GCMSOperationGuide (Ver4 4) MethodDevelopment PDF

225-28480
Sep. 2015
Gas Chromatograph Mass Spectrometer
GCMS-QP Series
GCMS-TQ Series
(Compatible with GCMSsolution Ver. 4.4 or later)
Operation Guide
Method Development
Read the instruction manual thoroughly before you use the product.
Keep this instruction manual for future reference.
This page is intentionally left blank.
Introduction
Read this Instruction Manual thoroughly before using the product.
Thank you for purchasing the GCMS-QP series and GCMS-TQ series gas chromatograph mass spectrometer.
This manual is intended to explain basic operations to first-time users. Read this manual thoroughly before using the
product and operate the product in accordance with the instructions in this manual.
Also, keep this manual for future reference.
This manual assumes that the reader is knowledgeable of basic operations of Windows. For the operation of
Windows, refer to the instruction manual that comes with that product.
Important
• If the user or installation location changes, ensure that this Instruction Manual is transferred with the product.
• If this manual is lost or damaged, immediately contact your Shimadzu representative to request a replacement.
• To ensure safe operation, read all Safety Instructions before using the product.
• To ensure safe operation, contact your Shimadzu representative if product installation, adjustment, or reinstallation
(after the product is moved) is required.
© 2015 Shimadzu Corporation. All rights reserved.
Original version is approved in English.
Method Development Guide i

Introduction
• All rights are reserved, including those to reproduce this manual or parts thereof in any form without written
permission from Shimadzu Corporation.
• Information in this manual is subject to change without notice and does not represent a commitment on the part of
the vendor.
• Any errors or omissions which may have occurred in this manual despite the utmost care taken in its production will
be corrected as soon as possible, although not necessarily immediately after detection.
• Shimadzu Corporation is not responsible for errors or injuries resulting from following the instructions in this
document.
• Shimadzu Corporation is not responsible for errors or injuries resulting from the use of equipment by the customer.
• The 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.
• Microsoft, Windows and Excel are registered trademarks of Microsoft Corporation in the United States and/or other
countries.
Other company names and product names mentioned in this manual are trademarks or registered trademarks of
their respective companies.
The TM and R symbols are omitted in this manual.
• Replacement parts for this product will be available for a period of seven (7) years after the product is discontinued.
ii Method Development Guide

Product Warranty
Shimadzu Corporation provides the following warranty for this product.

Details
1. Period: Please contact your Shimadzu representative for information about the period of this
warranty.
2. Description: If a product/part failure occurs for reasons attributable to Shimadzu during the warranty
period, Shimadzu will repair or replace the product/part free of charge. However, in the
case of products which are usually available on the market only for a short time, such as
personal computers and their peripherals/parts, Shimadzu may not be able to provide
identical replacement products.
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. Exceptions: Failures caused by the following are excluded from the warranty, even if they occur during
the warranty period.
1) Improper product handling
2) Repairs or modifications performed by parties other than Shimadzu or Shimadzu
designated companies
3) Product use in combination with hardware or software other than that designated by
Shimadzu
4) Computer viruses leading to device failures and damage to data and software, including the
product’s basic software
5) Power failures, including power outages and sudden voltage drops, leading to device
failures and damage to data and software, including the product’s basic software
6) Turning OFF the product without following the proper shutdown procedure leading to device
failures and damage to data and software, including the product’s basic software
7) Reasons unrelated to the product itself
8) Product use in harsh environments, such as those subject to high temperature or humidity
levels, corrosive gasses, or strong vibrations
9) Fires, earthquakes or any other act of nature, contamination by radioactive or hazardous
substances, or any other force majeure event, including wars, riots, and crimes
10) Product movement or transportation after installation
11) Consumable items
Note:Recording media, such as floppy disks and CD-ROMs are considered consumable
items.
* If there is a document such as a warranty provided with the product, or there is a separate contact agreed upon that includes warranty
conditions, the provisions of those documents shall apply.
The warranty period for products with special specifications or for system products is specified separately.
Method Development Guide iii

About This Operation Guide
Notation
This operation guide uses the notation described below.
Notation Meaning
! 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.

