwards forepump for approximately 15 minutes with the gas ballast valve open This allows enough time to return the oil to the forepump and to remove volatile solvents such as water from the oil 5 After you have ballasted the forepump to remove volatile solvents close the gas ballast valve by turning the gas ballast knob clockwise until you feel resistance Note Operating the forepump with the gas ballast valve open increases the rate of oil loss from the pump During normal operations run the forepump with the gas ballast valve closed Preparing the LC for Operation Thermo Scientific Before you tune your MSQ Plus Mass Detector or begin a sequence run check the status of your LC system Verify that the solvent bottles contain the appropriate solvents and that the solvent lines are free of air If the modules of your liquid chromatograph are controlled from the Xcalibur data system verify that they are communicating with the data system and are ready for operation If you have an Accela LC system ensure that the wash bottle contains solvent and that the syringe of the Accela autosampler and the four solvent reservoir lines are free of air If necessary use the Flush command to remove air from the syringe and the tubing that conne
23. compounds which include biological polymers for example proteins peptides glycoproteins and nucleotides pharmaceuticals and their metabolites and industrial polymers You can use ESI mode in either the positive or negative ion polarity mode Matching the charge on the ESI probe to the charge on the preformed ions in solution increases the sensitivity of the analysis Therefore select the ion polarity mode according to the polarity of the preformed ions in solution Acidic molecules form negative ions in high pH solution and basic molecules form positive ions in low pH solution You can vary the flow rate in ESI mode from the LC into the mass detector from 10 uL min to 2000 uL min In ESI the buffer type and the buffer strength both have a noticeable effect on sensitivity Therefore it is important to choose these variables correctly In the case of higher molecular weight proteins or peptides the resulting mass spectrum typically consists of a series of peaks corresponding to a distribution of multiply charged analyte ions The droplet size surface charge liquid surface tension solvent volatility and ion solvation strength all affect the ESI process Large droplets with high surface tension low volatility strong ion solvation low surface charge and high conductivity prevent good electrospray Mixed organic aqueous solvent systems that include organic solvents such as methanol acetonitrile and isopropyl alcohol are superio
24. consists of an ion source a mass analyzer a vacuum system and an ion detector The ion source performs four functions it separates the analytes from the solvent molecules it ionizes the analytes it drives the ionized solutes from the liquid phase to the gas phase and it provides efficient transfer of the ions to the mass analyzer The vacuum system provides the driving force for drawing ions into the mass analyzer and the environment in which the ions can reach the detector without colliding with other gaseous molecules The mass analyzer produces an electric field or a magnetic field or both that allow only ions within a specified mass to charge range to reach the ion detector The ion detector detects the presence of ions as they exit the mass analyzer The MSQ Plus Mass Detector performs two types of complementary atmospheric pressure ionization electrospray ESI and atmospheric pressure chemical ionization APC I It uses a transfer lens to transmit ions to the mass analyzer The mass analyzer consists of a single round quadrupole with an upper mass range limit of 2000 Da at unit resolution The vacuum system consists of an external forepump and an internal turbomolecular pump The external forepump operates from atmospheric pressure down to 107 torr and handles high gas loads of approximately 30 m h at 1 torr The internal turbomolecular pump provides a high 6 vacuum of 10 torr The ion detector is a conversion dynode which allows
25. e Install or update the Xcalibur software Perform a mass scale calibration if you notice a small drift in mass accuracy A full system autotune does the following 1 Resets all tune parameters to their default values 2 Performs a deep tune 3 Performs a resolution set up 4 Performs a mass scale calibration The default tune parameters for your MSQ Plus Mass Detector are set at the factory For information on tuning and calibrating the MSQ Plus Mass Detector see Calibrating the MSQ Plus Mass Detector on page 23 How Do I Optimize the Mass Detector Parameters for My Analytes Optimize the run acquisition parameters for your MSQ Plus Mass Detector from the Tune window For ESI mode optimize the probe temperature needle voltage and cone voltage For APCI mode optimize the probe temperature corona current and cone voltage The optimization procedure requires the use of an LC system containing both an LC pump and an autosampler The autosampler introduces your sample into the solvent flow produced by the LC pump An LC column is not required for this procedure However because LC pumps require a minimum backpressure of 3 bar 40 psi for optimal performance you might need to connect a backpressure regulator between the LC outlet and mass detector inlet After you optimize these settings in the Tune window save them in a tune file When you create an instrument method import the tune file into the Method Editor The Xcalibur
26. file name the data system appends the date and time at which you start data acquisition to the file name 4 Open and download the parameters from a stored tune file a Click the button to the right of the Tune Filename box to open the Select Tune Parameter File Name dialog box shown in Figure 27 Figure 27 Select Tune Parameter File Name dialog box Select Tune Parameter File Name Look in e methods gt a EA Ea templates a detector conditioning tune a peak switching tune a apci leakage current tune 5 detector gain tune 5 phthalate tune fa apcineg tune a electronic noise tune a pre cursor tune ja apcipos tune a esineg tune a quadrupole transmission tune a cali tune E esipos tune a resolution subcon tune a charging tune alhv test tune ba resolution tune a dark current tune a ion energy spread tune a sodium iodide tune a default tune ba mass drift tune a switching tune Filename eps Files of type Tune Files tune z Cancel b Select an appropriate tune file or create a new tune file c Ifyou are a novice user and you want to experiment with the tune parameters open the esipos tune file as shown in Figure 28 MSQ Plus Mass Detector Getting Started Guide 43 5 Manual Tuning in ESI Mode Acquiring and Viewing a Raw Data File Figure 28 Displaying the tune parameters contained in the esipos tune file in the Tune window C Thermolin
27. in your country WEEE Konformitat Dieses Produkt muss die EU Waste Electrical amp Electronic Equipment WEEE Richtlinie 2002 96 EC erf llen Das Produkt ist durch folgendes Symbol gekennzeichnet Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs Entsorgungsfirmen in allen EU Mitgliedsstaaten getroffen damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann Mehr Information ber die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific ber die Verwerter und weitere Hinweise die n tzlich sind um die Produkte zu identifizieren die unter diese ROHS Anweisung fallen finden sie unter www thermoscientific com rohsweee Thermo SCIENTIFIC Conformite DEEE Ce produit doit tre conforme a la directive europ enne 2002 96 EC des Dechets d Equipements Electriques et Electroniques DEEE Il est marqu par le symbole suivant Thermo Fisher Scientific s est associ avec une ou plusieurs compagnies de recyclage dans chaque tat membre de Punion europ enne et ce produit devrait tre collect ou recycl par celles ci Davantage d informations sur la conformit de Thermo Fisher Scientific 4 ces directives les recycleurs dans votre pays et les informations sur les produits Thermo Fisher Scientific qui peuvent aider la detection des substances sujettes la directive RoHS sont disponibles sur www thermoscientific com rohsweee Contents PICIAG G2 ee ee a a E E e A ahnen xi Related
28. method for a specific reagent or solvent Material safety data sheets MSDS summarize information on the hazard and toxicity of specific chemical compounds They also describe the proper handling of compounds first aid for accidental exposure and procedures for cleaning up spills or leaks Producers and suppliers of chemical compounds are required by law to provide their customers with the most current health and safety information in the form of an MSDS Read the material safety data sheets for each chemical you use CAUTION Avoid exposure to potentially harmful materials Always wear protective gloves and safety glasses when you use solvents or corrosives Also contain waste streams and use proper ventilation Refer to your supplier s material safety data sheets MSDS for procedures that describe how to handle a particular solvent corrosive substance or both MSQ Plus Mass Detector Getting Started Guide 101 A Sample Formulations Sensitivity Test Solutions Sensitivity Test Solutions The MSQ Sensitivity Test Kit part number FM104284 contains two 25 mL glass vials One vial contains 10 mg of erythromycin and the other vial contains 10 mg of p nitrophenol The stock solutions which can be stored under refrigeration for up to three months are prepared by adding 10 mL of solvent to each of these vials The working solutions that are used to perform the sensitivity test are prepared by diluting aliquots of the stock solutions Pre
29. that is shipped with your mass detector For most analytes the RF lens bias and ion energy parameters are optimized at 1 0 V and 0 8 V respectively The suggested sensitivity test solution for the positive ion polarity mode is a 5 pg uL solution of erythromycin The preparation of these test solutions is described in Sample Formulations on page 101 If you are an advanced user see the Help for information on the advanced options in the Tune window LC for Direct Control During the manual tuning process you make several injections If your LC system is controlled from the Xcalibur data system open the Instrument Setup window before you open the Tune window so that you can access the Direct Control dialog boxes for the LC pump and the autosampler To open the Instrument Setup window and adjust its size as follows 1 For Xcalibur 2 2 SP1 or later choose Start gt Programs gt Thermo Xcalibur gt Xcalibur On the Roadmap view of the Xcalibur data system click the Instrument Setup icon 40 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 5 Manual Tuning in ESI Mode Selecting Your Tune Options The Xcalibur data system displays the Instrument Setup window with icons for all of the currently configured devices for your LC MS instrument arranged down the left side of the view Instrument Setup pages and dialog boxes for the selected device are displayed on the right side of the view You can access additional dialo
30. the system or leave the system unused for a period of several months For information about the status of the MSQ Plus Mass Detector use the Server icon shown in Figure 6 and the Information view of the Xcalibur data system shown in Figure 7 The server software handles the communication between the MSQ Plus Mass Detector and the Xcalibur data system The Xcalibur data system controls the modules of your LC MS system Figure 6 Server icon Server icon aut Figure 7 Xcalibur Roadmap view Thermo Xcalibur Roadmap un Manager N a Ready To Download quence i ample Name Working On Position jaw File Roadmap view Information 4 view The Server icon shown in Figure 6 mimics a tristate LED display red green yellow Its states have the following meanings e Steady red when the power is on and the instrument is vented or an error has occurred within the system e Flashing yellow when the instrument is pumping down Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 17 3 Preparing Your LC MS for Operation Checking the Oil Level in the Oil Mist Filter and the Forepump e Steady yellow when the instrument is pumped down but not in Operate mode e Steady green when the instrument is pumped down and in Operate mode To check the status of your LC MS instrument 1 Launch the Xcalibur data system by doing one of the following e From the Windows desktop double click the Xcalibur icon
31. x Xcalibur or e For the Xcalibur 2 2 SP1 data system or later choose Start gt Programs gt Thermo Xcalibur gt Xcalibur The data system opens to the Thermo Xcalibur Roadmap view shown in Figure 7 on page 17 If your instrument configuration contains an MSQ Plus Mass Detector the Server icon appears in the system tray of the Windows taskbar next to the time display If the Server icon does not appear when you start the data system check the configuration of your instrument and the USB cable connection to the MSQ Plus Mass Detector You do not need to add specific configuration information for the MSQ Plus Mass Detector but you do have to add the mass detector to your instrument configuration See Configuring Your LC MS Instrument on page 11 and the Help for information on configuring your instrument display it Figure 7 shows the Status page of the Information view on the Roadmap view for an LC MS instrument that includes an Accela autosampler an Accela pump and an MSQ Plus Mass Detector 3 Click the listing of each configured device to display its status in the lower portion of the Status page Checking the Oil Level in the Oil Mist Filter and the Forepump 18 The forepump is external to the MSQ Plus Mass Detector and requires routine maintenance to keep it running at its optimum performance level Note You can find more information on operating and maintaining the forepump in the manual that a
32. 0 10 0 190 00 195 00 oo 00 205 00 Show SIM Scans Spectrum view Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 61 1 Creating Instrument Methods Method Editor Per Method Parameters Table You can use the Per Method Parameters table shown in Figure 44 to select the ionization mode ESI or APCI and set the probe temperature Typical probe temperature settings range from 350 to 650 C depending on the ionization mode and the flow rate of the mobile phase See Table 1 on page 7 and Table 2 on page 7 If the Per Methods Parameters table is not displayed click the Show Per Method Parameters Table bar to display it Figure 44 Per Method Parameters table Per Method Parameters Description Setpoint lonization Mode ESI Probe Temperature C 350 00 Hide Per Method Parameters Full Scan Events Table Use the Full Scan Events table shown in Figure 45 to define all the full scan events that you want to acquire in your method The parameters available to you in the Full Scan Events table are listed in Table 7 on page 69 Figure 45 Full Scan Events table showing one full scan event Full Scan Events Name Mass Range Time Range min Peak Format Scan Time s Polarity Cone Fou 1 00 00 10 00 5 00 i 200 00 To perform source fragmentation you can create two or more identical scan events and then enter increasing cone voltages into the Cone V
33. 12 Materials and equipment required to prepare calibrant Sheet 2 of 2 Materials and equipment Quantity 125 mL Erlenmeyer flask or equivalent 1 250 mL plastic graduated cylinder 1 1 mL adjustable mechanical pipette calibrated or equivalent 1 Analytical balance 1 Preparing a Concentrated Stock Solution of the Calibration Mixture The stock solution contains 10 mM cesium iodide MW 259 8 g mole 25 mM potassium iodide MW 166 0 g mole and 650 mM sodium iodide MW 149 9 g mole in 50 50 isopropanol water To prepare a stock solution of the calibration mixture 1 Add 50 mL of HPLC grade water to the 125 mL Erlenmeyer flask 2 Weigh out 260 mg 10 mg of cesium iodide Then quantitatively transfer the cesium iodide to the flask Record the actual weight manufacturer and lot number of the cesium iodide CsI used 3 Weigh out 415 mg 10 mg of potassium iodide Then quantitatively transfer the potassium iodide to the flask Record the actual weight manufacturer and lot number of the potassium iodide KI used 4 Weigh out 9 74 g 0 10 g of sodium iodide Then quantitatively transfer the sodium iodide to the flask Record the actual weight manufacturer and lot number of the sodium iodide Nal used 5 Add 50 mL of isopropanol to the flask and swirl to mix the solution 6 Allow the solution to cool and transfer the solution to a 100 mL glass bottle 7 Label the bottle 10 mM CsI 25 mM KI and 650 mM Nal
34. 297 14 99267578 7501953125 1 00585938 4 96093750 24 05273438 4 26757813 69 70214844 536 02539063 3 07617188 8 98437500 5 03417969 15 23437500 14 62890625 5 09765625 0 00000000 9 76562500 1 90429688 9 08203125 9 Using Qual Browser Viewing Reports 5 Choose View gt Report gt Tune Method to display the Tune Method report The Tune Method report displays the settings that were determined during the full system autotune procedure as shown in Figure 73 MSQ Plus Mass Detector Getting Started Guide 97 9 Using Qual Browser Viewing the Mass Spectrum for a Specific Time Point Figure 73 Report for autotune settings C iMy Documentsi 20ppm_caf_sim1 MSQ Plus 20612 2 0 SP1 Build 1 11 11 2008 3 49 20 PM 20ppm_caf_siml Segment 1 Lowest Calibrated Mass Highest Calibrated Mass Number of Coeffs Coeff 0 Coeff 1 Coeff 2 Calibration Deviation Calibration Delta RMS Nitrogen Gas Calibrant Resevoir Switch Flow Operate Vacuum Pre filter Pulse RF Frequency LM Res Mid Point HM Res Mid Point Pre scan Ion Counting Threshold Vacuum OK Vacuum Status 22 98980000 1971 61490000 3 0 00716622 1 00002063 0 00000000 0 04550802 0 05333739 On off off On 1 On 236755120 63 13766 On The non zero and non unity values for the three coefficients indicate that a successful autotune has been stored on this system A clean installation or a reinstallation of the softwar
35. 4 37 772 39 0 01 922 36 920 28 924 28 922 35 0 07 0 137 1072 25 1070 24 1074 24 1072 26 0 01 0 00 Be 1222 14 1220 15 1224 15 1222 12 0 02 j as ra 1372 04 1370 01 1374 01 1372 06 0 03 0 13 1521 93 1519 96 1523 96 1521 97 0 03 22 99 1971 61 1671 83 1669 86 1673 86 1671 87 0 04 i i 1821 72 1819 76 1823 76 1821 71 0 01 Diagnostic Messages 1971 61 1969 61 1973 61 1971 60 0 01 No Messages AutoTune Status Pass Reviewed By ___ Date Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 33 4 Calibrating the MSO Plus Mass Detector Performing a Mass Scale Calibration Performing a Mass Scale Calibration Perform a mass scale calibration every three to six months as part of a standard maintenance program or if you notice a drift in the mass accuracy of the mass detector Note Always perform the mass scale calibration procedure in ESI mode Before you perform a mass scale calibration prepare your system as described in Preparing the MSQ Plus Mass Detector for Calibration on page 24 To perform a mass scale calibration 1 Set the LC pump to deliver a solvent composition of 50 50 acetonitrile water at a flow rate of 0 2 mL min 2 Right click the Server icon to display the shortcut menu shown in Figure 19 on page 32 and choose Instrument Tune and Calibration to open the Instrument Tuning and Calibration wizard shown in Figure 20 on page 32 3 Select the Mass Scale Calibration option and click Ne
