Exactive Operating Manual Rev C

© 2010 Thermo Fisher Scientific Inc. All rights reserved. PEEK polymer is a trademark of Victrex plc. PEEKSil is a trademark of SGE International Pty. Ltd. SEQUEST is a registered trademark of University of Washington. Sigma-Aldrich is a trademark of Sigma-Aldrich Biotechnology. SOGEVAC is a registered trademark of Leybold Vacuum GmbH. Swagelok is a registered trademark of the Crawford Fitting Company. Teflon and Vespel are registered trademarks of E. I. du Pont de Nemours & Co. Tygon is a registered trademark of Saint-Gobain Performance Plastics Company. 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, omissions, damage or loss that might result from any use of this document, even if the information in the document is followed properly. This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of Sale shall govern all conflicting information between the two documents.

Release History: Revision A released in January 2009. Revision B released in July 2009. Revision C released in April 2010. For Research Use Only. Not for use in diagnostic procedures.

FCC Compliance Statement THIS DEVICE COMPLIES WITH PART 18 OF THE FCC RULES.

Read This First Welcome to the Thermo Scientific, Exactive™ system! Exactive is a member of the Thermo Scientific family of advanced mass spectrometer (MS) detectors.

About This Guide This Exactive Operating Manual describes the modes of operation and principle hardware components of your Exactive instrument. In addition, this manual provides step-by-step instructions for cleaning and maintaining your instrument.

Who Uses This Guide This Exactive Operating Manual is intended for all personnel that need a thorough understanding of the instrument (to perform maintenance or troubleshooting, for example). This manual should be kept near the instrument to be available for quick reference.

Scope of This Guide This manual includes the following chapters:

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Chapter 1: “Functional Description” describes the principal components of the Exactive.

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Chapter 2: “Daily Operation” outlines the checks and cleaning procedures of the Exactive system that should be performed every day to ensure the proper operation of your system.

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Chapter 3: “User Maintenance” outlines the maintenance procedures that you should perform on a regular basis to maintain optimum MS detector performance.

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Chapter 4: “System Shutdown, Startup, and Reset” provides procedures for shutting down and starting up the Exactive.

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Chapter 5: “Replaceable Parts” lists the replaceable parts for the MS detector and data system.

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Appendix A: “Calibration Solutions” provides information about preparing the calibration solutions for the Exactive.

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Appendix B: “Getting Connected” provides information on how to connect your Exactive mass spectrometer to external devices and describes the specifications for the peripheral control connections.

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Read This First Related Documentation

Related Documentation In addition to this guide, Thermo Fisher Scientific provides the following documents for Exactive: •

Exactive Preinstallation Requirements Guide

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Exactive Software Manual

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Exactive QuickStart Guide

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Ion Max and Ion Max-S API Source Hardware Manual

You can access PDF files of the documents listed above from the data system computer. The software also provides Help.

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Read This First Contacting Us

Contacting Us There are several ways to contact Thermo Fisher Scientific.

Assistance For technical support and ordering information, visit us on the Web: www.thermo.com/advancedms

Customer Information Service cis.thermo-bremen.com is the Customer Information Service site aimed at providing instant access to •

latest software updates

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manuals, application reports, and brochures.

Note Thermo Fisher Scientific recommends that you register with the site as early as possible. ▲ To register, visit register.thermo-bremen.com/form/cis and fill in the registration form. Once your registration has been finalized, you will receive confirmation by e-mail.

Changes to the Manual ❖

To suggest changes to this manual

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Please send your comments (in German or English) to: Editors, Technical Documentation Thermo Fisher Scientific (Bremen) GmbH Hanna-Kunath-Str. 11 28199 Bremen Germany

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Send an e-mail message to the Technical Editor at [email protected]

You are encouraged to report errors or omissions in the text or index. Thank you.

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Read This First Typographical Conventions

Typographical Conventions This section describes typographical conventions that have been established for Thermo Fisher Scientific manuals.

Data Input Throughout this manual, the following conventions indicate data input and output via the computer: •

Messages displayed on the screen are represented by capitalizing the initial letter of each word and by italicizing each word.

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Input that you enter by keyboard is identified by quotation marks: single quotes for single characters, double quotes for strings.