Indicates information provided to improve product performance.
[ ] Indicates items displayed on the screen, such as buttons, menu selections, settings, windows, and
icons. Example: Click [OK].
iv Method Development Guide

Safety Precautions
To ensure safe product operation, read these important safety instructions carefully before use and follow all
DANGER, WARNING and CAUTION instructions given in this section.
! WARNING
• For repairs, contact Shimadzu or your Shimadzu representative.
Not doing so could cause a fire, electrical shock, or injury.
• Do not modify or disassemble the instrument without the express approval of an authorized
Shimadzu representative.
Doing so could cause an accident from electric shock or a short circuit. It could also cause injury or
instrument failure.
• 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.
 Installation Site Precautions
! 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 install this instrument in a location with flammable or explosive gases or liquids.
Because this product is not designed to be explosion proof, doing so could cause a fire or explosion.
• Do not place flammable materials near the column oven exhaust at the back of the instrument, as
they could ignite and cause a fire.
• The lab table or other surface on which this instrument is installed should be level, stable, and
sufficiently strong to support the instrument's weight.
Otherwise, the unit could tip over or fall off the surface.
Do not install the instrument in a location with corrosive gases, gases containing organic solvents, halogen compounds,
or siloxanes, oil mist, or high levels of debris/dust. The instrument performance could be affected and its service life
hortened.
Do not operate the instrument in an environment where condensation may form. Doing so could cause it to malfunction.
Method Development Guide v

 High-Pressure Gas Precautions
! WARNING
• A high-pressure gas cylinder will be used to supply the carrier gas. When handling the gas cylinders,
observe the following suggestions.
• Keep gas cylinders in a well-ventilated area outside of the instrument installation site. Avoid exposure to
direct sunlight. Use lines to transport the gas from the cylinders to the instrument. For flammable gases, this
precaution is required by law.
• Do not place the high-pressure gas cylinder in a location where the temperature can exceed 40 °C.
• Choose an instrument installation site with sufficient ventilation, and include checking for gas leaks using an
electronic gas leak detector in your daily inspection procedure. Do not smoke or use open flames within 5 m
of the instrument when using highly combustible gases, such as acetylene and hydrogen, or potentially
combustible gases, such as oxygen and nitrous oxide. Install and maintain effective fire extinguishers.
• Secure the high-pressure gas cylinder with a cylinder stand or chain, etc., so that it does not fall over.
• Be sure to use a pressure release valve specified as "not to be used with oil." Also, do not use a pressure
release valve having piping, that is in contact with gas, whose inner surface is oily.
• When finished using the gas, immediately close the main cylinder valve.
• Verify that the pressure gauges are functional at least once every three months.
• Warning signs (adhesive aluminum plates) are available to indicate hydrogen gas use. Ask your Shimadzu
representative for more details. Signs are supplied free of charge to sites in which they are mandatory.
• Legal authorization is required to use cylinders with a capacity of 300 m3 or greater.
 Operation Precautions
! WARNING
• Always wear safety glasses or goggles when handling solvents. If solvent gets into the eyes,
blindness could result. Should solvent get into the eyes, immediately flush with large amounts of
water and seek medical attention.
• Do not place solvents near PCs, printers or other instruments, as fire or instrument damage could
result.
• Do not use flammable sprays (hair sprays, insecticide sprays, etc.) near this instrument, as they could
ignite and cause a fire.
vi Method Development Guide

Handling Emergencies
The following measures should be taken in the event of an emergency such as a malfunction of the gas
chromatograph mass spectrometer.
Take adequate precautions and contact your Shimadzu representative as necessary before resuming use of the
instrument.
 Emergency Shutdown Procedure

1 Turn OFF the gas chromatograph mass spectrometer.
2 Turn OFF all accessories.
3 Close the valves for the pipes supplying carrier gas, CID 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.
Method Development Guide vii

This page is intentionally left blank.
viii Method Development Guide

Contents
1 Overview 1
1.1 Measurement Modes ...........................................................................................1
1.1.1 Measurement Modes for the GCMS-QP Series ................................................. 1
1.1.2 Measurement Modes for the GCMS-TQ Series ................................................. 2
1.2 Overview of Smart Database...............................................................................3

1.2.1 Smart Database Storage Location ..................................................................... 3
1.2.2 Operating Environment ...................................................................................... 3
1.2.3 Compatible Equipment ....................................................................................... 3
1.2.4 Configuration ...................................................................................................... 4
1.2.5 Method Creation Functions(Smart MRM and Smart SIM).................................. 5
1.2.6 Automatic Retention Time Correction Function (AART)..................................... 6
2 Creating Method Files 7