36. 57 Method Ruin sans re DE a AA 58 Method Options View ony ine en ee A DE 60 Chiro Mate rainy Views asien ee re Sai 61 Per Method Parameters Table csi ya ar 62 Full Scan vents Bible ns 2a nie 62 SIM Seam Events Table usa ara ee ee 63 Mein seen ea re Re 63 Creating an LC MS Instrument Method u aa 65 Opening the Instrument Setup Window 1 2 0 0 00 eee eee ee eee 65 Specifying the Method Parameters for the MSQ Plus Mass Detector 65 Specifying the Method Parameters for the LC System 0 70 Saving the Wishes mas Be aah hie Sethe 71 Chapter8 Creating and Running Sequences 0 0eee cece eee eee eens 75 Creating a Single Sample Sequence u 5 ul ae en ee een 75 Opening Sequence Setup Window in ei 75 Creating the Sequence au le ae T Saving the Sequence ssr an ra eee ea Seah EEE dl de P R 79 viii MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Thermo Scientific Chapter 9 Appendix A Contents Starting Data Acquisition 6 cc nenn nenn 80 Openinga sequence Files san een le 81 Selecting the Rows That You Want to Run a ee 82 Selecting the Run Options and Starting the Run 00 82 Viewing the Data as It Is Acquired u a dee eee hopews 85 Reviewing Real Time Data a daw Bol Seiner het 85 Adding Cells to the Displays toca town Frust Rt re ala 86 Using Qual Browser 00 e cece eee eee eee eee nennen 89 Cell Sites ses enter 89
37. 78 Column Arrangement icon 78 compliance FCC iii regulatory iii compliance WEEE v cone voltage 40 46 50 55 Confirm Set Electron Multiplier Voltage dialog box 37 contacting us xiv corona current 6 8 9 50 55 68 corona pin 49 deep tune 7 8 detector gain calibration 23 34 35 Direct Control dialog box 25 40 51 55 documentation survey xv E Edwards forepumps 19 electromagnetic compatibility iii electron multiplier gain 35 electrospray effect of buffers on sensitivity 4 effect of solvent pH 5 factors affecting 4 molecular weights of compounds 4 MSQ Plus Mass Detector Getting Started Guide 109 Index F parameters to optimize 8 performed by MSQ Plus Mass Detector 2 polar compounds 3 4 polarity modes 4 probe temperature 6 recommendations for generating stable 4 setting up for calibration 24 spectra produced 4 tuning acquiring data in raw file 44 optimizing acquisition parameters 39 erythromycin 102 erythromycin stock solution 102 ESI probes 2 25 50 ESI See electrospray esineg tune file 9 esipos tune file 9 40 43 F FCC compliance iii File Save Audit Trail dialog box 72 File Summary Information dialog box 71 79 flow rates 5 fluorescence detectors forepumps checking oil level in 18 draining oil from 20 Edwards 19 function 2 Full Scan Events table opening 58 parameters on 68 purpose 62 switching to SIM Scan Events table 60 viewing mass spectrum of calibrant solution 30 full system a
38. File gt Save As to open the Save As dialog box shown in Figure 51 Figure 51 Save As dialog box Save As Save in methods Eh templates File name Instrument Controlmeth Save as type Methods meth Cancel Help Header Information No file selected 2 Browse through the directory tree to find the Drive Xcalibur methods directory 3 Type a file name in the File Name box 4 Click Save to open the File Summary Information dialog box shown in Figure 52 Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 71 7 Creating Instrument Methods Creating an LC MS Instrument Method Figure 52 File Summary Information dialog box File Summary Information x 5 Type a description of the Method file in the Description box 6 Click OK to open the File Save Audit Trail dialog box shown in Figure 53 Figure 53 File Save Audit Trail dialog box File Save Audit Trail x New Instrument Method 72 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 7 Creating Instrument Methods Creating an LC MS Instrument Method 7 Type a comment concerning the changes you made to the instrument method into the Comment box 8 Click Continue to close the File Save Audit Trail dialog box and save the Instrument Method Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 73 Creating and Running Sequences This chapter describes how to a
39. Getting Started Guide Thermo Scientific 8 Creating and Running Sequences Starting Data Acquisition Opening a Sequence File Start data acquisition by opening a sequence file containing the sample that you want to run To open a sequence file 1 From the Sequence Setup view in the Xcalibur Roadmap view choose File gt Open to display the Open dialog box shown in Figure 60 Figure 60 Open dialog box showing the selection of a sequence file Look in E methods ef templates iy Test Mix Sequence sid File name Test Mix Sequence sld Files of type Xcalibur Sequences sld v Cancel Help Header Information Created Monday January 12 2004 3 42 22 PM By acook Logon ID acook Times saved 1 Last edited Monday January 12 2004 3 42 22 PM By acook Logon ID acook Summary info New Sequence 2 Browse to the appropriate folder 3 Select the sequence that contains the sample you want to run 4 Sequence files are identified by their sld file extension 5 Click Open The Xcalibur data system opens the selected sequence Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 81 8 Creating and Running Sequences Starting Data Acquisition Selecting the Rows That You Want to Run Next select the rows that you want to run To select the row or rows that you want to run 1 Highlight the sequence row or rows that you want to run even if the sequence co
40. PR PA AA AR PE AA AAAA AAAA PR PT PA AT PE PA AA AE PT eA PAE AE PE PAN rE rE PPA PN rR PE AAAA PR PT AN AL PE A AL rR RP EE NOT SAVED A A A A A A A A A A 2 J A 2 A 2 A 2 A A 2 2 A A A Aj A A 2 2 A A A 2 A 2 A A A 2 MSQ Plus For information on making automated injections consult the following chapters in this manual e For information on creating tune files for ESI experiments see Manual Tuning in ESI Mode on page 39 e For information on creating tune files for APCI experiments see Manual Tuning in the APCI Mode on page 49 e For information on creating instrument methods see Creating Instrument Methods on page 57 e For information on creating a sequence spreadsheet to automate the injection of a set of samples see Creating and Running Sequences on page 75 10 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Configuring Your LC MS Instrument This chapter describes how to configure your LC MS instrument The typical inlet for the MSQ Plus Mass Detector is a liquid chromatograph The Xcalibur 2 2 SP1 data system supports liquid chromatography systems manufactured by Thermo Fisher Scientific and other manufacturers During installation a Thermo Fisher Scientific service engineer will connect your MSQ Plus Mass Detector and a supported liquid chromatograph In addition the service engineer will add these supported devices to your Xcali
41. Q Plus Mass Detector Getting Started Guide 29 4 Calibrating the MSO Plus Mass Detector Preparing the MSQ Plus Mass Detector for Calibration The MSQ Plus Mass Detector is ready for calibration To view a mass spectrum of the calibrant solution before you calibrate your mass detector go to the next topic Viewing the Mass Spectrum of the Calibrant Solution Optional Viewing the Mass Spectrum of the Calibrant Solution Optional You can optionally view the mass spectrum produced by infusing the calibrant solution To view the mass spectrum of the calibrant 1 Open the Advanced Options version of the Per Method Parameters table For instructions on displaying the Advanced Options parameters see Flushing Air from the Lines of the Reference Inlet System on page 28 2 If the nitrogen gas is off turn it on by clicking the Nitrogen Gas On Off toggle button 3 If the MSQ Plus Mass Detector is not in Operate mode start its operation by clicking the Operate toggle button 4 In the Per Method Parameters table set the following parameters Ifthe probe temperature is not already set to 350 C click the Probe Temperature Setpoint box type 350 and then press ENTER Ifthe needle voltage is not already set to 3 kV click the Needle kV Setpoint box type 3 and then press ENTER 5 In the Full Scan Events table shown in Figure 17 set the scan parameters so that you can view the entire mass spectrum of the calibrant sol
42. SDS 101 Thermo Scientific meth file 71 Method Editor Chromatogram view 61 components of 58 Full Scan Events table 62 Method Options view 60 Per Method Parameters table 62 Preview menu 64 Scan menu 64 selecting method options 67 SIM Scan Events table 63 Welcome page 66 Method Options view 58 60 67 microbore LC 6 MSQ Plus button 66 MSQ Plus Configuration dialog box 11 12 MSQ Plus Mass Detector communication with Xcalibur data system 17 components of 2 configuring 11 default tune parameters 8 features of 1 2 interface to Accela LC system 2 5 levels of calibration in 23 Method Editor See Method Editor 58 preparing for calibration 24 purpose of 1 serial number of 13 setting up for ESI mode 24 states of 16 types of ionization performed 2 3 Welcome page 57 MSQ Plus Mass Detector Calmix Kit 105 MSQ Plus Method Editor dialog box 10 MSQ Sensitivity Test Kit 102 needle voltage 6 8 9 39 40 46 68 97 New Sequence Template dialog box 75 76 nitrogen gas 6 15 16 26 nitrogen regulators 15 non polar compounds 3 non volatile buffers 6 0 oil mist filters contamination of 18 draining oil from 20 Open dialog box 81 Open Raw File dialog box 45 55 93 Thermo Scientific Index N P Per Method Parameters table displaying 27 44 62 purpose 62 phosphate 6 pin icon 85 89 p nitrophenol 102 p nitrophenol sensitivity test solution 104 p nitrophenol stock solution 102 polar compounds 3 4 polarity switching 62 Pr
43. Safety and Special Notices e Safety Precautions e Contacting Us To suggest changes to documentation or to Help Complete a brief survey about this document by clicking the button below Thank you in advance for your help SURVEY Related Documentation In addition to this guide Thermo Fisher Scientific provides the following documents as PDF files for the MSQ Plus Mass Detector MSQ Plus Mass Detector Hardware Manual MSQ Plus Mass Detector Getting Connected Guide MSQ Plus Mass Detector Preinstallation Guide MSQ Plus Mass Detector Calmix Kit Preparation Guide e Dionex AXP AXP MS Metering Pump Operators Manual Thermo Scientific MSQ Plus Mass Detector Getting Started Guide xi Preface Safety and Special Notices Dionex Chromelon MSQ Plus Operators Guide Dionex MSQ Plus Facilities Preinstallation Requirements Guide Dionex MSQ Hardware Manual e Dionex Installation and Commissioning Guide Dionex MSQ Preventive Maintenance e Dionex MSQIOLA Nitrogen Generator for Mass Spectrometers e Dionex MSQI8LA Nitrogen Generator for Mass Spectrometers Dionex N118LOA N418LA Unpacking amp Installation e Dionex N 18KLA Nitrogen Generator User Manual Dionex MSQ Getting Started e Safety and Regulatory Guide You also receive a printed copy of the Safety and Regulatory Guide with your MSQ Plus Mass Detector This guide contains important safety information about Thermo Scientific LC and MS systems Make sure tha
44. Viewing the Mass Spectrum of the Calibrant Solution Optional Verifying that the MSO Plus Mass Detector is Set Up for ESI Mode 24 To perform a full system autotune or a mass scale calibration the MSQ Plus Mass Detector must be set up in ESI mode Figure 10 shows an MSQ Plus Mass Detector set up for operation in ESI mode Figure 10 MSQ Plus Mass Detector set up for operation in the ESI mode To verify that the mass detector is set up for ESI mode 1 Open the front door of the mass detector by depressing the latch on the left side of the mass detector MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 4 Calibrating the MSO Plus Mass Detector Preparing the MSQ Plus Mass Detector for Calibration Note When the front door is open do not attempt to insert a screwdriver or other device into the safety interlock switch because a severe shock can result 2 Ensure that the ESI probe is connected and that the corona pin knob is in the vertical position For instructions on switching your mass detector to ESI mode see the MSQ Plus Mass Detector Hardware Manual Setting Up the LC System To perform a full system autotune or a mass scale calibration connect an LC pump to your MSQ Plus Mass Detector The LC pump must be set to deliver 50 50 acetonitrile water at a flow rate of 200 uL min If your LC system is set up for chromatography remove the LC column and replace it with a backpressure regulator
45. a scan event Full Scan ES Start time 0 00 mins End time 2 02 mins Duration 2 02 mins 4 To move the scan window of an event place the cursor on the colored bar until this icon appears 5 Drag the bar to the retention time window that you want A pop up window appears showing the event name start time end time and duration to assist in the positioning of the bar The new values are automatically updated in the Time Range column of the events table Specifying the Method Parameters for the LC System In the Instrument Setup view icons for all of the currently configured instrument components appear on the left side of the view Instrument Setup pages and dialog boxes for the selected instrument component appear on the right side of the view To create an instrument method that controls your LC system 1 Select the device that you want to set up by clicking its icon in the View bar The Xcalibur data system displays the Instrument Setup view for the instrument that you selected This view can consist of one or more pages or dialog boxes 2 Select the Instrument Setup options that are appropriate for your application 70 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 7 Creating Instrument Methods Creating an LC MS Instrument Method Saving the Method You can save the instrument method in a file with a meth file name extension To save the instrument method as a METH file 1 Choose
46. a time interval of 200 milliseconds for switching between positive and negative polarity modes The MSQ Plus Mass Detector measures only 30 cm 12 in wide and integrates seamlessly with the Accela LC system The following new innovations for this mass detector make it ideal for the chromatographer e ESI and APCI FastLoc probes which allow you to switch between the two ionization modes in less than a minute e Wipe clean M Path ion source with a patented cone wash system for ultra rugged performance with non volatile phosphate buffers e Automated full system autotune e Interactive method setup with 10 built in editable templates The M Path source and the cone wash system allow you to use mobile phases that would ordinarily be prohibited because of their tendency to clog the entrance cone of the ion source The positioning of the probe insert directs non volatile components such as those from mobile phase buffers and ion pairing agents or sample matrices away from the orifice of the entrance cone A low flow of solvent 100 to 250 L min from the cone wash system spraying the edge of the entrance orifice helps to prevent a build up of non volatiles during an LC MS run The tuning and calibration process that is required for all quadrupole mass analyzers to optimize their mass range mass accuracy and mass resolution is completely automated with wizards Figure 1 shows the user interface for these wizards The service enginee
47. acquisition method 44 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Thermo Scientific 5 Manual Tuning in ESI Mode Acquiring and Viewing a Raw Data File 3 Start the acquisition of data by clicking the Start Acquiring icon shown in Figure 29 in the Tune window toolbar Figure 29 Start Acquiring and Stop Acquiring icons in the Tune window toolbar File View Help 2153 amp ce e Stop Acquiring button Start Acquiring button From the Roadmap view double click the Qual Browser icon sae to open the Qual Browser window shown in Figure 30 Figure 30 Qual Browser window FR Qual Browser Eile View Tools Help sle S Hel bite 8 Eee Az m See gt Bl dal till D Ready 5 Open your raw data file a From the Qual Browser menu bar choose File gt Open to open the Open Raw File dialog box b Select the raw data file that you are acquiring c Click Open to open the file in the Qual Browser window and close the Open Raw File dialog box shown in Figure 31 MSQ Plus Mass Detector Getting Started Guide 45 5 Manual Tuning in ESI Mode Acquiring and Viewing a Raw Data File Figure 31 Open Raw File dialog box Open Raw File Look in e data Er Erythromyein_1 Files of type Raw Files raw Cancel m Header Information Replace Window C P it Default Layout v 6 In
48. an while you are acquiring data The Xcalibur data system does not include anti virus software Checking the Status of the LC MS Instrument If the MSQ Plus Mass Detector has not been in use recently it might be in one of four possible states e The system might be under vacuum with the nitrogen gas flowing e The system might be in Off mode which means that the nitrogen flow is reduced to a bleed through the API probe the electron multiplier and conversion dynode are turned off the power to the ion optics is turned off and the power to the probe heater is turned off but the system is still under vacuum e The system might be vented which means it is no longer under vacuum e The system might not be connected During typical usage the MSQ Plus Mass Detector is either left on with the nitrogen flowing or off with both the nitrogen flow and probe heater turned off The forepump is always left powered on and the source is always left under vacuum If the system has been moved or has been left unused for several months it might be vented or powered off For instructions on pumping down a vented system see the MSQ Plus Mass Detector Hardware Manual 16 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 3 Preparing Your LC MS for Operation Checking the Status of the LC MS Instrument Note Do nor vent the system unless you plan to move the MSQ Plus Mass Detector perform maintenance on an internal component of
49. and choose Manual Tune as shown in Figure 12 26 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 4 Calibrating the MSO Plus Mass Detector Preparing the MSQ Plus Mass Detector for Calibration Figure 12 Server shortcut menu Manual Tune Instrument Tune and Calibration Vent Exit 3 If it is not already open open the Per Method Parameters table of the Tune window shown in Figure 13 by clicking the Show Per Method Parameters bar at the top right of the Tune window Figure 13 View of Per Method Parameters table with Operate on and Nitrogen Gas on Description Readback Setpoint Tune Control Probe Temperature C 0 349 Needle kV 0 0 3 0 Acquisition Control Retention Time mins 0 00 n a General Control Operate n a On Nitrogen Gas n a On lonization Mode n a ESI m EEE 4 Click the Nitrogen Gas On Off toggle button to turn the nitrogen flow on The toggle button turns green and the text changes to On Within a few seconds you hear the flow of the nitrogen gas N Click the Operate toggle button to place the system in the operate mode Note The gas flows are preset and do not require adjustment 6 Click the Probe Temperature Setpoint box Type 350 in the box and then press ENTER The probe temperature rises to 350 C If the MSQ Plus Mass Detector has not been used recently or was last used in APCI mode go to the next topic Baking Out the Prob
