Shimadzu GCMS-QP2010 Series User manual

Read the instruction manual thoroughly before you use the product.
Keep this instruction manual for future reference.
225-18481
Mar. 2010
Gas Chromatograph Mass
Spectrometer
GCMS-QP2010 Series
Operation Guide
For GCMSsolution Ver. 2.6

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GCMS-QP2010 Series Operation Guide i
Microsoft and Windows are registered trademarks of Microsoft Corporation in the United States and other countries. Other product and company names mentioned herein are
trademarks or registered trademarks of their respective companies.
"Microsoft®Windows®" is abbreviated to "Windows".
© 2010 Shimadzu Corporation. All rights reserved.
<< Notices >>
zAll rights are reserved, including those to reproduce this document or parts there of in any form without permission in writing
from Shimadzu Corporation.
zInformation in this document is subject to change without notice and does not represent a commitment on the part of the
vendor.
zAny errors or omissions which may have occurred in this document despite the utmost care taken in its production will be
corrected as soon as possible, but not necessarily immediately upon detection. We appreciate notification of any errors or
omissions.
zShimadzu Corporation is not responsible for errors or injuries resulting from following the instructions in this document.
zShimadzu Corporation is not responsible for errors or injuries resulting from the use of equipment by the customer.
zReplacement parts for this product will be available for a period of seven (7) years after discontinuation of the product.
Thereafter, such parts may cease to be available. Note, however, that the availability of parts not manufactured by
Shimadzu Corporation is determined by the manufacturer of those parts.
zThe contents of PC hard drives may be lost due to unforeseen circumstances. In order to protect important data, be sure to
make backup copies on a regular basis.
In order to ensure the safe use of this product, observe the following points.
Follow the procedures described in the instruction manual.
Observe precautionary information.
Do not disassemble or modify this product without permission.
If repairs are required, contact your Shimadzu representative.

ii GCMS-QP2010 Series Operation Guide
Thank you for purchasing the GCMS-QP2010-series gas chromatograph mass spectrometer. This document is
intended to explain basic operations to first-time users. Refer to the instruction manual or the appendix of this
document for more details, including information related to maintenance and inspection.
This document assumes that the user has a working knowledge of Windows. There are references to functions and
terminology specific to Windows; refer to a Windows user manual as necessary. Users who have never worked with
Windows should read a Windows user manual before using this document.
Introduction

GCMS-QP2010 Series Operation Guide iii
Shimadzu Corporation provides the following warranty for this product.
Details
* If a warranty certificate or a similar form of document is provided with the product, or if a contract specifying warranty terms has been
signed, then the regulations specified in such a document take precedence.
The warranty period for products with special specifications or for system products is specified separately.
Product Warranty
1. Period: Please contact your Shimadzu representative for information concerning the extent of
your product's warranty.
2. Terms: If a fault attributable to Shimadzu Corporation occurs within the warranty period, we will
perform the necessary repairs or part replacement free of charge. Note, however, that it
may not be possible to replace products that have short life cycles, such as PCs and their
peripheral devices and parts, with the same models.
3. Limitation of Liability 1) In no event will Shimadzu be liable for any lost revenue, profit or data, or for special,
indirect, consequential, incidental or punitive damages, however caused regardless of the
theory of liability, arising out of or related to the use of or inability to use the product, even if
Shimadzu has been advised of the possibility of such damage.
2) In no event will Shimadzu's liability to you, whether in contract, tort (including negligence),
or otherwise, exceed the amount you paid for the product.
4. Items Not Covered: The following items are not covered by this warranty, even if they occur during the
warranty period.
1) Faults resulting from incorrect use
2) Faults resulting from repairs or modifications implemented by parties other than Shimadzu
Corporation or companies designated by Shimadzu Corporation
3) Faults occurring after use in combination with hardware or software other than that
designated by Shimadzu Corporation
4) Faults in equipment and damage to data and software, including the OS, resulting from
computer viruses
5) Faults in equipment and damage to data and software, including the OS, resulting from
power failures, including power interruptions and momentary voltage drops
6) Faults in equipment and damage to data and software, including the OS, resulting from
turning OFF the power switch on the equipment without following the proper shutdown
procedures
7) Faults not originating in the equipment itself
8) Faults occurring after use in severe environmental conditions, such as those subject to high
temperatures, high humidity levels, corrosive gases, or vibrations
9) Faults resulting from fires, earthquakes and other natural disasters, contamination by
radioactive or toxic substances, wars, riots, criminal activities, and other types of force
majeure
10) Faults occurring after the product is moved or transported following initial installation
11) Faults occurring in consumable parts or parts dependent on them
Note: Recording media, such as floppy disks and CD-ROMs, are also regarded as
consumable parts.