2.1 Steps for Creating Method Files with Smart Database........................................7
2.2 Preparing for Analysis..........................................................................................7
2.3 Measuring and Identifying n-Alkanes...................................................................8

2.3.1 Measure the mixed n-alkane standard sample. ................................................. 8
2.3.2 Identify the n-alkanes. ........................................................................................ 8
2.4 Creating a Compound Table and MS Table ......................................................10

2.4.1 Open Smart Database. .................................................................................... 10
2.4.2 Set the parameters........................................................................................... 12
2.4.3 Select the target compounds. .......................................................................... 13
2.4.4 Set the measurement mode. ............................................................................ 15
2.4.5 Select the ions.................................................................................................. 16
2.4.6 Create the MS table. ........................................................................................ 17
2.5 Correcting Method Files.....................................................................................20

2.5.1 Investigate the measurement conditions.......................................................... 20
2.5.2 Set quantitative parameters. ............................................................................ 22
2.5.3 Correct identification parameters. .................................................................... 25
3 Registering Compound Information in Smart Database 28

3.1 Steps for Registering Additional Compound Information in Various Types of Smart Database Files ......28
3.2 Preparing for Analysis........................................................................................28
Method Development Guide

Contents
3.3 Creating a Quantitative Method File for Scan Mode.......................................... 29

3.3.1 Acquire data for the target compounds in Scan mode. .................................... 29
3.3.2 Create the compound table.............................................................................. 29
3.3.3 Register the retention indices in the compound table. ..................................... 29
3.3.4 Create a quantitative method file. ................................................................... 33
3.4 Registering Compound Information................................................................... 34
3.5 Optimizing Transitions and Collision Energies (CEs) ................................. 37

3.5.1 Create a method file for product ion scan mode. ............................................. 37
3.5.2 Acquire data in product ion scan mode............................................................ 39
3.5.3 Determine the transitions and their optimal CE values. ................................... 42
3.6 Registering Additional Information for MRM Mode ..................................... 48
Appendix A Creating Method Files for Other Measurement Modes 51

A.1 Creating Method Files for Scan Mode .............................................................. 51
A.2 Creating Method Files Combining Multiple Measurement Modes .................... 53
A.2.1 Creating Method Files for Simultaneous Scan/MRM Measurement ....... 53
A.2.2 Creating Method Files for Simultaneous Scan/SIM Measurement ................. 56
A.2.3 Creating Method Files for Mixed SIM/MRM Measurement ..................... 59
Appendix B Correcting Retention Times Directly Without Using AART 62
Appendix C Correcting the Retention Times for Method Files Using AART 64
C.1 Measuring the Mixed n-Alkane Standard sample ............................................. 64

C.2 Identifying the n-Alkanes .................................................................................. 64
C.3 Correcting the Retention Times for Method Files Using AART ........................ 64
x Method Development Guide

Operation flow to create method file of MRM mode
Perform operations described in chapter "2 Creating Method Files" P.7 and after if you have a Smart DB file
(including Shimadzu database: Smart Pesticides Database) already created.
1 Measure the standard sample by scan mode
2 Create compound table

(Selection of Precursor Ion, etc. )
"3 Registering Compound Information
in Smart Database" ^P.28
3 Measure the standard sample by product ion scan mode
Smart Database
4 Find optimal transitions and collision energy

(Set reference ion ratio, etc.)
"2 Creating Method Files"

5 Create method file of MRM mode ^P.7
Method Creation Function

(Smart MRM)
Method file of MRM mode
Method Development Guide xi

Operation flow to create method file of SIM mode
1 Measure the standard sample by scan mode
2 Create compound table

(Selection of ion, etc. ) "3 Registering Compound Information
in Smart Database"
^P.28 to P.36
3 Create method file of MRM mode
Smart Database
Method file of SIM mode
"2 Creating Method Files"

^P.7
Method Creation Function

(Smart SIM)
xii Method Development Guide

1 1 Overview
Smart Database is a file in Microsoft Excel format.

