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2

Setting Up the Xcalibur Instrument Configuration

Specifying the Reagent Ion Source for the MS Detector

12

MS/ETD System Getting Started Guide

Thermo Scientific

5. Click

OK

.

A message box opens:

In order for the configuration changes to take effect, you will need to reboot the data
system and then the LTQ.

6. Click

OK

.

7. Reboot the data system.

8. Reboot the LTQ XL or LTQ Velos MS detector.

For instructions, refer to the

LTQ Series Hardware Manual

.

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Summary of Contents for ETD

Page 1: ...ETD Module Getting Started Guide for the LTQ XL and LTQ Velos MS Detectors compatible with LTQ Orbitrap XL and LTQ Orbitrap Velos 98000 97003 Revision C December 2010...

Page 2: ...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...

Page 3: ...ermo Fisher Scientific To ensure continued compliance with EMC and safety standards replacement parts and additional components options and peripherals must be ordered from Thermo Fisher Scientific or...

Page 4: ...trument This instrument is too heavy and or bulky for one person alone to handle safely EN 61326 1 2006 EN 61000 4 4 2004 EN 55011 2007 EN 61000 4 5 2005 EN 61000 3 2 2006 EN 61000 4 6 2007 EN 61000 3...

Page 5: ...r Scientific could impair any protection provided by the instrument Notice on the Susceptibility to Electromagnetic Transmissions Your instrument is designed to work in a controlled electromagnetic en...

Page 6: ......

Page 7: ...Directives and the recyclers in your country WEEE Konformit t Dieses Produkt muss die EU Waste Electrical Electronic Equipment WEEE Richtlinie 2002 96 EC erf llen Das Produkt ist durch folgendes Symb...

Page 8: ...ieurs compagnies de recyclage dans chaque tat membre de l union europ enne et ce produit devrait tre collect ou recycl par celles ci Davantage d informations sur la conformit de Thermo Fisher Scientif...

Page 9: ...he Reagent Ion Source for the MS Detector 10 Chapter 3 Tuning 13 Opening the Tune Plus Window 13 Tuning the Reagent Ion Optics 14 Automatic Tuning of the Reagent Ion Optics 15 Manually Tuning the Reag...

Page 10: ...bleshooting an AGC Target Error 35 Obtaining an ETD Spectrum for Angiotensin I 35 Optimizing the Reagent Ion Reaction Time 38 Chapter 6 Running an Xcalibur Experiment by Using ETD 41 Nth Order Double...

Page 11: ...XL 21 Figure 14 Semi Automatic page in the Tune dialog box 23 Figure 15 Reagent Ion Optics dialog box 24 Figure 16 Ion Trap page 26 Figure 17 Reagent page 27 Figure 18 Reagent Ion Source dialog box 28...

Page 12: ...de Thermo Fisher Scientific Figure 35 Data Dependent NL MS3 dialog box 47 Figure 36 Neutral loss masses table example 48 Figure 37 Data Dependent NL MS3 template 49 Figure 38 ETD Reagent fluoranthene...

Page 13: ...to documentation or to Help Complete a brief survey about this document by clicking the link below Thank you in advance for your help Related Documentation In addition to this guide Thermo Fisher Sci...

Page 14: ...tements that appear in the MS ETD System Getting Started Guide Table 1 LTQ XL ETD and LTQ Velos ETD system documentation Model Related documents LTQ XL and LTQ Velos LTQ Series Preinstallation Require...

Page 15: ...ngs Symbol Meaning General Hazard A hazard is present that is not included in the following categories This symbol also appears on the instrument Refer to the instructions in the instrument manual for...

Page 16: ...arted Guide Thermo Scientific To suggest changes to documentation or to Help Fill out a reader survey online at www surveymonkey com s PQM6P62 Send an e mail message to the Technical Publications Edit...

Page 17: ...e and flow restrictors ion volume and filament ion optics and heaters for these components The flow restrictors keep the internal pressure of the reagent vials below atmospheric pressure which prevent...