iv GCMS-QP2010 Series Operation Guide
This operation guide uses the notation described below.
About This Operation Guide
Notation
Notation Meaning
!WARNING Indicates a potentially hazardous situation which, if not avoided, could result in serious injury or
possibly death.
!CAUTION Indicates a potentially hazardous situation which, if not avoided, may result in minor to moderate
injury or equipment damage.
Indicates additional information that is provided to ensure the proper use of this product.
^Reference Indicates the location of related information.
"Items indicated by this notation mean that this (new) feature/function is downward compatible with
version 2.5. The new features are designed to make the software easier to use and/or increase
productivity. However, the user still has the option to either use the same method used in version 2.5
or use the new features by following the steps provided in this manual."
[ ] Indicates items displayed on the screen, such as buttons, menu selections, settings, windows, and
icons. Example: Click [OK].

GCMS-QP2010 Series Operation Guide v
These safety precautions contain important safety-related information. Be sure to read them before using the product
and observe them during use.
Installation Site Precautions
Do not install the product in locations subject to large amounts of corrosive gas or dust. Otherwise, performance may
be adversely affected and the product's service life may be shortened.
Safety Precautions
!WARNING
• Making internal repairs to the product is potentially dangerous. Such repairs must be performed by
specially trained Shimadzu personnel.
• Do not disassemble or modify the product without authorization.
Doing so may compromise safety.
• Read the instruction manual thoroughly before handling or operating the equipment, and be sure to
following the procedures described.
Not handling the equipment as described is potentially dangerous.
!WARNING
• The solvents used with the gas chromatograph mass spectrometer may be flammable or toxic. Install
the product in a well-ventilated room.
Otherwise, solvent vapors may cause poisoning, or ignite and cause a fire.
• Do not use this product in an environment containing combustible gases.
Doing so may cause a fire.
• Do not place flammable materials near the column oven exhaust at the back of the gas
chromatograph.
Doing so may cause a fire.
• Install the product on a surface that is level, stable, and strong enough to support the product's
weight.
Otherwise, the product may tip over or fall off the surface.

vi GCMS-QP2010 Series Operation Guide
High-Pressure Gas Precautions
Operation Precautions
!WARNING
• High-pressure gas cylinders are used to supply the carrier gas. Follow the instructions received from
the cylinder suppliers and handle the cylinders carefully.
Not doing so may cause poisoning or a fire.
• Keep the cylinders in a well-ventilated outdoor location that is not directly exposed to sunlight, and use pipes
to convey the gas indoors. For liquefied gases, this is required by law.
• Ensure that the temperature of gas cylinders never exceeds 40 ºC and that there are no naked flames within
2 m of the cylinders.
• Ensure that the installation site is well ventilated and, as part of the daily inspection procedure, check for gas
leaks using soapy water. Do not smoke or use open flames within 5 m of equipment using highly combustible
gases, such as acetylene, hydrogen, and propane, or potentially combustible gases, such as oxygen and
nitrous oxide. Keep a suitable fire extinguisher nearby at all times.
• Secure the cylinders with ropes or by some other method to prevent them from falling over.
• Be sure to use oil-free pressure reducing valves. Also, do not use pipes in which oil is present on the inner
surfaces that make contact with the gas.
• After using the gas, close the main valve immediately.
• Check that the pressure gauges are functional at least once every three months.
• Warning signs (adhesive aluminum plates) that indicate hydrogen gas use are provided free of charge.
Contact your Shimadzu representative in cases of particular necessity.
Legal authorization is required to use cylinders with a capacity of 300 m3or greater.
Refer to high-pressure gas control laws, liquid petroleum gas safety regulations, general high-pressure gas
safety regulations, and fire safety laws for more information.
!WARNING
• Wear safety glasses when handling solvents or when injecting samples into the gas chromatograph.
If solvent gets into the eyes, it may cause blindness. If solvent does get into the eyes, immediately flush with
large amounts of water and seek medical attention.
• Do not place solvents near PCs, printers, or other types of office equipment.
Doing so may cause a fire or equipment failure.
• Do not use flammable sprays (e.g., hair sprays and insecticide sprays) near the product.
They may ignite and cause a fire.