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For brevity, expressions such as “choose File > Directories” are used rather than “pull down the File menu and choose Directories.”

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Any command enclosed in angle brackets < > represents a single keystroke. For example, “press <F1>” means press the key labeled F1.

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Any command that requires pressing two or more keys simultaneously is shown with a plus sign connecting the keys. For example, “press <Shift> + <F1>” means press and hold the <Shift> key and then press the <F1> key.

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Any button that you click on the screen is represented in bold face letters. For example, “click Close”.

Topic Headings The following headings are used to show the organization of topics within a chapter:

Chapter 1 Chapter Name

Second Level Topics Third Level Topics Fourth Level Topics

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Read This First Safety and EMC Information

Safety and EMC Information In accordance with our commitment to customer service and safety, this instrument has satisfied the requirements for the European CE Mark including the Low Voltage Directive. Designed, manufactured and tested in an ISO9001 registered facility, this instrument has been shipped to you from our manufacturing facility in a safe condition. This instrument must be used as described in this manual. Any use of this instrument in a manner other than described here may result in instrument damage and/or operator injury. Notice on Lifting and Handling of Thermo Scientific Instruments For your safety, and in compliance with international regulations, the physical handling of this Thermo Scientific instrument requires a team effort for lifting and/or moving 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: If this instrument is used in a manner not specified by Thermo Fisher Scientific, the protection provided by the instrument could be impaired. 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.

Safety and Special Notices Make sure you follow the precautionary statements presented in this guide. The safety and other special notices appear different from the main flow of text. Safety and special notices include the following: Warning Warnings highlight hazards to human beings. Each Warning is accompanied by a Warning symbol. ▲

Caution Cautions highlight information necessary to protect your instrument from damage. ▲ Note Notes highlight information that can affect the quality of your data. In addition, notes often contain information that you might need if you are having trouble. ▲

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Identifying Safety Information The Exactive Operating Manual contains precautionary statements that can prevent personal injury, instrument damage, and loss of data if properly followed. Warning symbols alert the user to check for hazardous conditions. These appear throughout the manual, where applicable. The most common warning symbols are: Warning General Hazard. This general symbol indicates that a hazard is present that could result in injuries if it is not avoided. The source of danger is described in the accompanying text. ▲

Warning Electric Shock Hazard. High Voltages capable of causing personal injury are used in the instrument. The instrument must be shut down and disconnected from line power before service is performed. Do not operate the instrument with the top cover off. Do not remove protective covers from PCBs. ▲ Warning Burn Hazard. Treat heated zones with respect. Parts of the instrument might be very hot and might cause severe burns if touched. Allow hot components to cool before servicing them. ▲

Warning Corrosive Material. Wear gloves when handling toxic, carcinogenic, mutagenic, or corrosive/irritant chemicals. Use approved containers and procedures for disposal of waste solution. ▲ In addition to the above described, every instrument has specific hazards. So, be sure to read and comply with the precautions described in the subsequent chapters of this guide. They will help ensure the safe, long-term use of your system.

General Safety Precautions Observe the following safety precautions when you operate or perform service on your instrument:

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The system should be operated by trained personnel only. Read the manuals before starting the system and make sure that you are familiar to the warnings and safety precautions!

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Accurate results can be obtained only, if the system is in good condition and properly calibrated.

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Service by the customer should be performed by trained qualified personnel only and should be restricted to servicing mechanical parts! Service on electronical parts should be performed by Thermo Fisher Scientific Service Engineers only!

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Before plugging in any of the instrument modules or turning on the power, always make sure that the voltage and fuses are set appropriately for your local line voltage.

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Only use fuses of the type and current rating specified. Do not use repaired fuses and do not short-circuit the fuse holder.

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The supplied power cord must be inserted into a power outlet with a protective earth contact (ground). When using an extension cord, make sure that the cord also has an earth contact.

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Do not change the external or internal grounding connections. Tampering with or disconnecting these connections could endanger you and/or damage the system.

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The instrument is properly grounded in accordance with regulations when shipped. You do not need to make any changes to the electrical connections or to the instrument’s chassis to ensure safe operation.

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Never run the system without the housing on. Permanent damage can occur. When leaving the system, make sure that all protective covers and doors are properly connected and closed, and that heated areas are separated and marked to protect for unqualified personnel!