Page 18: ...mino acid side chains and important modifications such as phosphorylation are left intact Types of Experiments The New Method page of the Instrument Setup window for the LTQ XL Figure 1 or LTQ Velos M...

Page 19: ...1 Introduction Types of Experiments Thermo Scientific MS ETD System Getting Started Guide 3 Figure 1 LTQ XL ETD system New Method page...

Page 20: ...ree Ion Mapping ETD Experiment Types With the addition of the ETD module to the LTQ XL or LTQ Velos MS detector two other experiment templates are available Nth Order Double Play ETD This experiment i...

Page 21: ...e mass accuracy To tune and calibrate the LTQ XL ETD or LTQ Velos ETD system perform these basic steps Tune and calibrate the LTQ XL or LTQ Velos MS detector as described in the LTQ Series Getting Sta...

Page 22: ......

Page 23: ...D source and the LTQ XL or LTQ Velos MS detector from the Xcalibur data system add these devices to the Xcalibur instrument configuration To add the MS detector to the list of configured devices 1 Clo...

Page 24: ...ing Started Guide Thermo Scientific Figure 2 Thermo Foundation Instrument Configuration window 3 Select the devices to control from the Xcalibur data system as follows a In the Device Types list selec...

Page 25: ...nstrument Configuration Adding the MS Detector to the Xcalibur Instrument Configuration Thermo Scientific MS ETD System Getting Started Guide 9 Figure 3 Thermo Foundation Instrument Configuration wind...

Page 26: ...To specify the reagent ion source 1 In the Thermo Foundation Instrument Configuration window in the Configured Devices list double click the LTQ XL MS or LTQ Velos MS icon to open the Configuration d...

Page 27: ...shown is information about the contents of the reagent vials 4 Optional Select the Use Low Vial Temperature check box to heat the vial to 90 C rather than 108 C Figure 6 Figure 6 LTQ Velos Configurat...

Page 28: ...Getting Started Guide Thermo Scientific 5 Click OK A message box opens In order for the configuration changes to take effect you will need to reboot the data system and then the LTQ 6 Click OK 7 Rebo...

Page 29: ...n the Tune Plus window Figure 7 On the Windows taskbar choose Start Programs Thermo Instruments LTQ model Tune where model is your specific MS ETD system In the Xcalibur application choose Roadmap vie...

Page 30: ...thod for most situations Use manual tuning to manually optimize reagent ion optics parameters and reagent ion source parameters not automatically tuned such as CI gas pressure electron energy and emis...

Page 31: ...ctor heater source heater and the transfer line heater are not at their target temperatures When either the LTQ XL ETD or LTQ Velos ETD MS detector or the MS ETD System goes into standby mode Reagent...

Page 32: ...ent vials are not at their target temperature a message appears Reagent Vial NOT At Temperature Please wait The System LED on the ETD module flashes green to indicate that the reagent vial heaters are...

Page 33: ...s Thermo Scientific MS ETD System Getting Started Guide 17 5 In the Reagent Ion Source dialog box select the View Reagent Ion Spectra check box Figure 9 shows the reagent spectrum at peak m z 202 Figu...

Page 34: ...e The Status area displays the message Optimization Complete after completing automatic tuning This message also states the percentage change in the reagent ion signal m z 202 intensity relative to th...

Page 35: ...pectra check box 5 In the Tune Plus window click the Tune button to open this dialog box Figure 10 Note If the reagent vials are not at their target temperature a message appears Reagent Vial NOT At T...

Page 36: ...de Thermo Scientific 6 In the Tune Plus window choose Setup Reagent Ion Optics to open this dialog box Figure 11 Figure 11 Reagent Ion Optics dialog box 7 In the Tune dialog box Figure 10 on page 18 c...