GCMS-QP2010 Series Operation Guide vii
Take the measures described below in the event of an emergency, such as a malfunction of the gas chromatograph
mass spectrometer.
Before resuming operation, take appropriate precautions and, if necessary, contact your Shimadzu representative.
Handling Emergencies
Emergency Shutdown Procedure
1 Turn OFF the gas chromatograph mass spectrometer.
2 Turn OFF all accessories.
3 Close the main valves for the pipes supplying carrier gas, hydrogen, and air.
4 Disconnect the power supply.
If the power cable is attached to a switchboard, turn OFF the switchboard.
If the power cable is plugged into an outlet, unplug the cable.

viii GCMS-QP2010 Series Operation Guide
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GCMS-QP2010 Series Operation Guide ix
Contents
1 Overall Configuration of GCMSsolution
1.1 Programs .............................................................................................................1
1.2 Flowchart of Operating Procedure.......................................................................2
2 Starting GC/MS
2.1 Turning ON the Power .........................................................................................3
2.2 Layout of Operating Areas...................................................................................4
2.3 Inspecting Consumable Items and Maintenance Parts .......................................5
2.4 System Configuration ..........................................................................................6
2.4.1 Setting the Modules Used for Analysis............................................................... 6
2.4.2 Checking Column Information ............................................................................ 7
2.4.3 Enabling the Modules Used for Analysis............................................................ 9
2.5 Vacuum System Startup ....................................................................................10
2.6 Checking for Vacuum Leakage..........................................................................11
2.7 Autotuning..........................................................................................................13
2.7.1 Setting Analysis Conditions.............................................................................. 13
2.7.2 Executing Autotuning ....................................................................................... 14
2.7.3 Checking Autotuning Results ........................................................................... 17
3 Creating a Folder
3.1 Creating a Folder with Data Explorer.................................................................18
4 Qualitative Analysis
4.1 Creating a Method File ......................................................................................20
4.1.1 Setting Autosampler Parameters ..................................................................... 21
4.1.2 Setting GC Parameters .................................................................................... 21
4.1.3 Setting MS Parameters .................................................................................... 22
4.1.4 Setting Similarity Search Parameters............................................................... 23
4.1.5 Saving the Method File .................................................................................... 25

Contents
x GCMS-QP2010 Series Operation Guide
4.2 Repeating Autotuning........................................................................................ 25
4.3 Sequential Analysis ........................................................................................... 26
4.3.1 Creating a Batch File........................................................................................ 26
4.3.2 Editing a Batch File ^ Ver. 2.5 ................................................................... 29
4.3.3 Saving Batch Files ........................................................................................... 32
4.3.4 Executing Sequential Analysis ......................................................................... 33
4.4 Analyzing Data .................................................................................................. 34
4.4.1 Loading Data Files ........................................................................................... 34
4.4.2 Zoom in on a Peak in the Chromatogram and Displaying Mass Spectra......... 35
4.4.3 Removing the Background............................................................................... 37
4.4.4 Searching for Similarity ^ Ver. 2.5.............................................................. 38
4.4.5 Displaying Mass Chromatograms .................................................................... 39
4.4.6 Registering Spectra Displayed for Target Compounds
^ Ver. 2.5 .................................................................................................. 40
4.4.7 Editing the Spectrum Process Table................................................................ 40
4.4.8 Saving Data Files ............................................................................................. 42
4.5 Printing Qualitative Analysis Reports ................................................................ 43
4.5.1 Loading Report Formats .................................................................................. 43
4.5.2 Editing Report Formats .................................................................................... 44
4.5.3 Outputting Reports ........................................................................................... 47
5 Quantitative Analysis
5.1 Creating a Method File ...................................................................................... 48
5.1.1 Creating a Compound Table ............................................................................ 48
5.1.2 Creating a SIM Table ....................................................................................... 53
5.2 Sequential Analysis ........................................................................................... 55
5.2.1 Creating a Batch File........................................................................................ 55
5.2.2 Editing a Batch File ^ Ver. 2.5.................................................................... 58
5.2.3 Saving Batch Files ........................................................................................... 58
5.2.4 Executing Sequential Analysis ......................................................................... 59
5.3 Analyzing Data .................................................................................................. 60
5.3.1 Checking and Correcting Calibration Curves ................................................... 60
5.3.2 Re-quantifying after Correcting a Calibration Curve ........................................ 67
5.3.3 Checking and Correcting Quantitation Results ................................................ 69
5.4 Printing Quantitative Analysis Reports .............................................................. 73
5.4.1 Creating and Outputting Quantitative Analysis Reports ................................... 73