50. arameters open the apcipos tune file as shown in Figure 37 For most analytes the RF lens bias and ion energy parameters are optimized at 1 0 V and 0 8 V respectively Figure 37 Displaying the tune parameters from the apcipos tune file in the Tune window C Thermo instruments MSQ Cali methods apcipos tune MSInst Eile view Help 5 6 eo MSQ P us Tune ananin dk Description Readback Setpoint N o Tune Control 100 8F 0 00e 000 BPM 0 00 Probe Temperature C 0 550 Corona pA 0 0 10 0 Acquisition Control Retention Time mins 0 00 n a General Control Operate n a Off n a Off Nitrogen Gas lonization Mode n a BEI APCI mode ameters 5 2 3 2 2 5 u 3 0 732 5 733 0 733 5 734 0 7345 735 0 735 5 736 0 736 5 Name 1 Mass I Span Time Range Peak Format 1 Scan Time 1 Polarity 1 Cone Rdbk Zoom On Off NEE ee 734 50 4 00 0 00 Profile 0 20 ve 70 0 1 j Positive ion polarity mode ve Ready 000000 bytes sec d Click Open to download the tune parameters and close the dialog box Acquiring and Viewing a Raw Data File You can acquire a raw data file as you adjust the tune parameters for your compound of interest To acquire a raw data file as you adjust the tune parameters 1 Start the mass detector a Ifthe Per Method Parameters table is not open see Figure 13 on page 27 open it by clicking the Show Per Method Parameters bar b Turn on the nitrogen fl
51. at which the electron multiplier is operated Under normal operating conditions this decrease in detector gain which translates as a loss in sensitivity necessitates a detector gain calibration every three to four months If the detector is subject to heavy use you might need to perform a detector gain calibration every two months You can automatically calibrate the gain of the electron multiplier by running the detector gain calibration routine as described in the following procedure To calibrate the gain of the electron multiplier 1 Ensure that you have prepared your MSQ Plus Mass Detector for calibration as described in the Preparing the MSQ Plus Mass Detector for Calibration on page 24 2 In the area of the Tune window do the following e In the Peak Format list select Profile e In the Mass box type 300 or an equivalent value for the center mass corresponding to a relatively low intensity peak lt 104 cps IMPORTANT The gain routine strives to achieve conditions where it is receiving single ion counts Therefore it is important to scan a mass region where only low level chemical noise is present Avoid placing the center mass at a high intensity peak Doing so will make it harder for the software to control the ion flow rate and cause the tuning process to fail 3 Right click the Status Indicator and choose Instrument Tune and Calibration to open the Instrument Tuning and Calibration wizard See Figure 19 on
52. ate a processing method and reprocess your stored data files at a later date Processing methods have a pmd file extension 2 Set the parameters in the Samples area a Type 1 in the Number Of Samples box b Type 1 in the Number Of Injections box c Type the vial position in the Initial Vial Location box d Type an identifying name for the sample in the Base Sample ID text box e Labeling a sample with a base sample ID is optional If you do not enter a base sample ID the data system automatically uses the vial position as the base sample ID If you enter a base sample ID the data system automatically appends the vial position to your entry 3 Click OK to open your sequence spreadsheet as shown in Figure 56 Figure 56 Sequence Setup view showing a newly created one line sequence A Untitled Open Sequence Setup File Edit Change Actions Yiew GoTo Help Dede Sampl File Name Sample ID Path Inst Meth Unknown Test Mix01 First Injectiond 1 C Xcalibur methods Surveyor Instrument Control For Help press Fi NUM 1 12 2004 11 43 PM NOT SAVED Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 77 8 Creating and Running Sequences Creating a Single Sample Sequence The injection volume displayed in the Inj Vol column matches the injection volume contained in your instrument method You can override this injection volume value 4 If you want to change the injection volume double click the
53. boxes To perform polarity switching you can create two identical scan events one with the ve polarity and the other with the ve polarity 62 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 7 Creating Instrument Methods Method Editor SIM Scan Events Table Use the SIM Scan Events table shown in Figure 46 to monitor a limited number of mass to charge ratios characteristic of a target compound or set of compounds The mass analyzer switches between the selected mass to charge ratios each value being monitored for a period of time called the dwell time before moving on to the next event SIM selected ion monitoring scan events offer the following e Improved sensitivity because more time is spent monitoring the ions of interest rather than scanning across the full mass range e A wide and linear dynamic range without modification of the tuning parameters which is important in isotope dilution techniques that use co eluting labeled standards and in the analysis of trace components Better definition of the chromatographic peaks because more data points can be recorded across each peak e Reduced raw file sizes compared to a full scan because SIM scans record only a limited amount of data relating to the particular mass to charge ratio of interest Figure 46 lists the parameters available in the SIM Scan Events table Figure 46 SIM Scan Events table SIM Scan Events Name Mass Span Time Range min Dwell
54. bur instrument configuration To modify your LC MS instrument refer to the MSQ Plus Mass Detector Getting Connected Guide for instructions on connecting the modules of a liquid chromatograph to your MSQ Plus Mass Detector Various configuration options are available for each of the supported liquid chromatographs In addition you can specify the serial number and a location code company asset ID or custom label for the MSQ Plus Mass Detector Before you operate your system verify that your instrument contains the appropriate configuration settings Contents e Configuring the Mass Detector e Configuring the LC System Configuring the Mass Detector You can track the serial number of the MSQ Plus Mass Detector used in experiments by entering its serial number in the MSQ Plus Configuration dialog box The serial number appears in the autotune report To add the MSQ Plus Mass Detector to your instrument configuration 1 From the Windows taskbar in Xcalibur 2 2 SP lor later choose Start gt Programs gt Thermo Foundation x x gt Instrument Configuration The Thermo Foundation Instrument Configuration window appears as shown in Figure 3 Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 11 2 Configuring Your LC MS Instrument Configuring the Mass Detector Figure 3 Thermo Foundation Instrument Configuration window 22 Thermo Foundation Instrument Configuration Device Types Al Available Devic
55. ccompanies it As oil is vaporized by the forepump during normal operation the oil mist filter fills with condensed oil In addition the oil in the forepump becomes contaminated with volatile solvents which can cause corrosion and reduce the lifetime of the forepump Once the oil level in the oil mist filter rises above the maximum oil level mark the oil mist filter becomes ineffective in trapping exhaust fumes See Figure 8 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 3 Preparing Your LC MS for Operation Checking the Oil Level in the Oil Mist Filter and the Forepump Figure 8 Edwards forepump and attached oil mist filter showing the maximum oil level for efficient performance of the filter gt 00 MSQ Plus Mass Detector To MAINS ON OFF a exhaust vent PUMP OUT GASIN 6 BARS MAX MAINS IN Gas ballast knob Maximum oil level mark Oil return tubing a 220 V ac Check the level and color of the oil in the forepump also referred to as a backing pump a roughing pump or a rotary vane pump at least once a month Check the oil level in the oil mist filter that is attached to the Edwards forepump on a daily basis To check the oil level in the forepump look through the oil sight glass at one end of the forepump The oil level should be between the upper and lower marks positioned next to the win
56. ce inlet reservoir bottle through the tubing and into the 500 uL sample loop for 35 seconds At a flow rate of 200 uL min it takes 2 5 minutes to empty the sample loop During this time you can view a mass spectrum of the calibrant solution in the Peak Display area of the Tune window as shown in Figure 18 Figure 18 Mass spectrum of calibrant solution with centroid peak format 63 82 100 s0 50 Relative Abundance 1978 25 200 400 600 800 1000 1200 1400 1600 1800 2000 miz Performing a Full System Autotune After you move your MSQ Plus Mass Detector to a new environment perform maintenance on the inner components of the source block or reinstall or upgrade the Xcalibur software you must perform a full system autotune Note Always perform a full system autotune in ESI mode To perform a full system autotune 1 Ensure that you have prepared your mass detector for calibration as described in Preparing the MSQ Plus Mass Detector for Calibration on page 24 Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 31 4 Calibrating the MSO Plus Mass Detector Performing a Full System Autotune 2 Set the LC pump to deliver a solvent composition of 50 50 acetonitrile water at a flow rate of 0 2 mL min 3 Right click the Server icon to display a shortcut menu and then choose Instrument Tune and Calibration as shown in Figure 19 Figure 19 Server shortcut menu Manual Tune Instru
57. cquire and view real time data for a single sample Contents e Creating a Single Sample Sequence e Starting Data Acquisition e Viewing the Data as It Is Acquired Creating a Single Sample Sequence To set up a sequence to inject a single sample open the Sequence Setup window create the sequence and save the sequence Opening Sequence Setup Window From the Sequence Setup view you can open the New Sequence Template dialog box To open the New Sequence Template dialog box 1 Click the Sequence Setup icon igi on the Xcalibur Roadmap view to open the Sequence Setup view l A view similar to that shown in Figure 54 appears Figure 54 Sequence Setup view A Untitled Open Sequence Setup File Edit Change Actions View GoTo Help DB gt l pmu Sample Type FileName Sample ID Path Inst Meth Proc Meth Position Inj Vol Level 0 1 Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 75 8 Creating and Running Sequences Creating a Single Sample Sequence 2 From the Sequence Setup view choose File gt New A New Sequence Template dialog box similar to the one shown in Figure 55 appears The tray type and vial selections depend on the configuration of the autosampler Figure 55 New Sequence Template dialog box for an LC MS with an Accela autosampler New Sequence Template General Base File Name PO Starting Number Path Po Browse Instrument Method Browse Processing Method PY
58. cts the syringe to the wash bottle If you are using an Accela pump use a Purge command to remove air from the solvent reservoir lines or to draw fresh solvent through the lines For more information on the Accela LC system refer to the Accela UHPLC System User Guide for LC Devices Note If you are using a viscous wash solvent such as a methanol water mix reduce the flush speed for the Accela autosampler from its default of 400 to 100 uL s MSQ Plus Mass Detector Getting Started Guide 21 Calibrating the MSQ Plus Mass Detector The MSQ Plus Mass Detector software includes an automated wizard that provides three levels of calibration e Full system autotune This procedure is performed by a Thermo Fisher Scientific service engineer during the initial installation of the MSQ Plus Mass Detector You do not need to repeat this procedure unless you perform maintenance on the inner components of the source block or reinstall or upgrade the Xcalibur software e Mass scale calibration This procedure is a subset of the full system autotune procedure You should perform a mass scale calibration if you notice a drift in the mass accuracy of your analyses or every 3 to 6 months as part of your routine maintenance schedule for the MSQ Plus Mass Detector e Detector gain calibration This procedure resets the gain of the electron multiplier as it ages with use Note To perform any of these calibration procedures you must connect an LC p
59. d Guide vii Contents Chapter4 Calibrating the MSO Plus Mass Detector 0 0ee cece eee es 23 Preparing the MSQ Plus Mass Detector for Calibration 24 Verifying that the MSQ Plus Mass Detector is Set Up for ESI Mode 24 Setting Up the LC System na 25 Checking the Solvent Levels in the Reference Inlet System 25 Setting the Gas Flows and Probe Heater Temperature 26 Baking Out the Probe Optional na Brenn 28 Flushing Air from the Lines of the Reference Inlet System 28 Viewing the Mass Spectrum of the Calibrant Solution Optional 30 Performing a Full System Autotune ssa fie Sua pate ea 31 Performing a Mass Scale Calibration 0 0 eee 34 Performing a Detector Gain Calibration 0 0 0 00 c eee eee eee 34 Chapter5 Manual Tuning in ESI Mode 00 0 cece eee eee eee eens 39 Setting Up the LC for Direct Control u anne iets an mien wake ieee 40 Selecting Your Tune Options 22 2a aan ea a 41 Acquiring and Viewing a Raw Data File 0 24 ar sa ae 44 Chapter6 Manual Tuning in the APCI Mode zu222 ssenen eee cece nenn 49 Opening the Instrument Setup Window 2 2222 cece eee 51 Selecting Your Tune Options ew hoy UELI Eee oe 51 Acquiring and Viewing a Raw Data File ses 64 pena oA geass ee 54 Chapter7 Creating Instrument Methods 00cc cece eee eee eee eee eee 57 Welcome Ay een else
60. data system imports these parameters with the tune file e Needle voltage or corona current e RF lens bias 8 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 1 Introduction How Do Create Instrument Control Methods e Ion energy e Low mass resolution e High mass resolution You cannot modify the RF lens bias ion energy low mass resolution and high mass resolution parameters The correct values are embedded when you use any of the following files as a template for optimization the esipos tune esineg tune apcipos tune or apcineg tune file After you import the tune file into the Method Editor you must manually enter the optimal probe temperature and cone voltages for your application For information on creating tune files for ESI experiments see Manual Tuning in ESI Mode on page 39 For information on creating tune files for APCI experiments see Manual Tuning in the APCI Mode on page 49 For information on creating instrument methods see Creating Instrument Methods on page 57 How Do I Create Instrument Control Methods Thermo Scientific Create instrument methods which control all the modules of your LC MS instrument from the Xcalibur Instrument Setup window You manually enter the parameters for the modules of your instrument with the exception of either the needle voltage or the corona current value for the MSQ Plus Mass Detector For ESI mode import a tune tune file that con
61. dow See Figure 9 The oil color should be a clear light yellow Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 19 3 Preparing Your LC MS for Operation Checking the Oil Level in the Oil Mist Filter and the Forepump Figure 9 End of Edwards forepump showing oil level window i DULU 0000 2M 0il mist filter Edwards forepump Oil level window Perform maintenance as necessary e If the oil level is near or below the lower mark add more oil as described in the manual that comes with the Edwards forepump Ifthe oil has turned red in color or if the forepump has been in operation for more than 3000 hours since the oil was replaced replace the oil as described in the manual that comes with the Edwards forepump To drain the oil from the oil mist filter and to purge the oil of volatile contaminants 1 If the LC pump is pumping solvent turn the pump flow off 2 Put the MSQ Plus Mass Detector in Off mode by doing one of the following e From the Status page of the Information view in the Xcalibur data system right click the MSQ Plus listing to display a shortcut menu and choose Turn Device Off from the menu or e Open the Per Method Parameters table in the Tune window Take the system out of Operate mode by clicking the Operate On Off toggle button Then turn off the nitrogen gas by clicking the Nitrogen Gas On Off toggle button 3 Open the gas ballast valve on the Edwards forepump
62. e Optional on page 28 If you do not need to bake out the probe go to Flushing Air from the Lines of the Reference Inlet System on page 28 CAUTION Ensure that switching Operate to On also turns the Nitrogen Gas to On High probe temperature in the absence of nitrogen gas could damage the probe heater Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 27 4 Calibrating the MSO Plus Mass Detector Preparing the MSQ Plus Mass Detector for Calibration Baking Out the Probe Optional If the MSQ Plus Mass Detector has not been used recently or was last used in APCI mode bake out the probe before starting the LC flow To do this set the probe temperature to 550 C and leave the nitrogen gas flowing for approximately 5 min Then reset the probe temperature to 350 C Flushing Air from the Lines of the Reference Inlet System Before you start the Instrument Tune and Calibration wizard flush the air out of the tubing that connects the reference inlet reservoir to the injection valve of the mass detector Flushing air out of the lines helps to ensure a successful calibration To flush air out of the reference inlet system 1 Display the advanced parameters in the Per Method Parameters table a From the menu bar of the Manual Tune window choose View gt Options as shown in Figure 14 to open the Tune Options dialog box Figure 14 View menu C Thermo instruments MSQ metho File BYES Help v Toolbar v Sta
63. e min 213 06 4000000 3500000 3000000 2500000 Intensity 2000000 1500000 1000000 500000 270 77 miz Inu ma Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 283 00 302 10 321 08 353 35 380 73 395 45 434 39 455 94 477 33 499 18 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 ba Mix 4 10ppm 1 205 RT 3 52 AV 1 NL 4 3666 o 99 Sample Formulations Thermo Scientific This appendix provides instructions for preparing the sensitivity testing solutions and the calibrant solution A Thermo Fisher Scientific field service engineer uses the 5 pg pL solution of erythromycin to perform the sensitivity tests for the positive ion ESI and APCI modes and the 2 pg uL solution of p nitrophenol to perform the sensitivity tests for the negative ion ESI and APCI modes The calibrant solution for systems running on the MSQ 2 0 software version contains the reference compounds Csl KI and Nal in 50 50 isopropanol water v v that are used to perform a full system autotune and a mass scale calibration Contents e Sensitivity Test Solutions e Preparing the MSQ Plus Mass Detector Calibration Solution e Calibrant Solution CAUTION Always take safety precautions when you handle chemicals and unknown samples Ensure that you read and understand the hazards of the chemicals used in the following preparations Dispose of all laboratory reagents by the appropriate