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Do not turn the instrument on if you suspect that it has incurred any kind of electrical damage. Instead, disconnect the power cord and contact a Thermo Fisher Scientific Service Engineer for a product evaluation. Do not attempt to use the instrument until it has been evaluated. (Electrical damage may have occurred if the system shows visible signs of damage, or has been transported under severe stress.)

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Damage can also result if the instrument is stored for prolonged periods under unfavorable conditions (e.g., subjected to heat, water, etc.).

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Always disconnect the power cord before attempting any type of maintenance.

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Capacitors inside the instrument may still be charged even if the instrument is turned off.

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Never try to repair or replace any component of the system that is not described in this manual without the assistance of your Thermo Fisher Scientific Service Engineer.

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Do not place any objects – especially not containers with liquids – upon the instrument. Leaking liquids might get into contact with electronic components and cause a short circuit.

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Safety Advice for Possible Contamination Hazardous Material Might Contaminate Certain Parts of Your System During Analysis. In order to protect our employees, we ask you to adhere to special precautions when returning parts for exchange or repair. If hazardous materials have contaminated mass spectrometer parts, Thermo Fisher Scientific can only accept these parts for repair if they have been properly decontaminated. Materials, which due to their structure and the applied concentration might be toxic or which in publications are reported to be toxic, are regarded as hazardous. Materials that will generate synergetic hazardous effects in combination with other present materials are also considered hazardous. Your signature on the Repair-Covering letter confirms that the returned parts have been decontaminated and are free of hazardous materials. The Repair-Covering letter can be ordered from your service engineer or downloaded from the Customer Information Service (CIS) site. Please register under http://register.thermo-bremen.com/form/cis. Parts contaminated by radioisotopes are not subject to return to Thermo Fisher Scientific – either under warranty or the exchange part program. If parts of the system may be possibly contaminated by hazardous material, please make sure the Field engineer is informed before the engineer starts working on the system.

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Contents Chapter 1

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Functional Description...1-1 General Description ... 1-2 Instrument Layout ... 1-2 Placing the Instrument... 1-4 Control Elements... 1-7 System Status LEDs ... 1-7 Power Panel ... 1-8 Power Column... 1-11 API Source ... 1-13 Ion Max Ion Source ... 1-14 Ion Source Mount... 1-15 Ion Source Interface ... 1-16 Ion Optics... 1-18 Source Ion Optics ... 1-19 Analyzer Ion Optics ... 1-19 Orbitrap Analyzer ... 1-21 Curved Linear Trap ... 1-21 Extraction of Ion Packets ... 1-22 Measuring Principle ... 1-23 Ion Detection... 1-23 HCD Collision Cell... 1-25 Additional Hardware... 1-26 Syringe Pump ... 1-26 Switching Valves ... 1-27 Vacuum System ... 1-28 Forepump ... 1-29 Turbomolecular Pumps... 1-31 Vacuum System Controls... 1-32 System Bakeout... 1-35 Cooling Fans... 1-36 Gas Supply... 1-37 Nitrogen Gas Distribution ... 1-38 Collision Gas Distribution ... 1-38 Printed Circuit Boards ... 1-40 Preamplifier ... 1-40 Source Board... 1-40 8 kV Power Supply ... 1-41 Ion Optic Supply DC Board ... 1-41 Ion Optic Supply RF Board ... 1-41 FT Adapter Board ... 1-41 Data Acquisition Board (DAQ Board) ... 1-42 Internal Computer (Data Acquisition Unit)... 1-42 Vacuum Control Board... 1-42

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CLT-RF Board ... 1-43 CE HV Supply Board ... 1-43 CE Pulser Board... 1-43 Power Supply DAQ Board... 1-44 I/O Board ... 1-44

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Chapter 2

Daily Operation ... 2-1 Things to Do Before Operating the Exactive System... 2-2 Checking the Argon and Nitrogen Supplies ... 2-2 Checking the ESI Fused-Silica Sample Tube for Elongation ... 2-2 Checking the System Vacuum Levels ... 2-3 Checking the Disk Space on the Data System ... 2-5 Checking the Mass Accuracy of the Instrument ... 2-5 Things to Do After Operating the Exactive System ... 2-7 Flushing Sample Transfer Line, Sample Tube, and API Probe ... 2-7 Flushing Ion Sweep Cone and Ion Transfer Capillary ... 2-8 Purging the Oil in the Forepump... 2-11 Empty the Solvent Waste Container ... 2-11