GCMS-QP2010 Series Operation Guide xi
Contents
6 Shutting Down GC/MS
6.1 Vacuum System Shutdown................................................................................76
6.2 Turning OFF the Power .....................................................................................77
Appendix A File Format
Appendix B Viewing Help
B.1 Viewing Help .....................................................................................................79
B.1.1 Displaying Help from the Assistant Bar ........................................................... 79
B.1.2 Displaying Help from the Menu Bar ................................................................. 79
B.1.3 Displaying Help with the F1 Key ...................................................................... 80
Appendix C Using Data Explorer
Appendix D Maintenance
D.1 Maintenance .....................................................................................................83
D.2 Easy sTop
(Applicable to QP2010 Ultra and QP2010 SE models) ....................................85
D.3 Reset Procedure for Usage Frequencies and Usage Times ^ Ver.2.5 .......87
D.4 Changing Replacement Guidelines for septa and Glass Inserts ......................89
Appendix E Single Analysis (Manual Injection)
Appendix F Index Searches
Appendix G Displaying Chromatograms
G.1 Displaying Chromatograms from Fragment Tables ..........................................96
G.2 Displaying Chromatograms from Mass Spectra ...............................................98

Contents
xii GCMS-QP2010 Series Operation Guide
Appendix H Editing and Adding Batch Files During Sequential
Analysis
H.1 Editing Batch Files ............................................................................................ 99
H.2 Adding Batch Files (Batch Queue) ................................................................. 101
H.2.1 Creating Batch Files to Add .......................................................................... 101
H.2.2 Adding Batch Files ........................................................................................ 102
Appendix I Reducing the Carrier Gas Flow Rate After Sequential
Analysis and Using the Ecology Mode
I.1 Reducing the Carrier Gas Flow Rate After Sequential Analysis ..................... 105
I.1.1 Creating a Method File That Reduces the Carrier Gas Flow Rate ................ 105
I.1.2 Creating Batch Files ...................................................................................... 106
I.2 Ecology Mode
(This feature applies to QP2010 Ultra and QP2010 SE models.) .................. 109
I.2.1 Setting the Mode Manually ............................................................................ 109
I.2.2 Setting the Mode Using Batch Processing .................................................... 110
Appendix J Printing Reports
J.1 Printing Images
(Printing Spectra and Chromatograms Displayed in Windows) ...................... 112
J.2 Creating Reports ............................................................................................ 114
J.2.1 Using Templates ........................................................................................... 114
J.2.2 Using Previously Created Report Files ......................................................... 115
J.2.3 Manually Setting Report Content .................................................................. 116

GCMS-QP2010 Series Operation Guide 1
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1 Overall Configuration of
GCMSsolution
1.1 Programs
GCMSsolution is made up of the programs described below.
Select the program that is appropriate for the purpose (e.g., analysis or data processing).
^ Ver. 2.5
This manual describes operating instructions primarily for new features added in GCMSsolution Version 2.6.
However, items indicated with "
^ Ver. 2.5" can also be performed using previous methods. Use
whichever procedure is easier.
Icons and windows for functions that can only be used on QP2010 Ultra or QP2010 SE model will not be
displayed on the software if the GCMS model used is QP2010, QP2010 Plus or QP2010S.
Icon Name Description
GCMS Real
Time Analysis
Used to start up and shut down the instrument, make configuration
settings, and perform analysis.
GCMS Analysis
Editor
Used to create and edit method files and batch files during analysis.
GCMS Postrun
Analysis
Used to perform qualitative and quantitative processing, print reports, and
perform other tasks involving data processing.
GCMS Browser Used to perform qualitative and quantitative processing, print reports, and
perform other data processing tasks for multiple data files.