64. e in the Tune window You cannot alter cone voltage while data acquisition is in progress Note When you create an instrument method you import the tune file that contains the optimized needle voltage for your application You must manually enter the optimal probe temperature and cone voltage into the instrument method Repeat step 6 to step 8 until you finish optimizing the parameters for your compound After you finish optimizing the parameters for your compound stop the data acquisition by clicking the Stop Acquiring icon shown in Figure 38 in the Tune window toolbar Save your tune file a Choose File gt Save As from the Tune window menu bar to open the Save Tune Parameters dialog box shown in Figure 39 MSQ Plus Mass Detector Getting Started Guide 55 6 Manual Tuning in the APCI Mode Acquiring and Viewing a Raw Data File Figure 39 Save Tune Parameters dialog box Save Tune Parameters Save in data e cf m Save as type Tune Parameter Files tune Cancel b Type an appropriate name in the File name box c Click Save to save the tune file with the optimized MS parameters for your compound of interest Note Default tune files are read only 56 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Creating Instrument Methods You create an instrument method from the Instrument Setup window in the Xcalibur data system to automatically control the
65. e might reset the RF Frequency HM Res Mid Point and Detector Voltage parameters to default values For optimized settings refer to a previously successful autotune report Viewing the Mass Spectrum for a Specific Time Point You can view a mass spectrum for a specific time point in the chromatogram To view a spectrum for a specific time point in the chromatogram 1 Open a raw data file into the Qual Browser facility 2 If the grid does not contain both a Chromatogram cell and a Spectrum cell add the appropriate cell to the grid as described in Adding Cells to the Grid on page 94 3 Pin the Spectrum cell 4 In the Chromatogram cell click a time point that you are interested in The mass spectrum for the selected time point appears in the Spectrum cell as shown in Figure 74 98 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 9 Using Qual Browser Viewing the Mass Spectrum for a Specific Time Point Figure 74 Qual Browser window displaying the mass spectrum for the 3 76 minute time point Mix A 10ppm 1 7 22 2009 4 40 39 PM RT 0 00 8 00 352 744 NL 100 1 6787 6 29 7 03 Tic MS Mix A 3 63 6 32 x 80 ia 6 22 10ppm 1 Pio 031 064 5 48 5 39 70 0 69 5 44 5 72 m 90 4 28 60 416 074 4 63 6 44 7 27 w 083 278 297 74 5 87 I 7 87 Ih alei 2s 288 Were 477 508 40 173 Pe Relative Abundance 30 20 10 0 0 0 os 10 15 2 0 25 3 0 35 40 45 5 0 55 6 0 65 7 0 75 8 0 Tim
66. e of the mobile phase capillary Typical values range from 3 to 5 KV Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 39 5 Manual Tuning in ESI Mode Setting Up the LC for Direct Control Table 5 Tune controls in the ESI mode Sheet 2 of 2 Tune window control Probe Temperature Description Typical value Temperature setting of the The optimal value depends on the flow rate of the mobile probe heater phase In general you must increase the probe temperature as you increase the flow rate of the mobile phase See Table 1 on page 7 Cone V Setting Up the Voltage that is placed on The optimal value depends on the structure of your the source block and the analyte entrance cone Increasing the cone voltage can decrease adduct formation and give rise to fragmentation which provides structural information about your analyte Typical cone voltage values range from 75 to 150 V Note To enter an optimal needle voltage for your application into an instrument method you must empirically determine the optimal needle voltage from the Tune window save the value in a tune file and then import the tune file into an instrument method If you are a novice user you might want to experiment with the manual tuning features of the MSQ Plus Mass Detector by starting with one of the tune files included with the data system For ESI mode start with the esipos tune file and inject the sensitivity test compound
67. e sequence by following this procedure To save the sequence 1 Choose File gt Save As The File Summary Information dialog box appears as shown in Figure 58 Figure 58 File Summary Information dialog box File Summary Information User Jacook Header File ID Finnigan Created Monday January 12 2004 1 36 26 PM User ID acook Logon ID acook Not changed Description New Sequence 2 Type an appropriate description in the Description box and click OK The Save As dialog box appears as shown in Figure 59 Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 79 8 Creating and Running Sequences Starting Data Acquisition Figure 59 Save As dialog box Save As Save in methods e BE Uhl Test Mix Sequence sid File name Test Mix Sequence sid Save as type Xcalibur Sequences sld Cancel Help Header Information Created Monday January 12 2004 3 40 00 PM By acook Logon ID acook Times saved 1 Last edited Monday January 12 2004 3 40 00 PM By acook Logon ID acook Summary info New Sequence 3 Browse to the appropriate folder where you want to save the sequence 4 Type a file name in the File Name box 5 Click Save Starting Data Acquisition To inject a sample and start data acquisition open a sequence file select the row that you want to run select the run options and start the run 80 MSQ Plus Mass Detector
68. ector and your LC system To check the hardware of the mass detector and the LC system 1 Verify that the power communication and nitrogen supply lines are correctly connected For instructions on connecting the MSQ Plus Mass Detector refer to the MSQ Plus Mass Detector Getting Connected Guide 2 Check that the LC system is properly connected Instructions for connecting a Thermo Scientific LC are included in the manuals stored on the LC devices CD that is part of the media kit For detailed instructions on connecting an Accela LC system refer to the Accela Getting Connected Guide 3 Verify that the nitrogen gas supply for the mass detector is adequate The MSQ Plus Mass Detector uses a maximum of 720 L h in ESI mode 4 Verify that the nitrogen regulator is set to 5 2 bar 75 psi for ESI mode or 3 1 bar 45 psi for APCI mode The nitrogen regulator shown in Figure 5 is located below the source compartment of the mass detector Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 15 3 Preparing Your LC MS for Operation Checking the Status of the LC MS Instrument Figure 5 Nitrogen regulator Pressure gauge Control dial 5 Verify that the hard drive on your data system computer contains sufficient storage space Note Anti virus software uses a large portion of your computer s memory as it scans the hard drive for viruses Ensure that the anti virus software is not set to perform a sc
69. ed by ESI and non polar compounds such as steroids are best analyzed by APCI Sample ions can carry a single charge or multiple charges The number of charges carried by the sample ions depends on the structure of the analyte of interest the mobile phase and the ionization mode MSQ Plus Mass Detector Getting Started Guide 3 1 Introduction Is ESI or APCI Better for Analyzing My Samples Electrospray ESI ESI mode generally produces mass spectra consisting of singly charged ions but it depends on the structure of the analyte and the solvent When multiply charged ions are produced the Xcalibur data system can mathematically transform the resulting mass spectrum to express the molecular weight of the sample ESI mode transfers ions in solution into the gas phase Because the ESI process does not use heat to nebulize the analyte ions you can use it to analyze heat labile compounds or high molecular weight compounds You can use ESI mode to analyze any polar compound that makes a preformed ion in solution Preformed ions can include adduct ions For example polyethylene glycols can be analyzed from a solution containing ammonium acetate because of adduct formation between the NH ions in the solution and oxygen atoms in the polymer With ESI the MSQ Plus Mass Detector can analyze compounds with molecular weights that are greater than 100000 Da because of multiple charging ESI is especially useful for the mass analysis of polar
70. efore you begin the procedures that are provided in this chapter Figure 33 shows the APCI setup for the MSQ Plus Mass Detector For instructions on switching the probes refer to the MSQ Plus Mass Detector Hardware Manual Figure 33 MSQ Plus Mass Detector setup for the APC mode 50 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 6 Manual Tuning in the APCI Mode Opening the Instrument Setup Window The corona pin position might be dropped by as much as 1 to 2 centimeters if it improves the signal If you are a novice user you might want to experiment with the manual tuning features of the MSQ Plus Mass Detector by starting with one of the tune files included with the data system For the APCI mode start with the apcipos tune file and inject the sensitivity test compound that is shipped with your mass detector For most analytes the RF lens bias and ion energy parameters are optimized at 1 0 V and 0 8 V respectively The suggested sensitivity test solution for the positive ion polarity mode is a 5 pg uL solution of erythromycin The preparation of this test solution is described in Sample Formulations on page 101 Ifyou are an advanced user see the Help for information on the advanced options in the Tune window Opening the Instrument Setup Window If your LC system is controlled from the Xcalibur data system open the Instrument Setup window before you open the Tune window To open the Instrument Setu
71. ell makes it the pinned cell within the grid A pinned cell is an active cell that cannot be made inactive by clicking in another cell Instead actions performed in the inactive cells affect the pinned cell as described in Cursor Actions on page 92 The lower cell in Figure 67 is a pinned cell If you want to automatically change the range of a cell by clicking in the grid you must pin the cell For example if you want to display the spectrum for the 1 minute time point without opening the Spectrum Ranges dialog box pin the Spectrum cell Then click the 1 minute time point in the inactive chromatogram cell 90 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 9 Using Qual Browser Cell States Figure 66 Qual Browser window displaying an active TIC chromatogram cell and an inactive mass spectrum cell Gray border Active cell 06 24 2003 10 30 04 AM Unpinned Time min Inactive cell Figure 67 Qual Browser window displaying an inactive cell and a pinned cell Inactive cell fil dataia raw C Xcaliburidata data14 06 24 2003 10 30 04 AM 221 OG Dar To eos Be Time min 100 346 2 g 50 0 345 8 346 0 346 2 346 4 346 6 miz Pinned cell Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 91 9 Using Qual Browser Cursor Actions Cursor Actions Within the cells of the grid you can use the cursor in three ways e Click in the cell to select a point e Drag a line parallel to an
72. en and the ending time point Dwell Time 0 01 to 8 00 Click the Scan Time box and type a length of time for the scan Range 0 05 0 25 Polarity ve or ve Click the Polarity list and select ve or ve from the list Cone V 0 00 to 200 00 Click the Cone V box and type the value of the optimal cone Thermo Scientific typical 70 00 to 150 00 voltage for your application Editing the Scan Events You can manually edit scan events as described in Table 7 and Table 8 or you can edit scan events by using the information stored in a previously acquired raw data file MSQ Plus Mass Detector Getting Started Guide 69 1 Creating Instrument Methods Creating an LC MS Instrument Method To change the start or end time of an event with the Chromatogram view 1 Click a scan event in either the Full Scan Events or the SIM Scan Events table to select it 2 Place the cursor at either end of the colored bar e Ifyour cursor is at the left end of the bar it will change to a right arrow He e Ifyour cursor is at the right end of the bar it will change to a left arrow H 3 Drag the cursor to the retention time that you want A pop up window appears showing the event name start time end time and duration to assist in the positioning of the cursor The new values are automatically updated in the Time Range column of the events table as shown in Figure 50 Figure 50 Pop up window that appears when you adjust the start or end time of
73. en reinstall the reservoir bottle into your MSQ Plus Mass Detector Ensure that the bottle cap is tightly closed See Figure 75 Figure 75 View of refilled reference inlet reservoir Nitrogen pressurization line BOTTLE CAP MUST BE CLOSED TIGHTLY Clip Clip Waste Reference inlet reservoir bottle containing calibrant 108 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Index A Accela LC system 2 5 21 acetic acid 6 active but unpinned cells 90 adduct ions 4 ammonium acetate 6 ammonium formate 6 ammonium hydroxide 6 analytical LC 6 anti virus software 16 APCI probes 2 50 APCI See atmospheric pressure chemical ionization apcineg tune file 9 apcipos tune file 9 54 atmospheric pressure chemical ionization 2 effect of acidity and basicity 5 flow rates 5 non polar compounds 3 5 parameters to optimize 8 polarity modes 5 probe temperature 6 tuning acquiring data in raw file 54 opening Instrument Setup view 51 optimizing acquisition parameters 49 selecting tune options 51 autosamplers function 1 8 introducing samples 5 specifying injection volume and vial location 46 autotuning borate 6 Thermo Scientific C calibrant solution contents of 25 preparing 101 105 107 viewing mass spectrum of 30 capillary LC 6 Change Instruments In Use dialog box 83 chromatogram cells 86 Chromatogram Ranges dialog box 86 87 Chromatogram view 58 60 61 70 Column Arrangement dialog box
74. entering the mass detector adjust the mass detector parameters e For ESI mode adjust the probe temperature and the needle voltage e For APCI mode adjust the probe temperature and the corona current 6 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 1 Introduction How Do Calibrate the MSQ Plus Mass Detector In general increase the probe temperature as you increase the flow rate from the LC pump Table 1 and Table 2 list the suggested starting probe temperatures for optimizing an analysis in ESI mode or APCI mode respectively You might find that the optimal probe temperature for your analysis differs from these values by as much as 50 C Table 1 Starting probe temperature values for ESI mode Flow rate Temperature 200 uL min 350 C 500 uL min 450 C 1000 pL min 575 C 2000 uL min 650 C Table 2 Starting probe temperature values for APC mode Flow rate Temperature 200 pL min 450 C 500 pL min 550 C 1000 uL min 650 C 2000 pL min 650 C How Do I Calibrate the MSO Plus Mass Detector Thermo Scientific The MSQ Plus Mass Detector includes a comprehensive autotune system that offers two levels of instrument calibration full system autotune and mass scale calibration When installing the system the Thermo Fisher Scientific service engineer performs a full system autotune which includes a mass scale calibration After receiving a full system autotune the mass detecto
75. ents MSQ Caliireport Folders Thermo B Instruments amp msq 30 cali data methods ref oz data methods E system autoecal_10 autoecal_10 MSQ_status 38 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Manual Tuning in ESI Mode Before you create an instrument method you must optimize the acquisition parameters of the MSQ Plus Mass Detector for your compound of interest The process of optimizing the acquisition parameters of the MSQ Plus Mass Detector for a particular compound or family of compounds is referred to as manual tuning and is performed from the Tune window This chapter describes how to optimize the tune parameters for a compound of interest Perform the procedures that are provided in this chapter in the following order If your LC devices are controlled by the Xcalibur data system begin with Setting Up the LC for Direct Control on page 40 Otherwise begin with Selecting Your Tune Options on page 41 Contents e Setting Up the LC for Direct Control e Selecting Your Tune Options e Acquiring and Viewing a Raw Data File In the ESI mode you optimize the parameters listed in Table 5 Table 5 Tune controls in the ESI mode Sheet 1 of 2 Tune window control Description Typical value Needle kV Voltage that is placed on The optimal value depends on the structure of your the stainless steel insert analyte and the flow rat
76. es Configured Devices HE Accela AS Accela PDA Accela AS Accela 1250 Pump Accela 1250 Pump MSO Plus MSO Plus 2 If the MSQ Plus Mass Detector is not shown in the Configured Devices list scroll down through the devices shown in the Available Device list Double click the MSQ Plus button to copy it to the Configured Devices list 3 Double click the MSQ Plus icon in the Configured Devices pane to open the MSQ Plus Configuration dialog box shown in Figure 4 12 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 2 Configuring Your LC MS Instrument Configuring the LC System Figure 4 MSQ Plus Configuration dialog box MSQ Plus Configuration Serial number User defined information Label Value User Label gt v Cancel Help 4 Optional To enter the serial number of the mass detector click in the Serial number box and then type the serial number The serial number is located on the back of the MSQ Plus Mass Detector 5 Optional To enter user defined information select or type a value of up to 20 characters in the Label box The available selections are Company Asset ID and Location code 6 Type a value of up to 20 characters for the location code company asset ID or user defined label in the Value box 7 Click OK to close the MSQ Plus Configuration dialog box 8 Complete the configuration of your LC MS system and then click Done to exit the Inst
77. escribed in this topic e Method Options View e Chromatogram View e Per Method Parameters Table e Full Scan Events Table e SIM Scan Events Table e Menus You cannot have the Method Options view and the Chromatogram view open simultaneously nor can you have the Full Scan Events and the SIM Scan Events tables open simultaneously The Method Options view and the Full Scan Events table are shown in Figure 41 The Chromatogram view and the SIM Scan Events table are shown in Figure 42 on page 60 58 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 7 Creating Instrument Methods Method Editor Figure 41 Method Editor with menus method options Per Method Parameters table and Full Scan Events table visible Per Method Method options Parameters table MSQ Pius t r es 5 Per Method Parameters Description Setpoint Preview Display til All Scans lonization Mode ESI Full Scans Rawfile optional Probe Temperature C 350 00 SIM Scans Menus W Parameters Tune Options Seans Use current tune file Vv Add Full Add SIM Use selected tune file Event Control Delete Continue to end of LC O a 4 c 5 5 a v id f v po p Hide Method Options bar Full Scan Events ruil scan Events d t bl Name Mass Range Time Range min Peak Format Scan Time s Polarity jCone Y able IFS 1 100 00 1000 00 0 00 5 00 Centro