Chapter 3

User Maintenance... 3-1 General Remarks on Maintenance... 3-2 Returning Parts ... 3-3 Cleaning the Surface of the Instrument ... 3-3 Checking Warning Labels ... 3-4 Leak-Checking Gas Lines... 3-4 Maintaining the Vacuum System ... 3-5 Pumps Maintenance... 3-5 Baking Out the System ... 3-7 Maintenance of the Fan Filters... 3-9 API Source Maintenance... 3-11 Frequency of Cleaning ... 3-11 Removing and Reinstalling the Ion Max Ion Source Housing ... 3-12 Ion Sweep Cone and Ion Transfer Capillary Maintenance ... 3-16 Maintaining the API Probes ... 3-20 Maintaining the Ion Source Interface... 3-20

Chapter 4

System Shutdown, Startup, and Reset ... 4-1 Shutting Down the System in an Emergency ... 4-2 Behavior of the System in Case of a Main Failure... 4-2 Placing the System in Standby Condition ... 4-4 Shutting Down the System ... 4-5 Starting Up the System after a Shutdown... 4-6 Starting Up the Instrument ... 4-6

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Setting Up Conditions for Operation... 4-7 Resetting the System ... 4-8 Chapter 5

Replaceable Parts...5-1

Appendix A Calibration Solutions...A-1 Obtaining Ready-to-Use Calibration Solutions ...A-2 Calibration- and Test-Chemicals...A-3 Preparing the Positive Ion Mode Calibration Solution ...A-4 Preparing the Negative Ion Mode Calibration Solution ...A-6 Appendix B Getting Connected ...B-1 Connecting the API Probe to the MS Detector ... B-2 Connecting the Inlet Plumbing...B-3 Sample Introduction ... B-3 Fittings, Tubing, Unions, and Sample Loops ... B-4 Setting Up the Inlet for Direct Infusion ... B-6 Setting Up the Inlet for High-Flow Infusion... B-9 Setting Up the Inlet for Loop Injections (Flow Injection Analyses) ... B-14 Setting Up the Inlet for an LC/MS System with an Autosampler... B-17 Connecting the Grounding Union to the ESI Probe Sample Inlet... B-18 Establishing Power Supply and Communication for the Syringe Pump... B-19 Establishing Power Supply and Communication for the Switching Valve(s)... B-19 User I/O Connections... B-21 Output Specifications ...B-21 Input Specifications... B-22 Glossary ...G-1 Index ... I-1

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Figures Exactive front view ... 1-2 Instrument dimensions ... 1-4 System status LEDs ... 1-7 Rear side view of the instrument ... 1-8 Power panel ... 1-9 Power column ... 1-11 Ion Max ion source with ESI probe attached ... 1-13 Ion source mount ... 1-16 Cross sectional view of the ion source interface ... 1-17 Schematic view of the Exactive ... 1-18 Schematic view of the Orbitrap cell and example of a stable ion trajectory ... 1-21 Principle of electrodynamic squeezing of ions in the Orbitrap as the field strength is increased ... 1-22 Approximate shape of ion packets of different m/q after stabilization of voltages ... 1-24 Exactive with Chemyx Fusion 100 syringe pump ... 1-26 Schematic view of vacuum system ... 1-28 Forepump with noise reduction cover and drip pan ... 1-29 Forepump with On/Off switch ... 1-30 Overload protection for forepump without On/Off switch ... 1-30 Schematic view of the gas supply ... 1-37 Sweep gas supply port in the API cone seal ... 2-10 Ion sweep cone, showing the gas inlet ... 2-10 Vacuum / Bakeout window ... 3-7 Bakeout dialog box ... 3-8 Message box: Vacuum Bakeout active ... 3-8 Ventilation slots at the rear side of the instrument ... 3-9 Removing a fan filter from the filter bracket ... 3-9 Ion Max source housing, showing detail of components ... 3-12 Rear view of the Ion Max ion source housing ... 3-13 Ion source mount showing ion source housing guide pins and ion source interface release lever ... 3-14 View of the Ion Max API source and the drainage system ... 3-15 Spray cone, O-ring, ion transfer capillary, and ion sweep cone of the ion source interface ... 3-18 Ion source interface, showing the sweep gas supply port in the API cone seal ... 3-19 Ion sweep cone, showing the gas inlet ... 3-19 Removing the ion source interface ... 3-22 Exploded view of ion source interface assembly ... 3-25 Power panel, showing main power circuit breaker switch and reset button ... 4-2