It contains compound information (including compound names, retention times, ions (m/z), ion ratio
information, and standard spectra), so you can create method files for various measurement modes.
1
In addition, compound information can be added from existing method files or using an MRM conditions
optimization tool (MRM_Optimization_Tool.xlsm).
This manual describes the procedures for creating method files using Smart DB and for registering
1
compound information in Smart DB.
1
1.1 Measurement Modes
1
This section describes the measurement modes noted in this operation guide.
1.1.1 Measurement Modes for the GCMS-QP Series

1
1
Scan: All ions (m/z) in a configured mass range are measured at given time intervals.
It is used mainly for qualitative analysis.
SIM: Only specific ions (m/z) are selectively measured. Enabling high-sensitivity quantitative
analysis, and the sensitivity is 10 to 50 times better than in Scan mode.
1
1
1
1
1
1
1
1
1
1
Method Development Guide 1
1 Overview
1.1.2 Measurement Modes for the GCMS-TQ Series

In the GCMS-TQ series, the mass separator includes two types of quadrupole mass filters (Q1 and Q3)
and a collision cell (Q2).
Q1 and the collision cell transmit the ions (transmission mode), and Scan or SIM mode can be selected via
Q3 in the same manner as with the GCMS-QP series.
Analysis Mode Q1 Collision Cell Q3

Q3 Scan Transmission mode Scan
Q3 SIM Transmission mode SIM
In addition, product ions are generated by selecting specific ions (precursor ions) with Q1, and then
subjecting the precursor ions to CID (Collision-Induced Dissociation) with argon gas inside the collision
cell. The following four types of measurement modes can be selected by combining the Q1 and Q3 modes.
Analysis Mode Q1 Collision Cell Q3

Precursor Ion Scan Scan SIM
Product Ion Scan SIM Scan
CID
Neutral Loss Scan Scan Scan
MRM SIM SIM
MRM (Multiple Reaction Monitoring):

A specific m/z value is fixed for both Q1 and Q3, and the transitions (product ions generated
from specific precursor ions) are measured. This mode is less affected by impurities than SIM
mode, enabling quantitative analysis with high selectivity. Accordingly, it is effective for the
quantitation of trace components in high-matrix samples.
Product Ion Scan:

In this mode, Q1 is fixed to a specific m/z value, and the product ions produced by CID are all
measured with Q3.
Since spectra for the product ions are obtained, it is used to search for the optimal MRM
measurement conditions (transitions and their collision energies).
2 Method Development Guide

1.2 Overview of Smart Database

1.2.1 Smart Database Storage Location
Under default conditions, Smart Database is installed in the following folder when GCMSsolution is
installed.
1
Folder C:\GCMSsolution\SmartDatabase
Smart Database file of default SmartDatabase_Blank.xlsm
condition
n-alkane acquisition method AART_SmartDatabase_default.qgm
file
Under default conditions, no compound information is registered in Smart Database

("SmartDatabase_Blank.xlsm").
1.2.2 Operating Environment

Use Smart Database in the following environment.
OS Microsoft Windows 7 Professional

Excel Microsoft Excel 2010 (32-bit version), Excel 2013 (32-bit version)
Workstation software GCMSsolution Ver. 4.20 or later
1.2.3 Compatible Equipment

Method files created with Smart Database can be used with the following equipment.
GCMS-TQ Series: GCMS-TQ8030 and GCMS-TQ8040
GCMS-QP Series: GCMS-QP2010 Ultra, GCMS-QP2010 SE and GCMS-QP2020
Method files created with Smart Database are not compatible with the GCMS-QP2010, GCMS-QP2010
Plus, or GCMS-QP2010S, so they cannot be used
Compatible models are indicated by the following labels in the titles for chapters and sections.
: Indicates procedures that can be used with the GCMS-TQ series only.

1 Overview
1.2.4 Configuration
Smart Database consists of the following three sheets.
• [Database] Sheet
This sheet contains compound information, including compound names, retention indices, CAS numbers,
MRM transitions, Scan and SIM measurement ions, and standard spectra.
In addition, method files can be created for measuring taeget compounds.
• [MSTableView] Sheet
The measurement range for compounds in method files created with the [Database] sheet can be checked
on a chart.
• [n-alkaneIndexTable] Sheet
When method files have been created with the [Database] sheet, the information for the n-alkanes used (for
retention time correction) can be checked.

1.2.5 Method Creation Functions(Smart MRM and Smart SIM)

Smart DB includes a function to flexibly create method
files based on the required processing time and the loop
time.
Using these functions makes it easy to create method files
for measuring multiple components with high sensitivity in
MRM or SIM mode. 1
Required Processing Time:Time range for acquiring data
mainly on each compound
Loop Time: Data acquisition interval
Illustration of the MS Table created by Smart MRM or Smart SIM function.