78. eview menu 64 probe heaters 26 27 probe temperature APCI 6 50 55 ESI 6 40 46 resetting 28 setting 62 68 Q Qual Browser active but unpinned cells 90 adding cells to the grid 94 inactive cells 90 opening raw files 92 purpose 89 viewing mass spectrum for a time point 98 viewing reports 95 Qual Browser icon 45 92 Qual Browser window 45 55 raw files acquiring data in 44 54 creating file name for 41 51 opening in Qual Browser 89 opening in Qual browser 92 opening previously acquired 61 storing 77 Real Time Plot View icon 85 reference inlet reservoirs 26 108 reference inlet system 5 checking solvent levels 25 flushing air out of 28 use in autotuning use in mass scale calibration 1 refractive index detectors 1 regulatory compliance iii resolution set up 7 RF lens bias 8 9 40 51 54 MSQ Plus Mass Detector Getting Started Guide 111 Index S Roadmap view 18 Run Sample icon 82 Run Sequence dialog box 82 S safety precautions xiii safety standards iii Save As dialog box 71 79 Save Tune Parameters dialog box 47 56 scan events 69 Scan menu 64 Select Tune Parameter File Name dialog box 43 53 Select Tune Raw File Name dialog box 42 53 sensitivity test solutions erythromycin 103 p nitrophenol 104 preparing 101 sequence file 81 Sequence Setup icon 75 Sequence Setup view 75 77 sequences 75 serial number of the mass detector 13 Server icon appearance on starting Xcalibur data system 18 states of 17 sta
79. g boxes for the device by clicking the device listing in the menu bar 2 Leave the Instrument Setup window open but adjust its size to half the size of your view screen or minimize it When you acquire data in the Tune window use the Direct Control dialog box for the LC pump to start the mobile phase flow You use the Direct Control dialog box for the autosampler to inject your analyte Selecting Your Tune Options Thermo Scientific The display in the Tune window contains a mass spectrum corresponding to each row in the Scan Events table at the bottom of the window As you optimize the MS parameters for a particular compound the mass spectra displayed in the Tune window will change To record the changes in the mass spectra collect the data in a raw data raw file If you are a novice user you might want to experiment with the tune parameters for your compound by starting with one of the tune files that is shipped with the data system The following procedure describes how to create a file name for the raw raw data file that is created by the data system after you start data acquisition from the Tune window It also explains how to select a stored tune tune file from the Tune window that you use as a template To select your tune options 1 Right click the Server icon to display a shortcut menu and choose Manual Tune to open the Tune window 2 Choose View gt Options to open the Tune Options dialog box shown in Figure
80. hat Types of Buffers Can I Use e How Do I Set Up the Mass Detector for Various LC Flow Rates How Do I Calibrate the MSQ Plus Mass Detector e How Do I Optimize the Mass Detector Parameters for My Analytes e How Do I Create Instrument Control Methods The MSQ Plus Mass Detector is a high performance single quadrupole mass spectrometer It includes a reference inlet system an atmospheric pressure ionization API source and the Xcalibur data system The reference inlet system is used for autotuning and mass scale calibration In liquid chromatography mass spectrometry LC MS analysis an autosampler injects a sample onto an LC column The sample separates into its various components The components elute from the LC column and pass into the mass detector where they are analyzed The Xcalibur data system then stores and processes the data from the mass detector Why Use the MSQ Plus Mass Detector The MSQ Plus Mass Detector can increase the specificity and detection limits for applications that use any of the classic detectors such as UV fluorescence light scattering or refractive index Applications using classic detectors rely primarily on chromatographic retention times to identify analytes In contrast a mass detector allows mass identification for the components of chromatographic peaks Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 1 1 Introduction Why Use the MSQ Plus Mass Detector A mass detector
81. id 1 we 75 00 Show SIM Scans bar Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 59 7 Creating Instrument Methods Method Editor Figure 42 Method Editor with menus Chromatogram view Per Method Parameters table and SIM Events table visible Chromatogram view Per Method Parameters table MSO PUSE reneis EE Per Method Parameters Show Method Description Setpoint v lonization Mode ESI j Alls Options bar Full a 100 Probe Temperature C 350 00 SIM Scans 90 2 Parameters 80 Menus Scans gt 70 5 Add Full 350 a Add SIM D Create Group 50 jroup 40 3 Delete 30 5 20 F 10 I 0 y a a Wi r T hi Pr Pens 0 00 1 00 200 300 400 500 600 700 800 900 Time minutes SIM Scan Events Name Mass Span Time Range min Dwell Time s Polarity Cone SIM 1 00 00 1 00 0 00 1 00 1 00 ve 200 00 E Show Full Scans bar SIM Scan Events table To switch between the Chromatogram view and the Method Options view click the Hide Method Options or the Show Method Options bar To switch between the SIM Scan Events table and the Full Scan Events table click the Show SIM Scans or the Show Full Scans bar Method Options View You can use the Method Options view shown in Figure 43 to do the following e Open an existing raw file so that you can preview a chromatogram e Use the settings in the current tune file or a specific tune file CAUTION The MSQ Pl
82. ientific or prepare your own calibration solution See Calibrant Solution on page 106 for a suggested procedure for preparing the calibration solution MSQ Plus Mass Detector Getting Started Guide 25 4 Calibrating the MSO Plus Mass Detector Preparing the MSQ Plus Mass Detector for Calibration To check the solvent levels in the reservoir bottles 1 Open the front door of the MSQ Plus Mass Detector by depressing the door latch on the left side of the mass detector as you pull forward on the door 2 Check the level of the calibrant solution in the reference inlet reservoir which is the bottle on the right See Figure 11 Figure 11 View of reference inlet reservoir bottle and waste bottle Connected to Connected to port 6 of valve u port 5 of valve Nitrogen pressurization line BOTTLE CAP MUST BE CLOSED TIGHTLY 3 If the volume of calibrant solution is less than 50 mL refill the bottle After you refill the bottle ensure that the bottle cap is closed tightly 4 Check the level of waste solution in the waste bottle the bottle on the left see Figure 11 5 If the waste bottle is full of solvent empty it Setting the Gas Flows and Probe Heater Temperature Turn on the nitrogen gas and the probe heater To turn on the nitrogen gas and the probe heater 1 Verify that the nitrogen regulator is set to 5 2 bar 75 psi See Figure 5 on page 16 2 Right click the Server icon in the Windows taskbar
83. in 50 50 IPA H2O In addition label the bottles as specified in step 2 step 3 and step 4 Preparing the Working Calibration Solution The working calibration solution used to calibrate the MSQ Plus Mass Detector can be prepared by diluting the stock solution 500 fold with a pre mixed solution of 50 50 isopropanol water v v Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 107 A Sample Formulations Calibrant Solution To prepare the working calibration solution 1 Prepare approximately 250 mL of the 50 50 isopropanol water v v diluent 2 Unscrew the cap of the reference reservoir bottle and remove the bottle from the MSQ Plus Mass Detector 3 Dispose of any leftover calibrant solution from the reference reservoir bottle and rinse the reference reservoir bottle with 50 50 isopropanol water to remove any remaining residue 4 Add approximately 100 mL of the premixed 50 50 isopropanol water v v to a 250 mL plastic graduated cylinder 5 Using a 1 mL adjustable mechanical pipette calibrated or equivalent add 0 5 mL of the stock solution 10 mM CsI 25 mM KI and 650 mM Nal in 50 50 IPA H O v v to the graduated cylinder 6 Fill the graduated cylinder to the 250 mL mark with premixed 50 50 isopropanol water v v The working calibration solution contains 1 3 mM Nal 0 05 mM KI and 0 02 mM CsI in 50 50 isopropanol water 7 Transfer the calibrant solution to the clean reference reservoir bottle Th
84. ing Us There are several ways to contact Thermo Fisher Scientific for the information you need To contact Technical Support Phone 800 532 4752 Fax 561 688 8736 E mail us techsupport analyze thermofisher com Knowledge base www thermokb com Find software updates and utilities to download at mssupport thermo com To contact Customer Service for ordering information Phone 800 532 4752 Fax 561 688 8731 E mail us customer support analyze thermofisher com Web site www thermo com ms xiv MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Thermo Scientific Preface Contacting Us To get local contact information for sales or service Go to www thermoscientific com wps portal ts contactus To copy manuals from the Internet Go to mssupport thermo com agree to the Terms and Conditions and then click Customer Manuals in the left margin of the window To suggest changes to documentation or to Help e Fill out a reader survey online at www surveymonkey com s PQM6P62 e Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com MSQ Plus Mass Detector Getting Started Guide xv Introduction This chapter explains the basic functionality of the MSQ Plus Mass Detector and the preparations for using the tool Contents e Why Use the MSQ Plus Mass Detector e Is ESI or APCI Better for Analyzing My Samples e How Do I Introduce My Samples into the Mass Detector e W
85. ing the MSQ Plus Mass Detector Calibration Solution Kit Contents This section describes how to prepare the MSQ Plus Mass Detector calibration solution for autotune and mass calibration You can also find these instructions in the MSQ Plus Mass Detector Calmix Kit Preparation Guide The MSQ Plus Mass Detector Calmix Kit Part Number 60111 62021 includes a concentrated stock calibration solution of three inorganic salts with the following concentrations e Sodium iodide Nal 130 mM e Potassium iodide KI 5 mM e Cesium iodide CsI 2 mM The inorganic salts are dissolved in 2 5 mL 1 of solvent and packaged in a sealed ampoule The solvent is a 92 8 mixture of HPLC grade water H O and reagent grade isopropanol IPA The neck of the ampoule is scored for easy and safe opening Three ampoules and three labels are included in the Calmix Kit The labels denote the expiration date 36 months from date of manufacture the lot number and the Thermo Fisher Scientific and supplier provided part numbers The Calmix Kit contains a gravimetric certificate of analysis corresponding to the lot number It also includes the Material Safety Data Sheet MSDS for the calibration solution Preparing the Calibration Solution Thermo Scientific Follow these steps to prepare the calibration solution To prepare the working concentration of calibration solution 1 In a graduated cylinder prepare 250 mL 20 mL of diluent e 125 mL 10
86. ions Figure 35 Select Tune Raw File Name dialog box Select Tune Raw File Name O E Files of type Raw Files raw Cancel b Browse to the directory where you want to store your raw data Then type an appropriate file name into the File Name box c Click Open to create the file and close the Select Tune Raw File Name dialog box 4 Open and download the parameters from a stored tune file a Click the button to the right of the Tune File Name box to open the Select Tune Parameter File Name dialog box shown in Figure 36 Figure 36 Select Tune Parameter File Name dialog box Select Tune Parameter File Name Look in E methods Bf apci leakage current tune LM RF ramp tune apcineg tune LM transmission tune apcipos tune massdrift tune E charging tune E peak switching tune dark current tune phthalate tune detector conditioning tune pre cursor tune detector gain tune quad transmission tune electronic noise tune resolution subcon tune esineg tune resolution tune esipos tune sodium iodide tune hy test tune stability tune ion energy spread tune switching tune LM RF Gen tune tune File name Files of type Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 53 6 Manual Tuning in the APCI Mode Acquiring and Viewing a Raw Data File b Select an appropriate tune file or create a new tune file c Ifyou are a novice user and you want to experiment with the tune p
87. ject your sample If your autosampler is controlled by the Xcalibur data system open its Direct Control dialog box from the Instrument Setup window Enter an appropriate injection volume and vial location Click Apply 7 From the Qual Browser window observe the chromatogram To view the data as it is acquired periodically press F5 8 From the Tune window change the parameters for the needle voltage probe temperature and cone voltage You cannot alter the cone voltage while data acquisition is in progress Note When you create an instrument method you import the tune file that contains the optimized needle voltage for your application You must manually enter the optimal probe temperature and cone voltage into the instrument method 9 Repeat step 6 through step 8 until you finish optimizing the parameters for your compound 46 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Thermo Scientific 5 Manual Tuning in ESI Mode Acquiring and Viewing a Raw Data File 10 After you finish optimizing the parameters for your compound stop the data acquisition by clicking the Stop Acquiring icon shown in Figure 29 on page 45 in the Tune window toolbar 11 Save your tune file a Choose File gt Save As from the Tune window menu bar to open the Save Tune Parameters dialog box shown in Figure 32 Figure 32 Save Tune Parameters dialog box Save Tune Parameters Save in Io data e gE
88. k the Chromatogram cell to make it the active cell with a gray border To display multiple chromatogram cells 2 Choose View gt Ranges to open the Chromatogram Ranges dialog box as shown in Figure 64 Figure 64 Chromatogram Ranges dialog box Chromatogram Ranges Ranges Automatic processing Range Time range minutes J Fixed scale Type Range _ Scan filter Delay min Scale Raw file TIC 0 00 C Documer Mass Range 180 00 220 00 0 0 c ESI corona sid 60 00 0 00 C Documer Base Peak 0 0 c ESI Icorona sid 60 00 0 00 C Documer Wavelength A 260 00 0 00 C Documer o oO o e o RS gt Plot properties Raw file c xcalibur data data14 raw x Detector ms bd Scan filter v Peak algorithm ficis Ed Plot type TIC Me l v Delay min 0 00 Fix Of 00 Cancel Help 86 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 8 Creating and Running Sequences Viewing the Data as It Is Acquired 3 For each cell that you want to add do the following a Selecta Type check box b From the Detector list select a detector c From the Plot Type list select a plot type 4 Click OK to close the Chromatogram Ranges dialog box 5 Choose View gt Lock Display to resume monitoring real time data acquisition Figure 65 shows the four traces resulting from the settings in the Chromatogram Ranges dialog box 1 The total ion chromatogram TIC
89. lay an important role in the APCI process In APCI mode you can vary the flow rate from the LC into the mass detector from 0 2 to 2 mL min You can use APCI in positive or negative ion polarity mode Molecules with basic sites produce a strong ion current in positive ion mode Molecules with acidic sites such as carboxylic acids and acid alcohols produce a strong ion current in negative ion mode Although in general fewer negative ions are produced than positive ions the negative ion polarity mode can be more specific because the negative ion polarity mode typically generates less chemical noise than does the positive mode Therefore the signal to noise ratio might be better in the negative ion mode than in the positive ion mode How Do Introduce My Samples into the Mass Detector Thermo Scientific Use an LC system containing an LC pump and an autosampler to introduce samples into the MSQ Plus Mass Detector The MSQ Plus Mass Detector has a reference inlet system for the introduction of the tuning and mass scale calibration solution The Xcalibur data system controls HPLC systems manufactured by Thermo Fisher Scientific and other manufacturers The Accela LC system manufactured by Thermo Fisher Scientific integrates seamlessly with the MSQ Plus Mass Detector MSQ Plus Mass Detector Getting Started Guide 5 1 Introduction What Types of Buffers Can Use What Types of Buffers Can Use Use volatile buffers when possible
90. lus Mass Detector Getting Started Guide 51 6 Manual Tuning in the APCI Mode Selecting Your Tune Options The following procedure describes how to create a file name for the raw raw data file that is created by the data system after you start data acquisition from the Tune window It also explains how to select a stored tune tune file from the Tune window that you use as a template To select your tune options 1 Right click the Server icon to display its shortcut menu and choose Manual Tune to open the Tune window 2 Choose View gt Options to open the Tune Options dialog box shown in Figure 34 Figure 34 Tune Options dialog box Tune Options MSQ Plus Tune Options Configure the tune and display parameters r Tune Number of tune masses a Acquisition filename Ic Thermo InstrumentsS MSOQ data defaultraw Tune filename EST hermo Instruments MS GQ methods default Display I Filled traces IV Automatic intensity ranging I Show advanced parameters Cancel Help 3 Enter an acquisition file name for the raw data file that will be created by the data system after you start data acquisition in the Tune window a Click the button to the right of the Acquisition File Name box to open the Select Tune Raw File Name dialog box shown in Figure 35 52 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 6 Manual Tuning in the APCI Mode Selecting Your Tune Opt
91. mL of HPLC grade H O e 125 mL 10 mL of reagent grade IPA Note The efficacy of the calibration solution depends on high quality diluent and clean glassware because the solvent adducts must be properly formed in the electrospray source and the reference masses must be detected against the background of electronic and chemical noise 2 Transfer 100 mL 10 mL of the diluent from the graduated cylinder to the 250 mL Nalgene bottle that is attached to the front panel inlet side of the MSQ Plus Mass Detector MSQ Plus Mass Detector Getting Started Guide 105 A Sample Formulations Calibrant Solution 3 Transfer the entire contents of a single ampoule to the Nalgene bottle You can use a transfer pipet to facilitate the transfer 4 Transfer the remaining volume of the diluent from the graduated cylinder to the Nalgene bottle 5 Attach one of the labels from the Calmix Kit to the Nalgene bottle 6 Firmly seal the Nalgene bottle of the MSQ Plus Mass Detector inlet reservoir and mix the solution by swirling the bottle Note The Nalgene bottle is pressurized from 1 0 to 1 5 bar during the autotune and mass calibration process requiring a leak tight seal 7 Once the autotune and mass calibration process is complete bypass the injection valve by attaching the transfer line from the HPLC system to the grounded union on the front panel of the mass detector This last step does not apply to MSQ systems that are grounded th