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Figures

Connection between ESI probe and syringe pump ... B-7 Connecting the syringe and the LC union ... B-8 Connecting the infusion line to the LC union and the grounding union ... B-9 Connecting the LC union to the union Tee ... B-10 Six-port switching valve connections ... B-11 Connecting the LC union to the union Tee ... B-11 Plumbing diagram showing APCI/MS sample introduction with high-flow infusion ... B-13 Connecting the union Tee to the grounding union used for the ESI probe ... B-13 Plumbing diagram showing ESI/MS sample introduction with high-flow infusion ... B-14 Switching valve set up for loop injections ... B-15 Plumbing diagram for loop injection into the solvent flow from an LC into an APCI probe ... B-16 Plumbing diagram for loop injection into the solvent flow from an LC into an ESI probe ... B-17 Connecting the grounding union to the sample inlet of the ESI probe ... B-18 Power panel of the Exactive MS ... B-19 Output equivalent schematic ... B-21 Start In input equivalent schematic ... B-22 Analog inputs equivalent schematic ... B-23

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Tables Measuring properties of the instrument ... 1-3 System status LEDs of the Exactive ... 1-7 Vacuum regions overview ... 1-28 Vacuum measurement regions in the Exactive ... 1-33 Typical pressure readings ... 2-4 User maintenance procedures ... 3-2 Maintenance schedule of the forepump ... 3-5 Solvent waste system parts ... 3-16 Parts for maintenance of the ion transfer capillary ... 3-17 Available calibration solution packages ...A-2 Exactive calibration- and test-chemicals ...A-3 Sample introduction and analytical techniques for ESI/MS and APCI/MS ... B-4 Frequently used parts for making plumbing connections for ESI/MS and APCI/MS ... B-5 Output circuit specifications ... B-21 Start In input circuit specifications ... B-22 Analog inputs circuit specifications ... B-23

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Procedures To suggest changes to this manual...iv To cut and reposition the end of the sample tube... 2-3 To determine the amount of available disk space... 2-5 To flush sample transfer line, sample tube, and API probe ... 2-7 To clean ion sweep cone and ion transfer capillary ... 2-8 To purge the oil in the forepump ... 2-11 To perform a leak check for a gas line ... 3-4 To perform a system bakeout ... 3-7 To check the fan filters... 3-9 To clean the fan filters... 3-10 To remove the ion source housing... 3-12 To reinstall the Ion Max ion source housing ... 3-13 To remove and clean the ion transfer capillary ... 3-17 To remove the ion source interface... 3-21 To remove tube lens and skimmer from the ion source interface assembly... 3-23 To remove the capillary heater assembly... 3-24 To reinstall tube lens and skimmer... 3-26 To reinstall the ion source interface assembly ... 3-26 To place the Exactive system in the Standby condition ... 4-4 To shut down the Exactive system... 4-5 To start up the Exactive ... 4-6 To set up your Exactive for operation... 4-7 To prepare the positive ion mode calibration solution...A-4 To prepare the negative ion mode calibration solution ...A-6 To connect liquid lines to the API probe... B-2 To fill the syringe, connect it to the LC union, and insert it into the syringe pump ... B-7 To connect an infusion line between the LC union and the grounding union ...B-8 To connect the syringe to the LC union Tee ... B-10 To connect the union Tee to the switching valve ... B-10 To connect the LC pump to the switching valve ... B-12 To connect the switching valve to a waste container... B-12 To connect the union Tee to the ion source ... B-12 To set up the inlet for loop injections... B-14 To connect the inlet plumbing for an LC/MS system with an autosampler... B-17 To establish power supply and communication between syringe pump and MS detector ... B-19 To establish power supply and communication between switching valve(s) and MS detector ... B-19

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