1 Overview
1.2.6 Automatic Retention Time Correction Function (AART)

If a column is cut or replaced with a column of a different lot, the retention time of each component
changes. Therefore, it is necessary to measure the standard sample and then correct MS instrument
parameters and setting time on the compound table.
The automatic adjustment of retention time (AART) function is to correct the retention times at one time
based on the retention indices assigned for compounds. By using AART, the retention times of several
hundred types of compounds can be corrected at one time.
To use the retention index, measurement needs to be performed under the same measurement conditions
using a column with the same specifications of that used to calculate the retention index.
Retention index: Expressed by a virtual carbon number where the retention time is converted into the
carbon number of straight-chain alkanes by utilizing the fact that straight-chain
alkanes elute at equal intervals in order of their carbon numbers. The virtual carbon
number determined this way is known as the methylene unit and one-hundred times a
number is called retention index.
<Mixed n-Alkane Standard sample>

Cat. No. 560295 Custom Retention Time Index Standard (hexane solution), 100 μg/mL, 1 mL
Components: C7 to C33 n-alkanes
Concentration: 200 μg/mL each of C15 and C30 to C33; 100 μg/mL of the other components
Manufacturer: Restek Corporation

2 2 Creating Method Files
This chapter describes the procedures for creating method files with Smart Database.
2
2.1 Steps for Creating Method Files with Smart
Database 2
Follow the steps below to create a method file.
2
1. Measure and identify n-alkanes.
2. Create a compound table and MS table.

2
2
3. Create a method file and modify it. 2
2
2.2 Preparing for Analysis 2
Attach an analysis column appropriate for the Smart Database file to be used. Then configure the
environmental settings and perform autotuning. Also create a folder for saving individual files.
2
For the procedures, refer to the GCMS Operation Guide - Basic Operation Guide.
2
If you have Smart Database provided by Shimadzu, copy the method file from the folder blow and paste it
the created folder.
2
Source Folder
Destination Folder
2
2
2
2
2 Creating Method Files
2.3 Measuring and Identifying n-Alkanes

Measure the mixed n-alkane standard sample in order to correct the retention times registered in Smart
Database. Correct the retention times for the target compounds based on the n-alkane identification
results and retention indice of target compounds (AART function).
Refer to "Appendix B Correcting Retention Times Directly Without Using AART" P.62 if you adjust retention
times directly without using AART function
2.3.1 Measure the mixed n-alkane standard sample.
1 Using the method file for n-alkane analysis, measure 5 μg/mL of the mixed n-alkane
standard sample.
Change the preparation concentration of n-alkane according to measurement conditions. The above
is an example of splitless analysis.
2.3.2 Identify the n-alkanes.
1 Start up the [GCMS Postrun Analysis] program. On the [Postrun] assistant bar, click the
(Create Compound Table) icon.

The [Create Compound Table] mode window is displayed.
2 Load the data file for the 5 μg/mL of n-alkane acquired in "2.3.2 Identify the n-alkanes.".

2.3 Measuring and Identifying n-Alkanes
3 Check and correct the identification results.

If the sample has been misidentified, perform either manual identification or manual peak integration to
identify it correctly.
Depending on the measurement conditions, the number of n-alkanes detected may differ from the
number registered in the compound table.
4 After the analysis, click the (Save) icon on the toolbar.

The identification results are saved in the data file.
Do not close the n-alkane data file, as it is needed for the next step.

2.4 Creating a Compound Table and MS Table

This section describes the procedures for creating compound tables and MS tables for method files using
Smart Database.
2.4.1 Open Smart Database.
1 On the [Compound Table] assistant bar, click the

The [Open Smart Database] window is displayed.
(Smart MRM/SIM) icon.
2 Select the Smart Database file (in Excel format) to be used, and click [Open].
The Smart Database file opens.
If the following message is displayed on the message bar on Excel, Click [Enable Content].

3 Open the [Database] sheet.
4 In the [Instrument Type] area, select the instrument to be used.
5 Click the [Lang.] button, and set the language for compound name notation and the
display. Click [OK].
Compound Name Lang: Select the language for compound name notation. Select from Japanese,
English, and Chinese.
Language: Select the display language for the Smart Database window.
The settings configured here will be stored by Smart Database.