92. ment Tune and Calibration vent Exit The Instrument Tuning and Calibration wizard shown in Figure 20 appears Figure 20 Instrument Tuning and Calibration wizard 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 Mass Scale Calibration Detector Gain Calibration 4 complete system tune and calibration using the in built calibration system Requires an LC system to be connected to the detector Cancel 4 Select the Full System Autotune option and then click Next A series of messages inform you of the progress of the tuning and the calibration procedure If the tuning or calibration procedure fails an error message appears 5 To accept the results of the autotune click Finish The software replaces the current tune and calibration files with the ones generated by the autotune 6 Click Print Report to print the calibration report An autotune report for a full system autotune is shown in Figure 21 32 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 4 Calibrating the MSO Plus Mass Detector Performing a Full System Autotune Figure 21 Autotune report for a full system autotune
93. mplate or an existing method or use the Method Editor to edit the method Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 65 7 Creating Instrument Methods Creating an LC MS Instrument Method Selecting a Template or an Existing Method You can select a template or an existing method from the Welcome page To open the Welcome page and choose from among its options 1 Click the MSQ Plus button in the View bar of the Instrument Setup window to display the Welcome page shown in Figure 48 The View bar is a vertical bar on the left of the Instrument Setup window It contains buttons for each of the instruments that you selected by using the Instrument Configuration program Figure 48 Welcome page for the MSQ Plus Mass Detector MSQ Pius Method Editor Templates File Create a new instrument method using an existing template Open an existing file A ESI Full Scan Positive Ion Tune B ESI Full Scan Negative Ion C ESI SIM Positive Ion Access to tune allowing you to optimize C ESI SIM Positve Ion or modify the system settings oO ESI SIM Negative Ion E ESI Positive Negative Switching F APCI Full Scan Positive Ion G APCI Full Scan Negative Ion H APCI SIM Positive Ion H APCI SIM Pasitve Ion I APCI SIM Negative Ion J APCI Positive Negative Switching 2 Select one of the options available to you e To create a new method click a template for the type of acquisition that you want t
94. n Thermo Scientific Use this procedure to prepare the erythromycin sensitivity test solution To prepare 10 mL of the erythromycin sensitivity test solution 1 Allow the 1 mg mL 1 ug uL stock solution of erythromycin to equilibrate to room temperature Then dilute it 100 fold a Using a 200 pL adjustable pipette transfer 100 pL of the stock solution of erythromycin into a clean dry 25 mL glass vial b Using a 10 mL adjustable pipette add 9 9 mL of 50 50 acetonitrile water v v to the vial and mix the solution c Label the resulting solution 10 ng pL Erythromycin 2 Dilute the 10 ng uL solution of erythromycin 100 fold a Using a 200 mL adjustable pipette transfer 100 mL of the 10 ng mL solution of erythromycin into a clean dry 25 mL glass vial MSQ Plus Mass Detector Getting Started Guide 103 A Sample Formulations Sensitivity Test Solutions b Using a 10 mL adjustable pipette add 9 9 mL of 50 50 acetonitrile water v v to the vial and mix the solution c Label the resulting solution 100 pg uL Erythromycin 3 Dilute the 100 pg pL solution of erythromycin 20 fold a Using a1 mL adjustable pipette transfer 0 50 mL of the 100 pg mL erythromycin solution into a clean dry 25 mL glass vial b Using a 10 mL adjustable pipette add 9 5 mL of 50 50 acetonitrile water v v to the vial and mix the solution c Label the resulting solution 5 pg uL Erythromycin Preparing the P Nitrophenol Sensitivity Te
95. nds to a low intensity region 7 Click Finish 36 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 4 Calibrating the MSO Plus Mass Detector Performing a Detector Gain Calibration The Confirm Set Electron Multiplier Voltage dialog box appears as shown in Figure 23 Figure 23 Confirm Set Electron Multiplier Voltage dialog box Confirm Set Electron Multipler oltage m x WARNING You are about to change the election multiplier voltage Excessive voltage will reduce the multialier life To set he voltage click OK To quit click Cancel Cancel WARNING To complete the detector gain calibration do one of the following e To apply the new voltage setting to the electron multiplier click OK The new voltage setting is stored in the registry e To keep the current detector voltage click Cancel After you complete the detector gain calibration the Tune page appears As Figure 24 shows the software automatically stores tune reports in the following directory for Xcalibur 2 2 SPlor later Drive Thermo Instruments MSQ Cali report Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 37 4 Calibrating the MSO Plus Mass Detector Performing a Detector Gain Calibration Figure 24 Contents of Thermo Instruments MSQO Cali Report for 2 3 C Thermo nstruments MSQ Cali report File Edit View Favorites Tools Help Q ex v amp ye Search By Folders m a Address E C ThermolInstrum
96. ng CTRL click the events that you want to add After you select the events that you want to group choose Create Group The group uses the time range and the polarity values listed in the first event You can edit the time range and polarity parameters for the group Tip Before an individual SIM event or group of SIM events is performed the mass detector performs a prefilter pulse to determine the baseline To reduce the amount of time spent on performing prefilter pulses group events that use the same time range polarity or both To ungroup the SIM events choose Ungroup If the individual events initially contained different settings for the time range polarity or both they now contain the same settings as the group e To delete a scan event or a group click the event or the group to select it and then choose Delete Creating an LC MS Instrument Method To create an instrument method follow the procedures in this section Opening the Instrument Setup Window Opening the Instrument Setup window is the first step in creating an instrument method To open the Instrument Setup window 1 For Xcalibur 2 2 SP1 or later choose Start gt Programs gt Thermo Xcalibur gt Xcalibur In the Roadmap view of the Xcalibur data system click the Instrument Setup icon Specifying the Method Parameters for the MSQ Plus Mass Detector To enter the instrument control parameters for the MSQ Plus Mass Detector you can select a te
97. ntains just one row See Figure 61 Figure 61 Sequence Setup view showing sequence with first row selected X Test Mix Sequence sld Open Sequence Setup File Edit Change Actions Yiew GoTo Help Sample Type FileName Sample ID Path Inst Meth 1 Unknown Test Mix01 First Injectiond 1 C Xcaliburkmethods Surveyor Instrument Control 14 1 For Help press Fi NUM 2 5 2004 5 58 PM NOTSAVED 2 Confirm that you have vials in the positions specified in the sequence rows that you plan to run Selecting the Run Options and Starting the Run Follow these steps to select the run options and start the run To select the run options and start the run 1 From the toolbar click the Run Sample icon dB to open the Run Sequence dialog box shown in Figure 62 82 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 8 Creating and Running Sequences Starting Data Acquisition Figure 62 Run Sequence dialog box Run Sequence m Acquisition Options User MSQPlus User Instrument Start Instrument MSO Plus Accela AS Accela Pump Run Rows f I Priority Sequence IV Start When Ready Instrument Method Start Up Browse T Quan M Qual Shut Down Browse J Reports emani I Programs Pre Acquisition Browse i J Create Quan Summary Post Acquisition Browse Run Synchronously I Pre Acquisition D Post Acquisition Processing Actions r
98. o perform The Method Editor opens with the default parameters for the template e To edit an existing method click the following link to display the Open dialog box Open an existing file In the Open dialog box select a method and click Open Click the MSQ Plus button in the view bar of the Instrument Setup window to display the method in the Method Editor e To open the Tune window click the following link Access to tune allowing you to optimize or modify the system settings 66 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 7 Creating Instrument Methods Creating an LC MS Instrument Method Using the Method Editor to Edit the Method To edit the method for the MSQ Plus Mass Detector follow these procedures e Selecting the Method Options e Selecting the Per Method Parameters e Selecting the Scan Events e Editing the Scan Events Selecting the Method Options Select the method options in the Method Editor view To select the method options in the Method Editor view 1 From the Method Editor click the Show Method Options bar to open the Method Options view shown in Figure 49 Figure 49 Method Editor with the Method Options view MSQ P us Method Editor Preview Display All Scans Full Scans Raufile optional FF SIM Scans Parameters Tune Options Scans Use current tune file v Add Full Event Control Continue to end of LC E v n a a E m 2 bj a D 3 i a
99. ons damage or loss that might result from any use of this document even if the information in the document is followed properly This document is not part of any sales contract between Thermo Fisher Scientific Inc and a purchaser This document shall in no way govern or modify any Terms and Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents Release history Revision A September 2013 Software version Thermo MSQ Plus Mass Detector 2 0 or later Xcalibur 2 2 SP1 or later Foundation 2 0 SP1 2 1 3 0 or later For Research Use Only Not for use in diagnostic procedures Regulatory Compliance Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with applicable domestic and international regulations When the system is delivered to you it meets all pertinent electromagnetic compatibility EMC and safety standards as described in the next section or sections by product name Changes that you make to your system may void compliance with one or more of these EMC and safety standards Changes to your system include replacing a part or adding components options or peripherals not specifically authorized and qualified by Thermo Fisher Scientific To ensure continued compliance with EMC and safety standards replacement parts and additional components options and peripherals must be ordered from Thermo Fisher Scientific o
100. ow to the API probe by clicking the Nitrogen Gas toggle button 54 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Thermo Scientific 10 11 6 Manual Tuning in the APCI Mode Acquiring and Viewing a Raw Data File c Start the operation of the MSQ Plus Mass Detector by clicking the Operate toggle button Start the LC flow Use the same mobile phase conditions that you plan to use when you create your acquisition method Start the acquisition of data by clicking the Start Acquiring icon shown in Figure 38 in the Tune window toolbar Figure 38 Start Acquiring and Stop Acquiring icons in the Tune window toolbar File View Help Bl 5 16 E R Stop Acquiring button Start Acquiring button Double click the Qual Browser icon s to Open the Qual Browser window shown in Figure 30 on page 45 from the Roadmap view From the Qual Browser menu bar choose File gt Open to open the Open Raw File dialog box Select the raw data file that you are acquiring Then click Open to open the file in the Qual Browser window Inject your sample If your autosampler is controlled by the Xcalibur data system open its Direct Control dialog box and select an appropriate injection volume and vial location Observe the chromatogram in Qual Browser To view the data as it is acquired periodically press F5 Change the parameters for the corona current probe temperature and cone voltag
101. p window 1 For Xcalibur 2 2 SP1 or later choose Start gt Programs gt Thermo Xcalibur gt Xcalibur On the Roadmap view of the Xcalibur data system click the Instrument Setup icon Xcalibur displays the Instrument Setup window with icons for all of the currently configured devices for your LC MS instrument arranged down the left side of the view Instrument Setup pages and dialog boxes for the selected device are displayed on the right side of the view You can access additional dialog boxes for the device by clicking the device listing in the menu bar 2 Leave the Instrument Setup window open but adjust its size to half the size of your view screen or minimize it When you acquire data in the Tune window use the Direct Control dialog box for the LC pump to start the mobile phase flow and the Direct Control dialog box for the autosampler to inject your analyte Selecting Your Tune Options The display section of the Tune window contains a mass spectrum for each row in the Scan Events table at the bottom of the window As you optimize the MS parameters for particular compound the intensities of the mass spectra displayed in the Tune window will change To record the changes in the mass spectra collect the data in a raw data raw file If you are a novice user you might want to experiment with the tune parameters for your compound by starting with one of the tune files that is shipped with the data system Thermo Scientific MSQ P
102. page 32 4 Select the Detector Gain Calibration option and then click Next The Detector Gain Calibration confirmation page appears 5 Ensure that you set up the LC MS system as described in step and step 2 of this procedure and click Next to start the automated calibration process During the automated calibration process the software performs the steps listed in Table 4 Table 4 Steps in the automated calibration process Sheet 1 of 2 Automated Detector Gain Routine Step 1 Turns off the ion flow and captures the electronic noise Step 2 Determines the peak to peak difference between the minimum and maximum values for the absolute analog to digital converter noise Step 3 Turns the ion flow on Step 4 Starting from 700 V increases the voltage in 50 V intervals until the peak to peak signal intensity is more than 10 times the noise signal MSQ Plus Mass Detector Getting Started Guide 35 4 Calibrating the MSO Plus Mass Detector Performing a Detector Gain Calibration Table 4 Steps in the automated calibration process Sheet 2 of 2 Automated Detector Gain Routine Step 5 Adjusts the ion flow rate to approximately 1000 counts per second Measures the multiplier output response to each ion event to determine gain at this multiplier voltage Step 6 Raises the multiplier voltage by 50 V and repeats step 5 This process is repeated several times Step 7 Creates a calibration curve over the measured multi
103. paring the Stock Solutions for the Sensitivity Tests The field service engineer uses two compounds to perform sensitivity testing Erythromycin is used to test the sensitivity of the instrument in the positive ion mode P nitrophenol is used to test the sensitivity of the instrument in the negative ion mode Stock Solution Erythromycin Follow this procedure to perform sensitivity testing with erythromycin To prepare a1 mg mL 1ug uL stock solution of erythromycin in 100 HPLC grade acetonitrile 1 Open the 25 mL glass vial that contains 10 mg of erythromycin 2 Using a 10 mL volumetric pipette or an adjustable mechanical pipette add 10 mL of HPLC grade acetonitrile to the vial 3 Screw the cap back onto the vial and mix 4 Label the vial Erythromycin Stock Solution 5 Store the erythromycin stock solution 1 mg mL in a refrigerator until it is needed When refrigerated this stock solution is stable for several months Stock Solution P Nitrophenol Follow this procedure to perform sensitivity testing with p nitrophenol To prepare a 1 mg mL 1mg mL stock solution of p nitrophenol in 100 HPLC grade methanol 1 Open the 25 mL glass vial that contains 10 mg of p nitrophenol 2 Using a 10 mL volumetric pipette or an adjustable mechanical pipette add 10 mL of HPLC grade methanol to the vial 3 Screw the cap back onto the vial and mix 4 Label the vial P Nitrophenol Stock Solution 102 MSQ Plus Mass Detector
104. plier voltage range and determines the multiplier voltage required to produce a gain of 450 000 Once the tune process successfully finishes the equation of the calibration curve appears and the Finish button becomes available as shown in Figure 22 Figure 22 Instrument Tuning and Calibration wizard showing the calibration curve produced by the tune process Instrument Tuning and Calibration Detector Gain Calibration Electron multiplier voltage optimization Flow 738 ions Single 20 Multiple 18 Peak 549 Flow 803 ion s Single 89 Multiple 14 Peak 512 Flow 736 ion s Single 27 Multiple 9 Peak 694 Flow 796 ion s Single 82 Multiple 14 Peak 537 Flow 782 ion s Single 70 Multiple 12 Peak 598 Flow 762 ion s Single 47 Multiple 15 Peak 593 Flow 718 ion s Single 708 Multiple 10 Peak 526 Flow 780 ion s Single 70 Multiple 10 Peak 616 Flow 745 ion s Single 35 Multiple 10 Peak 584 Woltge 1850 0 Area 3552970 567232 lon count 7582 Gain 4481078 043936 Multiplier voltage 438 116864 149 364028 In gain r 0 999429 Multiplier voltage for the Jain of 4 5E 5 1506 2 Tune process Sane F lt Back Cancel Run Time 7 59 The equation of the calibration curve produced by the tune event shown in Figure 22 is as follows Voltage 438 149 x In 450 000 Voltage 1506 6 If the calibration has not finished within 12 minutes click Cancel and verify that the value in the Mass box correspo
105. r is extremely stable in the region of 0 01 Da C In a normal air conditioned laboratory the mass detector rarely if ever needs a second full system autotune A deep tune is an automated operation that adjusts the operating frequency of the RF generator to match the natural resonant frequency of the quadrupole analyzer It ensures that the mass detector operates to the maximum value of its mass range Resolution set up is an automated operation that electronically adjusts the resolution of the peaks produced by the calibrant at both high and low mass 1971 6 m z and 172 8 m z respectively It is adjusted to give unit resolution by setting the peak width to 0 7 Da at the half height of the peak It also performs a linearity adjustment to the same criterion at mid mass 1072 24 m z MSQ Plus Mass Detector Getting Started Guide 7 1 Introduction How Do Optimize the Mass Detector Parameters for My Analytes Mass scale calibration is an automated procedure that compares the masses of the factory supplied calibrant solution to a reference file of the same compound The reference file contains the correct mass for each peak and the values of the acquired data file are corrected to match those in the reference file These correction factors are then applied to all subsequent acquisitions Perform a full system autotune when you do the following e Move the mass detector to a different environment e Perform maintenance on the source block