1 Overall Configuration of GCMSsolution
2GCMS-QP2010 Series Operation Guide
1.2 Flowchart of Operating Procedure
Start up GC/MS system
• Switch the power ON
• Specify maintenance and configuration settings, etc.
• Start up vacuum system
• Check for vacuum leaks
^ P. 1 3Execute autotuning
Qualitative Analysis Quantitative Analysis
1Create method file
• Specify instrument parameters
Specify Scan mode
• Specify similarity search
parameters
2 Acquire data
3 Analyze data
• Display mass spectrum
• Perform similarity search
• Register displayed spectrum
4 Print report
• Edit report
• Output report
1 Perform qualitative analysis
(standard sample)
Use standard samples to confirm retention
times for target compounds
2 Create method file
<Quantitative analysis using Scan mode>
• Create compound table
<Quantitative analysis using SIM mode>
• Create compound table
• Create SIM table
3 Acquire data
5 Print report
• Edit report
• Output report
4 Analyze data
• Check and correct
calibration curve
• Calculate quantitative
values for samples with
unknown concentrations
Shut down the instrument
• Shut down the vacuum system
• Switch the power OFF
^ P. 3
^ P. 2 0
^ P. 2 6
^ P. 3 4
^ P. 4 3
^ P. 2 0
^ P. 4 8
^ P. 5 5
^ P. 7 3
^ P. 6 0
^ P. 7 6

GCMS-QP2010 Series Operation Guide 3
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2 Starting GC/MS
2.1 Turning ON the Power
Switch ON any peripheral or accessory equipment connected to the system, before switching ON the
main GC/MS system.
1Turn ON the power to the GC.
2Turn ON the power to the MS.
3Turn ON the power to the PC, printer, and display.
GCMS
GC power switch
Front Side
MS power switch
Back Side

2 Starting GC/MS
4GCMS-QP2010 Series Operation Guide
4Double-click the (GCMS Real Time Analysis) icon.
The [GCMS Real Time Analysis] program starts.
5Click [OK].
2.2 Layout of Operating Areas
No. Name GCMS Program Explanation
1Title Bar Real Time Analysis,
Analysis Editor, Postrun
Analysis, and Browser
Displays the name of the program, process, and file
currently running or being processed.
2Menu Bar Real Time Analysis,
Analysis Editor, Postrun
Analysis, and Browser
Displays command menus corresponding to the window
currently open.
3Toolbar Real Time Analysis,
Analysis Editor, Postrun
Analysis, and Browser
Displays command tool buttons corresponding to the
window currently open.
1
4
2 3
65
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Title Bar
Menu Bar Toolbar
Assistant Bar
Data Explorer Instrument
Monitor 4
6
Assistant Bar
Data Explorer
Title Bar
Menu Bar Toolbar
GCMS Real Time Analysis GCMS Postrun Analysis

GCMS-QP2010 Series Operation Guide 5
2.3 Inspecting Consumable Items and Maintenance Parts
2
The assistant bar, instrument monitor, and Data Explorer can be shown or hidden by selecting [Show/Hide]
on the [View] menu.
2.3 Inspecting Consumable Items and Maintenance
Parts
Check the state of the GC/MS consumable items using the procedure described below.
1Move the mouse pointer over the icon for a consumable item in the instrument monitor
to display the current state and the recommended replacement point for the
corresponding item.
When a consumable item approaches its recommended maximum usage frequency, the background of
the corresponding icon turns black to alert the user.
This note is shown when mouse pointer is moved over the septum icon. This means that the septum has
been used 13 times out of a maximum 100 times.
When replacing the analysis column, or when a consumable item has passed its recommended
replacement point, perform maintenance with reference to "Appendix D Maintenance" P.83.
Depending on the analysis content, the appropriate replacement frequency may be greater than the
recommended frequency.
4Assistant Bar Real Time Analysis,
Analysis Editor, Postrun
Analysis, and Browser
Command icons are arranged in order of typical operation
sequence. The assistant bar is named according to the
window that is currently open. For example, when the
[Batch] window is open, the assistant bar is named the
[Batch] assistant bar.
5Instrument Monitor Real Time Analysis Displays analytical instrument parameter values in real
time.
6Data Explorer Real Time Analysis,
Analysis Editor, Postrun
Analysis, and Browser
Used to easily load analytical data or method files. It lists
files in the selected folder, according to file type.
No. Name GCMS Program Explanation

2 Starting GC/MS
6GCMS-QP2010 Series Operation Guide
2.4 System Configuration
Check and set the modules used for analysis using the procedures described below.
2.4.1 Setting the Modules Used for Analysis
1Click the [System Configuration] icon on the [Real Time] assistant bar.
The [System Configuration] window opens.
2Check that the components shown in the [Modules Used for Analysis] area correspond
to the actual modules in the GC/MS system that are to be used for the analysis.
If the modules to be used for current analysis do not correspond to the modules shown in
this window, set as shown in the following example:
1Select [AOC-20i+s] in the [Available Modules] area if for example, AOC-20i with AOC-20s are to be
used for analysis.
2Click to register the module in [Modules Used for Analysis].
1 2