Page 37: ...y appears Figure 13 You can observe The response of the reagent ion intensity to changes in the lens parameters in the Reagent Ion Optics dialog box Figure 11 on page 20 The emission current CI gas pr...

Page 38: ...the Reagent Ion Source dialog box select the View Reagent Ion Spectra check box 5 In the Tune Plus window click the Tune button to open this dialog box Figure 10 on page 18 Note If the reagent vials a...

Page 39: ...Figure 14 Semi Automatic page in the Tune dialog box 7 Under What to Optimize select one of the following items to tune Reagent ion lens 1 V Reagent ion gate lens V Reagent ion lens 2 V Reagent ion l...

Page 40: ...2 Choose Setup Reagent Ion Optics to open this dialog box Figure 15 The Reagent Ion Optics dialog box shows the optimized settings from the tuning process Figure 15 Reagent Ion Optics dialog box 3 Cl...

Page 41: ...em Mode Checking the Vacuum Pressure Checking the Gas Supplies Checking the System Mode Before beginning your daily work turn on the mass spectrometer To turn on the mass spectrometer 1 Open the Tune...

Page 42: ...e heater are not at their target temperatures When either the LTQ XL ETD or LTQ Velos ETD MS detector or the MS ETD System goes into standby mode Reagent vial nitrogen cooling turns on if the vials ar...

Page 43: ...h the tank pressure regulator 3 Verify that the pressure of the reagent carrier gas ultra high purity helium nitrogen or nitrogen at the ETD module is 275 35 kPa 39 9 5 psi If necessary adjust the pre...

Page 44: ...3 of gas should last approximately two years For more information about gas requirements refer to the LTQ Series Preinstallation Requirements Guide Turning On the Reagent Ion Source Even when the ETD...

Page 45: ...NOT At Temperature Please wait The System LED on the ETD module flashes green to indicate that the reagent vial heaters are turned on but not at their target temperatures the other heaters are at thei...

Page 46: ...ectrum 7 Check the spectrum and do one of the following If the spectrum is satisfactory proceed to step 8 If the spectrum is not satisfactory tune the reagent ion optics as described in Chapter 3 Tuni...

Page 47: ...Ion Source to open this dialog box Figure 20 Figure 20 Reagent Ion Source dialog box 3 Clear the Reagent Ion Source On check box When you clear this check box the ETD source and reagent heaters go in...

Page 48: ...TD System Getting Started Guide Thermo Scientific Purging the Oil in the Fore Pump Purge decontaminate the oil in the fore pump daily to remove water and other dissolved chemicals from the pump oil Fo...

Page 49: ...number of reagent ions admitted into the ion trap of the LTQ XL or LTQ Velos MS detector To view the injection reagent ion settings 1 Open the Tune Plus window see the instructions on page 13 2 Choos...

Page 50: ...s Specifies the maximum time that the system allows for anions to be injected into the trap The default value is 50 ms AGC Target Sets the target number of reagent anions to be injected into the trap...

Page 51: ...e to a dirty reagent ion source its optics or both A contaminated reagent ion source or its optics can also cause the maximum injection time limit to be exceeded Increase the emission current in the R...

Page 52: ...is dialog box Figure 23 Figure 23 Define Scan dialog box 5 Under MSn Settings in the n 2 row enter the Parent Mass m z of the 3 charge state of Angiotensin I The molecular weight of Angiotensin I acet...

Page 53: ...ETD Spectrum for Angiotensin I Thermo Scientific MS ETD System Getting Started Guide 37 7 Click OK The Define Scan dialog box closes and Tune Plus displays the ETD MS MS spectrum of Angiotensin I Fig...

Page 54: ...eagent ions as described in Turning On the Reagent Ion Source on page 28 To optimize the reagent ion reaction time 1 Turn on ETD activation for the analyte Angiotensin I in this case 2 Open the Tune P...

Page 55: ...window shows a reagent ion reaction time after completing the tune process A message prompts you to accept the optimized value If you accept the optimized value the reagent ion reaction time paramete...