106. r one of its authorized representatives EMC Directive 89 336 EEC as amended by 92 31 EEC and 93 68 EEC EMC compliance has been evaluated by UNDERWRITERS LABORATORY INC UL EN 55011 1998 EN 61000 4 3 2002 EN 61326 1 1998 EN 61000 4 4 2001 EN 61000 3 2 1995 EN 61000 4 5 2001 EN 61000 3 3 1995 EN 61000 4 6 2001 EN 61000 4 2 2001 EN 61000 4 11 2001 CFR 47 Part 15 Subpart B 2004 Code of Federal Regulations Part 15 Subpart B Radio Frequency Devices Unintentional Radiators Class A Low Voltage Safety Compliance This device complies with the EU directive 73 23 EEC equivalent to IEC 1010 1 1990 plus Amendment 1 1991 and Amendment 2 1995 by meeting the following standard EN 61010 1 2001 with Corrigendum No 1 and 2 FCC Compliance Statement THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES OPERATION IS SUBJECT TO THE FOLLOWING TWO CONDITIONS 1 THIS DEVICE MAY NOT CAUSE HARMFUL INTERFERENCE AND 2 THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION CAUTION Read and understand the various precautionary notes signs and symbols contained inside this manual pertaining to the safe use and operation of this product before using the device Notice on Lifting and Handling of Thermo Scientific Instruments For your safety and in compliance with international regulations the physical handling of this Thermo Fisher Scientific instrument req
107. r to water alone for ESI Volatile acids and bases are good but Thermo Fisher Scientific does not recommend salts above 10 mM Strong mineral acids and bases are extremely detrimental to the instrument Observe the following recommendations for generating stable electrospray e Refrain from using non volatile salts and buffers in the solvent system For example avoid the use of salts containing sodium or potassium and avoid the use of phosphates If necessary use ammonium salts instead e Use organic aqueous solvent systems 4 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 1 Introduction How Do Introduce My Samples into the Mass Detector e Use volatile acids and bases e If possible optimize the pH of the solvent system for your analyte of interest For example if your analyte of interest contains a primary or secondary amine use an acidic mobile phase pH 2 to 5 for your chromatographic separation The acidic pH tends to keep positive ions in solution Atmospheric Pressure Chemical lonization APCI Like ESI APC is a soft ionization technique as opposed to an electron ionization technique APCI provides molecular weight information for compounds of low polarity that are somewhat volatile APCI is typically used to analyze small molecules with molecular weights up to about 1000 Da APCI is a gas phase ionization technique Therefore the gas phase acidities and basicities of the analyte and solvent vapor p
108. r tunes and calibrates the detector at installation Perform an automated mass scale calibration whenever you notice a drift in the accuracy of the reported masses of your known standards 2 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 1 Introduction Is ESI or APCI Better for Analyzing My Samples Figure 1 Instrument Tuning and Calibration wizard 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 Mass Scale Calibration 4 complete system tune and calibration using the in built calibration system Requires an LC system to be connected to the detector Cancel To create an acquisition method for an LC MS system with an MSQ Plus Mass Detector use the Tune window to optimize the parameters for your analyte After determining the optimal mass detector settings for your analyte open a template from the Instrument Setup window import the Tune file that contains the optimal settings for your analyte and modify a few parameters if necessary Is ESI or APCI Better for Analyzing My Samples Thermo Scientific You can operate the MSQ Plus Mass Detector in either of two atmospheric pressure ionization modes electrospray ionization ESI or atmospheric pressure chemical ionization APC Typically polar compounds such as amines peptides and proteins are best analyz
109. rated Range Min m z 22 9898 22 9898 14 la Calibrated Range Max m z 1971 6149 1971 6149 N wy am Yu A oada La T tT T me 1 171 175 1070 1074 1970 1974 Peak widths are measured at 10 height Ref Peak Search From To Real Peak Mass Shift 22 99 18 99 26 99 23 05 0 06 Slow LM Shift 250 00 Da S Slow Mass Shift 250 00 Da S 38 96 37 03 41 03 38 92 0 05 0 59 pais ABE 83 05 81 00 85 00 83 07 0 03 H 132 91 130 93 134 93 132 90 0 00 0 00 aE 0 00 pE 172 88 168 88 176 88 172 92 0 04 472 67 470 71 474 74 472 63 0 05 0 59 lsa 622 57 620 52 624 54 622 49 0 08 22 99 172 88 172 88 1971 61 772 46 770 38 774 44 772 41 0 05 Slow Calibration 250 00 Da S 922 36 920 30 924 36 922 36 0 00 1072 25 1070 25 1074 27 1072 28 0 04 0 08 1222 14 1220 18 1224 18 1222 18 0 04 0 00 7 N 1372 04 1370 08 1374 09 1372 09 0 05 1521 93 1519 99 1523 99 1521 99 0 05 0 08 u gt 1671 83 1669 88 1673 86 1671 88 0 05 22 99 1971 61 1821 72 1819 77 1823 73 1821 75 0 03 1971 61 1969 64 1973 69 1971 60 0 02 R Ref Peak Search From To Real Peak Mass Shift Fast LM Shift 1000 00 Da S Fast Mass Shift 1000 00 Da S 22 99 18 99 26 99 23 06 0 07 0 59 0 50 5 B 38 96 37 04 41 04 38 83 0 13 a 4 83 05 80 91 84 91 83 07 0 02 0 00 0 00 TI 132 91 130 93 134 93 132 92 0 02 172 88 170 90 174 90 172 87 0 01 0 59 0 50 III 472 67 470 66 474 66 472 65 0 03 22 99 172 88 172 88 1971 61 622 57 620 54 624 54 622 47 0 10 Fast Calibration 1000 00 Da S 772 46 770 37 77
110. reach equilibrium temperature in 1 to 2 minutes when you turn the system back on 84 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 8 Creating and Running Sequences Viewing the Data as It Is Acquired 6 Leave the parameters in the other areas at their defaults Use the Instrument Method and Programs areas in the Run Sequence dialog box to specify particular acquisition or processing requirements For details on these parameters see the Help or Thermo Xcalibur Acquisition and Processing User Guide 7 Click OK to start the run Viewing the Data as It Is Acquired You can view the data as it is acquired by using the real time plot facilities To view the data as it is acquired using the real time plot facilities 1 Click the Real Time Plot View icon on the Roadmap view toolbar The screen is automatically locked so you can view the progress of your run in real time 2 If you want to freeze the run data click the Unlocked icon When the screen is unlocked you cannot monitor the real time progress of your run but you can review your data For example you can display the spectrum for a particular peak that has already eluted Data collection continues off screen as you review your data 3 To relock the display click the Locked icon la Reviewing Real Time Data Follow this procedure to review the data as it is being collected To review the data as it is being collected 1 Unlock the display b
111. rough the injection valve that is released before January 2005 serial number below 201 xx Calibrant Solution The automated full system autotune and mass scale calibration procedures use a calibrant solution that contains a mixture of 1 3 mM sodium iodide Nal 0 05 mM potassium iodide KI and 0 02 mM cesium iodide CsI in a solution of 50 50 isopropanol water You can purchase this calibrant solution as a new kit part number 60111 62021 containing Calmix concentrate and instructions This material ships with each new MSQ Plus Mass Detector as part of the MSQ chemical kit part number 60111 62023 Or you can prepare the solution yourself using the procedures in this section Preparing the calibrant solution requires the materials and equipment listed in Table 12 or their equivalents To prepare 250 mL of calibrant solution follow these procedures 1 Preparing a Concentrated Stock Solution of the Calibration Mixture 2 Preparing the Working Calibration Solution Table 12 Materials and equipment required to prepare calibrant Sheet 1 of 2 Materials and equipment Quantity Cesium iodide CsI gt 99 9 pure Approx 300 mg Potassium iodide KI A C S reagent grade 0 Approx 500mg Sodium iodide Nal A C S reagent grade Approx 10 g HPLC grade water Approx 200 mL Isopropanol Approx 200 mL 106 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific A Sample Formulations Calibrant Solution Table
112. rument Configuration application Configuring the LC System Thermo Scientific If your LC system is controlled from the Xcalibur data system you must add it or all of its devices to your instrument configuration RL bd 1 To add your LC system to the instrument configuration for your data system If a particular device is not listed in the Configured Devices pane in the Instrument Configuration dialog box double click its icon in the Available Devices pane to add it to the Configured Devices pane Double click each device in the Configured Device pane and check its configuration settings MSQ Plus Mass Detector Getting Started Guide 13 2 Configuring Your LC MS Instrument Configuring the LC System Information on the configuration settings for each device is available in the Help For additional information about your Accela LC system refer to the Accela UHPLC System User Guide for LC Devices 14 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific p Preparing Your LC MS for Operation This chapter describes how to prepare your LC MS instrument for operation Check the system before restarting its operation by performing the procedures in this chapter Contents e Checking the Hardware e Checking the Status of the LC MS Instrument e Checking the Oil Level in the Oil Mist Filter and the Forepump e Preparing the LC for Operation Checking the Hardware First check the hardware of your mass det
113. spreadsheet cell containing the injection volume value that you want to change highlight the current value and type a new value in the cell You can use the Column Arrangement icon to make the column cell visible E For details on the parameters in the New Sequence Template dialog box refer to the Xcalibur Help or the following documents For the Xcalibur 2 2 SP1 or later data system see the Xcalibur Help or the Thermo Xcalibur Data Acquisition and Processing User Guide 5 To alter the current column arrangement click the Column Arrangement toolbar button to display the Column Arrangement dialog box shown in Figure 57 To add a column to the sequence select the column from the Available Columns list and click Add To remove a column from the sequence select the column from the Displayed Columns list and click Remove To alter the position of the columns in the sequence select the column from the Displayed Columns list and click either Move Up or Move Down as appropriate Figure 57 Column Arrangement dialog box Column Arrangement Available Columns Client Sample Type Comment File Name Company id Dil Factor ISTD Corr Amt Ene Laboratory dickies Proc Meth Phone Position Sample Vol peis Inj Yol Sample Wt Level SampleN ame Study 78 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 8 Creating and Running Sequences Creating a Single Sample Sequence Saving the Sequence Save th
114. st Solution Use this procedure to prepare the p nitrophenol sensitivity test solution To prepare 10 mL of the p nitrophenol sensitivity test solution 1 Allow the 1 mg mL 1 ug uL stock solution of p nitrophenol to equilibrate to room temperature Then dilute it 100 fold a Using a 200 pL adjustable pipette transfer 100 pL of the stock solution of p nitrophenol into a clean dry 25 mL glass vial b Using a 10 mL adjustable pipette add 9 9 mL of 50 50 methanol water v v to the vial and mix the solution c Label the resulting solution 10 ng pL P nitrophenol 2 Dilute the 10 ng uL solution of p nitrophenol 100 fold a Using a 200 pL adjustable pipette transfer 100 pL of the 10 ng uL solution of erythromycin into a clean dry 25 mL glass vial b Using a 10 mL adjustable pipette add 9 9 mL of 50 50 methanol water v v to the vial and mix the solution c Label the resulting solution 100 pg uL P nitrophenol 3 Dilute the 100 pg uL solution of p nitrophenol 50 fold a Using a 200 mL adjustable pipette transfer 200 pL of the 100 pg pL p nitrophenol solution into a clean dry 25 mL glass vial b Using a 10 mL adjustable pipette add 9 8 mL of 50 50 methanol water v v to the vial and mix the solution c Label the resulting solution 2 pg uL P nitrophenol 104 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific A Sample Formulations Preparing the MSO Plus Mass Detector Calibration Solution Prepar
115. start time and end time appears Choose SIM Scans to display scan events defined in the SIM Scan Events table in the Chromatogram view Each scan event is displayed as a green bar If you hover the cursor over a bar a tooltip showing the event name start time and end time appears Choose Parameters to display a report of the method parameters Click Print to print the report or click Back to return to the Method Editor The Scan menu contains the Add Full Add SIM Create Group and Ungroup commands With these commands you can do the following Add and delete full and SIM scan events Group and ungroup retention time ranges 64 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 7 Creating Instrument Methods Creating an LC MS Instrument Method To use the commands in the Scan menu e To adda full scan event to the Full Scan Events table choose Add Full If you select a full scan event the new scan uses the values of the selected event If do not select a scan the values of the last row in the table are used Note Selected table rows are highlighted in green e To adda SIM scan event to the SIM Scan Events table choose Add SIM If you select a SIM scan event the new scan uses the values of the selected event If you do not select a scan the values of the last row in the table are used e To create a group for a particular time range click the first SIM event that you want to add to the group Pressi
116. struments MSQ Calilmethodslesipos tune MSInst File View Help 33 amp eo MSQ P us Tune Description l Readback Setpoint Width 1 2H 0 016 RI 0 Tune Control 100 BF 0 00e 000 BPM 0 00 Probe Temperature C 0 550 Needle kV 0 00 3 00 Acquisition Control Retention Time mins 0 00 na General Control Operate n a on Nitrogen Gas n a Off lonization Mode n a ESI I i ESI mode a 5 3 3 E 3 5 a 3 0 4 T T 1 7325 733 0 733 5 734 0 734 5 735 0 735 5 736 0 736 5 Name Mass Span Time Range Peak Format 1 Scan Time 1 Polarity i Cone Rdbk 1 Zoom On Off Fi 734 50 4 00 0 00 Profile 0 20 ve 70 0 1005 On 7 Positive ion polarity mode ve 000000 bytes sec d Click Open to download the tune parameters and close the Select Tune Parameter File Name dialog box Acquiring and Viewing a Raw Data File Follow the steps in this section to acquire and view a raw data file To acquire and view a raw data file 1 Start the mass detector a Ifthe Per Method Parameters table is not open open it by clicking the Show Per Method Parameters bar b Turn on the nitrogen flow to the API probe by clicking the Nitrogen Gas toggle button c Start the operation of the MSQ Plus Mass Detector by clicking the Operate toggle button 2 Start the LC flow Use the same mobile phase conditions that you plan to use when you create your
117. t all lab personnel have read and have access to this document The software also provides Help Safety and Special Notices Make sure you follow the precautionary statements presented in this guide The safety and other special notices appear in boxes Safety and special notices include the following CAUTION Highlights hazards to humans property or the environment Each CAUTION notice is accompanied by an appropriate CAUTION symbol IMPORTANT Highlights information necessary to prevent damage to software loss of data or invalid test results or might contain information that is critical for optimal performance of the system Note Highlights information of general interest Tip Highlights helpful information that can make a task easier xii MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Preface Safety Precautions Safety Precautions Observe the following safety precautions when you operate or perform service on the MSQ Plus Mass Detector CAUTION Do not perform any servicing other than that contained in the MSQ Plus Mass Detector Hardware Manual To avoid personal injury or damage to the instrument do not perform any servicing other than that contained in the MSQ Plus Mass Detector Hardware Manual or related manuals unless you are qualified to do so CAUTION Shut down the mass detector and disconnect it from line power before you service it High voltages capable of causing personal inj
118. tains the appropriate needle voltage for your application For APCI mode import a tune tune file that contains the appropriate corona current for your application The Use Current Tune file check box is selected by default as shown in Figure 2 This means that the mass detector uses the needle voltage or the corona current value in the current tune file To use the needle voltage value or the corona current value from a stored tune file you must deselect this check box click the Browse button to the right of the Use Selected Tune File box and select an appropriate tune file MSQ Plus Mass Detector Getting Started Guide 9 1 Introduction How Do Create Instrument Control Methods Figure 2 MSQ Plus Method Editor dialog box Use current tune file Browse button check box E Untitled Thermo Xcalibur Instrument Setup File Help olaja 8 x12 Foc A COL A BB CC COL CL DOL BCC CEL COL C O BB CCDC O E CCC COL COL E A BoC CAL E CA MSO Pius Method Editor Preview Display All Scans Full Scans Rawfile optional SIM Scans Parameters Tune Options Accela AS rs e Scans Add Full Add SIM Use selected tune file Create Gro eate Use current tune file Ungroup Event Control Delete Accela 1250 Pump Continue to end of LC Show Per Method Paramet Hide Method Options DSN ANA NENNEN a a a a pa NNN NN INN NN NNN NNN NNN NNN NNN NN NNN NTN NNN Ee AE AA AA AAAA rE AM AR AR PR AAAA AT PA AR PR AT PM AR
119. the run automatically select the Start When Ready check box The Xcalibur data system starts the run after you click OK in the Run Sequence dialog box If your system contains an Accela pump the run begins after the pump sends a pump ready signal to the Accela autosampler The Accela pump is not ready until it monitors a stable backpressure as defined in the instrument method Note To manually start an acquisition clear the Start When Ready check box and choose Actions gt Start Analysis from the Sequence Setup menu To subsequently control the acquisition choose Actions gt Pause Analysis or Actions gt Stop Analysis 5 In the After Sequence Set System area make the following selections e Select the On option if you want Xcalibur to leave the devices in the On state after the sequence ends Select the Off option if you want Xcalibur to turn off the pump flow and place the mass detector in the Off mode after the sequence ends In the Off mode the nitrogen gas probe heater and high voltages are turned off If your instrument contains a UV detector Xcalibur turns off the detector s lamps Select the Standby option if you want to the LC pump flow to stop after the sequence ends Note The MSQ Plus Mass Detector application has no standby mode If you are actively developing an instrument method leave the system on Otherwise turn the system off at the end of a sequence to save nitrogen gas The probe heater will