2.4.2 Set the parameters.
1 On the [Ret. Index for AART] drop-down menu, select the retention index for the
analysis column attached to the instrument.
2 Check that the data file opened in section "2.3 Measuring and Identifying n-Alkanes" P.8
is loaded.
3 Click (Load) for [Template Method File] and select the template method file.

The setting values of the file specified by the template method file are used for GC/MS measurement
parameters (e.g. GC measurement parameters, detector voltage) other than ones in the MS table of
the method file to be created as well as analysis parameters (e.g. quantitative parameters,
qualitative parameters).
When using Smart DB Ver. 3.00, a template method file cannot be specified by this procedure.
Conditions specified at [n-alkane data file] are set for GC/MS measurement conditions other than
ones in the MS table. Conditions of the initial file (see the filename below) are set for analysis
parameters when one of [Ret. Index 1] to [Ret. Index 3] is selected at [Ret Index for AART]. When 2
[Not Use AART] is selected at [Ret Index for AART], conditions of the method file specified at
[Template Method File] are set.
GCMS-TQ Series: SmartDB_MethodTQ.qgm in the \System folder of the GCMSsolution
installation folder.
GCMS-QP Series: SmartDB_Method.qgm in the \System folder of the GCMSsolution
installation folder.
The settings configured by clicking [Advanced] in the parameters area are only used for analyses
with the odor analysis system. Normally, these settings do not need to be changed.
2.4.3 Select the target compounds.
1 In the [Type] column, press the Delete key to erase "Target" from the fields for
compounds that will not be measured, leaving these fields blank.
Rows in which the [Type] fields are left blank (for compounds that will not be measured) will not be
included in the resulting compound table. Select [ISTD] when the compound is measured as an internal
standard substance.
When [Type] has been set to [ISTD], set the value for [ISTD Group]. If the value for [ISTD Group] is
not set, an error will be displayed during method creation, and the method will not be created.

In Smart Database files containing the information from the mixed standard sample, the following
setting procedure can be used to measure only the compounds contained in the mixed standard
sample.
2
1
1 Select the checkboxes for the mixed standard samples to be used.

Multiple mixed standard samples can be selected.
2 Click the [Filtering] button.
"Target" will now be configured for only those compounds contained in the mixed standard samples
selected, and the entries will be rearranged automatically.
To reset the rearrangement of compounds, click on the drop-down menu in the [Serial#] cell, and sort
the entries in ascending order.

2.4.4 Set the measurement mode.

Set the measurement mode, such as MRM or SIM mode.
• If you are creating method files for Scan mode, see "Appendix A.1 Creating Method Files for Scan Mode"
P.51.
• If you are specifying MRM mode, SIM mode, and Scan mode separately for measurements of each
compound, see "Appendix A.2 Creating Method Files Combining Multiple Measurement Modes" P.53.
1 In the [Acq. Mode] column, check that the fields for target compounds are set to "MRM."
If you are measuring in Q3SIM or SIM mode, select "SIM" on the drop-down menu in the [Acq.
Mode] cell in the first row. Then use copy & paste to set the [Acq. Mode] fields for the target
compounds to "SIM."

2.4.5 Select the ions.

• For MRM mode, select the transition (target ion) used for quantitation, and the transitions (reference ions)
used for identification.
• For Q3SIM or SIM mode, select target and reference ions.
Under default conditions, ion 1, ion 2, and some others are selected. To change these, make your
selections while checking the masses and ion ratios.
If you set the fields in the [Type] column to "T," it will be used as a target ion. If you set the fields in the
column to "Ref.," it will be used as a reference ion. You can configure one target ion and up to five
reference ions.
1 Check the registered transitions or ions.
2 To change or add ions, make your selection on the drop-down menu in the [Type] cell.
<Compounds Measured in MRM Mode>
<Compounds Measured in SIM Mode>

2.4.6 Create the MS table.

Set the parameters required to create the MS table.
1 Click [Create Method File].