Page 56: ......

Page 57: ...calibur Experiment by Using ETD This chapter describes the two ETD specific experiment templates provided by the Xcalibur data system For more information refer to the LTQ Series Getting Started Guide...

Page 58: ...ed Guide Thermo Scientific Nth Order Double Play ETD Experiment To create an Nth Order Double Play ETD method 1 Choose Start Programs Thermo Xcalibur Xcalibur Figure 28 Figure 28 Xcalibur Roadmap view...

Page 59: ...ur Experiment by Using ETD Nth Order Double Play ETD Experiment Thermo Scientific MS ETD System Getting Started Guide 43 2 Click the Instrument Setup icon Figure 29 Figure 29 Instrument Setup window f...

Page 60: ...or LTQ Velos MS icon to open the New Method page for the device Figure 30 New Method page for the LTQ XL ETD system 4 Under Select ETD Experiment Type click Nth Order Double Play ETD to open this dial...

Page 61: ...ument Setup window opens showing the Nth Order Double Play with ETD template Figure 32 Figure 32 Nth Order Double Play with ETD template 7 Enter the scan event settings by clicking the Scan Event 1 Sc...

Page 62: ...list click Activation to see the activation parameters Figure 34 The activation type is automatically set to ETD Figure 34 Activation parameters 10 In the Default Charge State box enter a value of 5 o...

Page 63: ...1 Choose Start Programs Xcalibur Xcalibur Figure 28 on page 42 2 Click the Instrument Setup icon Figure 29 on page 43 3 In the Available Devices pane click the LTQ XL MS or LTQ Velos MS icon to open...

Page 64: ...ollowing Type the mass and name for the neutral loss masses to identify Click Import to import a list of neutral loss masses from a tab delimited text file or from an XML file Figure 36 shows an examp...

Page 65: ...vent 2 and Scan Event 3 bars For Scan Event 2 and Scan Event 3 the Dependent Scan check box lower left corner and its adjacent Settings button become active 9 For Scan Event 2 and Scan Event 3 only Cl...

Page 66: ...The Normalized Collision Energy and Activation Q parameters are unavailable because they are not applicable to ETD 13 In the Activation Time ms box leave the default value or enter a different value a...

Page 67: ...eted the ETD reagent m z peak intensity diminishes m z 202 in negative polarity mode Periodically checking this peak intensity is a good way to monitor the ETD module consumables To view the ETD reage...

Page 68: ...cribed in the ETD Module Hardware Manual With the emission current at the correct level the m z 202 signal significantly drops within one hour The reagent vial might be empty Replace the fluoranthene...

Page 69: ...thod for a specific reagent or solvent By law producers and suppliers of chemical compounds are required to provide their customers with the most current health and safety information in the form of a...

Page 70: ...hermo Fluoranthene P N HAZMAT 00013 is Sigma Aldrich Supelco P N 48535 The fluoranthene MSDS is available on the following Web page http www sigmaaldrich com catalog search ProductDetail SUPELCO 48535...

Page 71: ...the most current health and safety information in the form of an MSDS The MSDS provides summarized information about the hazard and toxicity of specific chemical compounds Is also provides informatio...

Page 72: ...f methanol 8 L of glacial acetic acid 3 Mix the solution thoroughly To prepare an Angiotensin I sample solution 1 Pipet 100 L of the stock solution 1 nmol L of Angiotensin I into a clean polypropylene...

Page 73: ...experiments 2 F FCC compliance iv fluoranthene 53 fore pump oil purging 32 G gas release 31 H helium gas checking supply 27 I injection reagent ion settings 33 N nitrogen gas checking supply 27 nitro...

Page 74: ...ETD System Getting Started Guide Thermo Scientific Index V V vacuum pressure checking 26 W WEEE compliance vii X Xcalibur experiments for ETD 4 41 Xcalibur instrument configuration 7 Xcalibur templat...

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