120. to obtain the highest performance for your assays Volatile buffers include the following e Acetic acid e Ammonium acetate e Ammonium formate e Ammonium hydroxide e Triethylamine TEA e Trifluoroacetic acid TFA Some LC applications use non volatile buffers such as phosphate or borate buffers However the use of non volatile buffers can lead to a buildup of salt in the ion source and can cause a loss of sensitivity For LC applications that require non volatile buffers Thermo Fisher Scientific recommends installing the optional cone wash pump Note You might need to increase the frequency of ion source maintenance when using non volatile buffers How Do Set Up the Mass Detector for Various LC Flow Rates The ESI probe can generate ions from liquid flows of 10 pL min to 2 0 mL min This flow rate range lets you use a variety of separation techniques capillary LC microbore LC and analytical LC The APCI probe can generate ions from liquid flows of 0 2 to 2 0 mL min Within this flow rate range you can use the microbore LC analytical LC and semi preparative LC separation techniques CAUTION Do not heat the probe without the nitrogen gas flowing To prepare the mass detector for operation turn on the nitrogen gas turn on the probe heater and then turn on the LC flow After you finish an analysis turn off the LC flow turn off the heater and then turn off the nitrogen gas As you change the solvent flow rate
121. tus Bar Do b Select the Show Advanced Parameters check box see Figure 15 Then click OK to exit the dialog box 28 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 4 Calibrating the MSO Plus Mass Detector Preparing the MSQ Plus Mass Detector for Calibration Figure 15 Tune Options dialog box Tune Options MSQ Plus Tune Options Configure the tune and display parameters Tune Number of tune masses a Acquisition filename Ic Thermo Instruments M5 Q data default raw RA Tune filename Ic Thermo Instruments MSQ methods default El Display J Filled traces V Automatic intensity ranging I Show advanced parameters Cancel Help 2 In the Sequence Control area of the Per Method Parameters table click the Inject from Ref Inlet toggle button See Figure 16 Figure 16 Per Method Parameters table with advanced parameters Description Tune Control Probe Temperature C Needle kV Detector M Acquisition Control Retention Time mins General Control Operate Nitrogen Gas lonization Mode Sequence Control Inject from Ref Inlet Readback Setpoint _ 0 349 0 0 3 0 0 0 n a na On wm na On ESI n a Stated mm Inject from Ref Inlet toggle button The MSQ Plus Mass Detector draws calibrant from the reference inlet reservoir bottle through the tubing and into 500 uL sample loop for 35 seconds Thermo Scientific MS
122. tus of MSQ Plus Mass Detector 17 Server shortcut menu 27 server software 17 Show Full Scans bar 60 Show Method Options bar 60 67 Show Per Method Parameters Table bar 62 Show SIM Scans bar 60 SIM scan events 63 SIM Scan Events table opening 58 parameters on 68 purpose 63 switching to Full Scan Events table 60 wld files 81 source fragmentation 62 spectrum view 61 Start Acquiring icon 45 55 Status Log report 96 Stop Acquiring icon 45 47 55 survey link xv 112 MSQ Plus Mass Detector Getting Started Guide T Thermo Foundation Instrument Configuration dialog box 11 triethylamine TEA 6 trifluoroacetic acid TFA 6 tune files saving optimized settings in 8 selecting in Method Editor 68 Tune Method report 97 Tune Options dialog box 29 41 52 tune report locations 37 tuning calibrant 26 tuning in APCI mode See atmospheric pressure chemical ionization tuning in ESI mode See electrospray turbomolecular pumps 2 U Unlocked icon 85 USB cables 18 UV detectors 1 V vacuum system 2 View bar 66 volatile buffers 6 W waste bottle 26 WEEE compliance v Welcome page 57 66 X Xcalibur data system anti virus software 16 communication with MSQ Plus Mass Detector 17 icon 18 Information view 17 Instrument Setup view 40 51 65 parameters imported from tune file 8 Roadmap view 18 Sequence Setup view 75 77 server software 17 starting 18 Thermo Scientific
123. ue from the Tune file 5 To stop the acquisition after completing all the mass detector s scan events clear the Continue to End of LC check box shown in Figure 41 on page 59 Selecting the Per Method Parameters The per method parameters for the MSQ Plus Mass Detector are the ionization mode and the probe temperature To select the ionization mode and enter the probe temperature 1 If the Per Method Parameters table is not displayed open it by clicking the Show Per Method Parameters bar 2 If you want to change the ionization mode click the Ionization Mode Setpoint and select an appropriate ionization mode for your application 3 To change the probe temperature click the Probe Temperature Setpoint box Type an appropriate probe temperature in the box and then press ENTER Note The probe temperature setting is not imported with the tune file Use the temperature that you determined empirically when you optimized the tune parameters for your analytes Selecting the Scan Events Table 7 lists the allowable ranges for the parameters in the Full Scan Events table Table 8 lists the allowable ranges for the parameters in the SIM Scan Events table Your method can contain both SIM scan events and full scan events e Use SIM selected ion monitoring scan events for trace analysis and quantitation e Use full scan events for rapid screening and qualitative analysis 68 MSQ Plus Mass Detector Getting Started G
124. uide Thermo Scientific Table 7 Full Scan Events table parameters 7 Creating Instrument Methods Creating an LC MS Instrument Method Parameter Range Entry Name Alphanumeric characters Click the Name box and type a name consisting of alphanumeric characters Mass Range 1 00 2000 00 Click the Mass Range box and type the beginning mass a hyphen and the ending mass Time Range 0 00 9999 00 Click the Time Range box and type the beginning time point a hyphen and the ending time point Peak Format Centroid or Profile Click the Peak Format list and select Centroid or Profile from the list Scan Time 0 01 to 8 00 Click the Scan Time box and type a length of time for the scan Range 0 25 1 0 Polarity ve or ve Click the Polarity list and select ve or ve from the list Cone V 0 00 to 200 00 Click the Cone V box and type the value of the optimal cone typical 70 00 to 150 00 Table 8 SIM Scan Events table parameters voltage for your application Parameter Range Entering Name Alphanumeric characters Click the Name box and type a name consisting of alphanumeric characters Mass 1 00 2000 00 Click the Mass Range box and type the m z ratio of the ion that you want to monitor Span 0 00 to 1998 Click the Span box and type an appropriate span m z For SIM scan events typical values range between 0 05 and 0 5 Time Range 0 00 9999 00 Click the Time Range box and type the beginning time point a hyph
125. uires a team effort to lift and or move the instrument This instrument is too heavy and or bulky for one person alone to handle safely Notice on the Proper Use of Thermo Scientific Instruments In compliance with international regulations This instrument must be used in the manner specified by Thermo Fisher Scientific to ensure protections provided by the instrument are not impaired Deviations from specified instructions on the proper use of the instrument include changes to the system and part replacement Accordingly order replacement parts from Thermo Fisher Scientific or one of its authorized representatives Notice on the Susceptibility to Electromagnetic Transmissions Your instrument is designed to work in a controlled electromagnetic environment Do not use radio frequency transmitters such as mobile phones in close proximity to the instrument For manufacturing location see the label on the instrument WEEE Compliance This product is required to comply with the European Union s Waste Electrical amp Electronic Equipment WEEE Directive 2002 96 EC It is marked with the following symbol Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union EU Member State and these companies should dispose of or recycle this product See www thermoscientific com rohsweee for further information on Thermo Fisher Scientific s compliance with these Directives and the recyclers
126. ump that is capable of delivering solvent at a flow rate of 200 pL min to your MSQ Plus Mass Detector See the MSQ Plus Mass Detector Getting Connected Guide for instructions on connecting an LC system to your MSQ Plus Mass Detector Before you perform a full system autotune or a mass scale calibration prepare your MSQ Plus Mass Detector as described in Preparing Your LC MS for Operation on page 15 Contents e Preparing the MSQ Plus Mass Detector for Calibration e Performing a Full System Autotune e Performing a Mass Scale Calibration e Performing a Detector Gain Calibration Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 23 4 Calibrating the MSO Plus Mass Detector Preparing the MSQ Plus Mass Detector for Calibration Preparing the MSQ Plus Mass Detector for Calibration To perform a full system autotune mass scale calibration or detector gain calibration you must set up the mass detector for ESI mode and ensure that the reference inlet reservoir contains a sufficient volume of factory supplied calibrant To prepare the MSQ Plus Mass Detector for calibration follow these procedures 1 Verifying that the MSQ Plus Mass Detector is Set Up for ESI Mode 2 Setting Up the LC System Checking the Solvent Levels in the Reference Inlet System A amp Setting the Gas Flows and Probe Heater Temperature Nn Baking Out the Probe Optional 6 Flushing Air from the Lines of the Reference Inlet System 7
127. ury are used in the instrument Some maintenance procedures require that the mass detector be shut down and disconnected from line power before service is performed Do not operate the mass detector with the top or side covers off Do not remove protective covers from PCBs CAUTION Do not interfere with the safety interlock Interfering with the safety interlock will expose you to potentially lethal electrical hazards CAUTION Respect heated zones Treat heated zones with respect The ion transfer capillary and the APCI vaporizer might be very hot and might cause severe burns if touched Allow heated components to cool before you service them CAUTION Place the mass detector in Standby or Off mode before you open the atmospheric pressure ionization API source The presence of atmospheric oxygen in the API source when the mass detector is on could be unsafe The mass detector automatically goes into standby mode when you open the API source however take this added precaution for safety reasons CAUTION Take care when handling the corona pin The corona pin is sharp and can cause personal injury Take care when removing or installing the corona pin CAUTION Make sure you have sufficient nitrogen for your API source Before you begin normal operation each day make sure that you have sufficient nitrogen for your API gt gt PRP PP source The presence of atmospheric oxygen in the API source when the mass detector is on could be unsafe
128. us Mass Detector stops acquiring data after completing all the mass detector s scan events However if the Continue to End of LC check box shown in Figure 41 on page 59 is enabled the mass detector continues acquiring indefinitely or until you manually stop it 60 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 7 Creating Instrument Methods Method Editor Chromatogram View The Chromatogram view allows you to open a previously acquired raw file a file with the taw file extension and display its chromatogram You can right click the chromatogram to display a spectrum view which shows the most abundant ion at the selected retention time as shown in Figure 43 You can also use the information in the raw file to edit the retention times for the scan events in your method Figure 43 Chromatogram view showing a mass spectrum displayed by right clicking the chromatogram MSQ Pius Method Editor Per Method Parameters All Scans 100 lonization Mode ESI Probe Temperature C 350 00 Hide Per Method Parameters Full Scans SIM Scans 30 Parameters 80 Scans gt 70 Add Full 2 60 Add SIM 3 50 group AO Delete 30 20 10 Eh 400 500 6 00 Time minutes Spectrum Retention Time 3 66 minutes Scan 559 Top 20 Spectral Masses Rel Int 100 90 18 ee Peak Format Scan Time s Polarity Cone Centroid 1 00 ve 200 00 3 80 E Ea c 60 lt o 50 gt 3 40 cr 30 2
129. ution e Click the Mass box and type 1000 e Click the Span box and type 1997 e Click the Scan Time box and type 2 These settings let you to view the entire mass spectrum of the calibrant solution The characteristic peaks in the mass spectrum of the calibrant solution for the MSQ Plus Mass Detector are listed in Table 3 Figure 17 Full Scan Events table Name 1 Mass Span Time Range Peak Format Scan Time Polarity Cone Rdbk Zoom On Off Feil 1000 00 1997 00 0 00 Centroid 2 00 ve 75 B Table 3 Characteristic peaks in the mass spectrum of the calibrant solution Sheet 1 of 2 Peak Mass to charge ratio Peak Mass to charge ratio 1 22 99 8 1072 25 2 38 96 9 1222 14 3 83 05 10 1372 04 30 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 4 Calibrating the MSO Plus Mass Detector Performing a Full System Autotune Table 3 Characteristic peaks in the mass spectrum of the calibrant solution Sheet 2 of 2 Peak Mass to charge ratio Peak Mass to charge ratio 4 132 91 11 1521 93 5 172 88 12 1671 83 6 472 67 13 1821 72 7 622 57 14 1971 61 6 Turn on the solvent flow from the LC pump Ensure that the pump is set to deliver 50 50 acetonitrile water at a flow rate of 200 uL min 7 In the Sequence Control area of the Per Method Parameters table click the Inject from Ref Inlet toggle button shown in Figure 16 on page 29 The MSQ Plus Mass Detector draws calibrant from the referen
130. utotune performing 31 purpose 7 report 33 when to perform 8 23 G gain calibration 35 H hard drives 16 Hide Method Options bar 60 high mass resolution 9 110 MSQ Plus Mass Detector Getting Started Guide inactive cells 90 Info View icon 18 Information view displaying 18 purpose 17 Instrument Method report 95 instrument methods 65 Instrument Setup view 40 51 65 Instrument Tuning and Calibration wizard 32 34 35 ion energy 9 40 51 54 ion source 2 6 ionization mode 68 L LC pumps acquiring data in Tune window 41 51 draining oil from oil mist filter 20 increasing flow rate and temperature 7 introducing samples to MSQ Plus Mass Detector 5 minimum backpressure required 8 optimizing mass detector parameters 8 performing detector gain calibration 23 performing full system autotune 23 25 32 performing mass scale calibration 23 25 34 setting up 25 stopping after end of sequence 84 viewing calibrant mass spectrum 31 LC system checking hardware 15 configuring 13 connecting 15 creating instrument method controlling 70 opening Instrument Setup window 51 preparing for operation 21 setting up for calibration 25 setting up for manual tuning 40 light scattering detectors 1 liquid chromatography mass spectrometry LC MS 1 Locked icon 85 low mass resolution 9 mass analyzer 2 mass scale calibration performing 34 purpose 8 reference inlet system used in 1 when to perform 8 23 34 material safety data sheets M
131. xt A series of messages inform you of the progress of the calibration If the calibration fails an error message appears 4 To accept the results of the calibration click Finish The current calibration file is replaced with the one generated by the mass scale calibration procedure 5 Click Print Report to print the calibration report Performing a Detector Gain Calibration Note Detector gain calibration is only available in the engineering version of the Tune application As ions exit the mass analyzer the gain of an electron multiplier is the number of electrons created in each ion event The gain depends on the age of the electron multiplier and the velocity of the impinging electron which in turn depends on the voltage applied between the input and output of the multiplier At a given point in the lifetime of an electron multiplier a single ion event has a given gain As the electron multiplier ages its gain decreases because it does not release as many secondary electrons from a given ion event To maintain a gain of approximately 4 5 x 10 the voltage applied across the input and output of the multiplier must be increased 34 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific Thermo Scientific 4 Calibrating the MSO Plus Mass Detector Performing a Detector Gain Calibration The change in gain over time is directly related to the number of ions that impinge the detection system and the voltage
132. y axis to select a range e Drag a line in any diagonal direction to select an area The effect of these actions depends on the state of the cell Within an active cell cursor actions rescale the plot in the ways shown in Table 9 If one of the cells is pinned the cursor action in any of the inactive cells is always applied to the pinned cell as shown in Table 10 Table 9 Effect of cursor action in an active cell Cursor action Effect Drag parallel to X axis Rescale graph showing selected x range only same y range Drag parallel to Y axis Rescale graph showing selected y range only same x range Dragged area Rescale graph showing both the selected x and y ranges Table 10 Effect of cursor action in an inactive cell on the pinned cell Pinned cell Cursor action Effect Spectrum Click in a chromatogram cell The spectrum cell displays the spectrum at that retention time Chromatogram Click in a spectrum cell The chromatogram cell displays chromatogram for the wavelength selected in the spectrum cell Opening a Raw Data File in Qual Browser The data files containing the raw chromatographic and spectral data have the raw file extension To open a raw data file in Qual Browser 1 Click the Qual Browser icon on the Xcalibur Roadmap view or choose Go To gt Qual Browser to display the empty Qual Browser window shown in Figure 68 92 MSQ Plus Mass Detector Getting Started Guide Thermo Scientific 9 Using Qual Browser
133. y clicking the Locked icon After you unlock the display data collection continues off screen 2 Pin the Mass Spectrum cell by clicking the pin icon in the upper right corner of the cell The pin in the upper right corner of the Mass Spectrum cell turns green Cursor actions in other cells such as the chromatogram cell now affect the view displayed in the Spectrum cell 3 Click the peak of interest in the Chromatogram cell In the Mass Spectrum cell a mass spectrum appears for the time point that you clicked on 4 To resume monitoring real time data acquisition click the Locked icon again to lock the display Thermo Scientific MSQ Plus Mass Detector Getting Started Guide 85 8 Creating and Running Sequences Viewing the Data as It Is Acquired 5 Pin the Chromatogram cell by clicking the pin in the upper right corner of the cell The pin in the upper right corner of the Chromatogram cell turns green Cursor actions in other cells such as the Spectrum cell now affect the view displayed in the Chromatogram cell 6 Click the m z value of interest in the Mass Spectrum cell In the Chromatogram cell that contained the total ion chromatogram TIC a chromatogram appears for the m z value that you clicked 7 To resume monitoring real time data acquisition click the Locked icon a Adding Cells to the Display You can display multiple cells in the real time display view RL bd 1 Clic

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