The [MS Table Parameter] window is displayed.
2 Enter the parameters.
• Loop Time (MRM and SIM)

This is the sum total of the event times for all compounds configured to one group. If "0.3 sec" is
entered, for example, data for each compound will be acquired every 0.3 seconds. To ensure good
reproducibility, at least 10 data points must be acquired per peak. However, if the loop time is
shortened, the time required to collect a single transition or ion will be shortened, reducing the
sensitivity.
Recommended values:0.2 - 0.5 sec
• Required Processing Time

This indicates the time range for measurements, centered on the retention time for each
compound. For example, if "0.3 min" is entered, data will be acquired for each compound within a
range of the retention time ±0.3 min (i.e. for 0.6 minutes). Measure the standard sample or
unknown sample using the method file created and check for retention time offset. Check the
retention time offset caused by impurities and peak widths (tailing, etc.) and configure settings if
necessary
Recommended values: 0.2 - 0.5 min

The required processing time specified here is applied to all compounds being measured. To set
different required processing times for individual compounds, set the values in the [Required Proc.
Time for Each Comp.] column for the applicable compounds in the [Database] sheet, as shown
below.
For compounds with this setting left blank, the required processing time set in the [MS Table
Parameter] dialog will be used. Use this only for compounds for which to set a required processing
time that differs from the setting configured in the [MS Table Parameter] dialog.
3 Click [OK].
The [Progress Bar] window is displayed. A method file is automatically created with the MS table and
compound table set based on the parameters configured in step 2).
When the method file has been created, the [Save As] window is displayed.
4 Enter a file name, and then click [Save].

The [MSTableView] sheet is displayed.

5 Here, you can check the time range for MRM and SIM measurements of target
compounds.
1 2
1 You can use the [MSTableView] sheet to check the minimum value for the dwell time for all target
compounds.
Dwell Time: The measurement time for each transition (ion) for each compound targeted for
measurement is called dwell time. The longer the dwell time is, the higher-sensitivity
measurement can be performed at.
2 You can check the dwell time for each transition (ion) for each target compound.
Estimated elution time for peak
Compound name Dwell time Measurement time
6 Name the Smart Database file and save it.

2.5 Correcting Method Files

2.5.1 Investigate the measurement conditions.
Measure the standard sample or unknown sample using the method file created.
Check the sensitivity and separation on the acquired data and correct the method file if necessary.
Improving the Separation: 1. Change to transition ions unaffected by the matrix.

Improving the Sensitivity: 1. Change to high-intensity transition ions.
2. Reduce the number of transition ions.
(Configure a single reference ion, for example.)
3. Raise the detector voltage.
4. Partition the method file.
■ Changing Transition Ions

Change the transition ion by the procedures described in section "2.4.5 Select the ions." P.16 and after.
■ Changing the Detector Voltage
1 Open the [Acquisition] window. Load the method file saved in section "2.4.6 Create the
MS table." P.17.
2 On the [MS] tab, specify the [[Detector Voltage] setting.

SIM mode:
MRM mode:
Relative value from the tuning results:
Absolute value:
0.1 kV to 0.3 kV
1.6 kV to 2.0 kV
3 Save (overwrite) the method file.

■ Partitioning the Method File

The dwell time will become extremely short depending on the number of target compounds (300
compounds or more), or on the selected number of transitions or ions. If insufficient sensitivity is obtained,
the dwell time can be lengthened by partitioning the method file.
1 Open the [Database] sheet in the Smart Database file previously named and saved.
2 On the [Divide Method into] drop-down menu, select "2."
The numbers of the measurement method files will alternate down the rows in the [Method No.]
column.
Check the allotment of the target compounds to the method files.
The method numbers can be changed if necessary.
3 Click the [Create Method File] button.

From this stage, perform operations following the procedures described in section "2.4.6 Create the MS
table." P.17.
Save the method file according to the number of partitioned files.

2.5.2 Set quantitative parameters.

To perform quantitative analysis, configure settings for calibration curve information.
1 Start up the [GCMS Real Time Analysis] program. Display the [Acquisition] window.
2 Load a confirmed method file.
3 On the [Method] menu, click [Quantitative Parameters].
4 Click on the [Identification] tab, and select the [Use Reference Ions] checkbox.
This operation is unnecessary when the [Use Reference Ions] checkbox is already selected.

5 Click on the [Quantitative] tab, and enter the quantitative method and other parameters.
1
3 2
No. Item Explanation

1 Quantitative • External Standard:Quantitation is performed using a calibration curve
Method obtained from the absolute quantity (concentration) and the area or height
value of the target compound in a standard sample.
• Internal Standard:An internal standard is added to the sample, the sample is
analyzed, and quantitation is performed using the relationship between the
relative sensitivity and the quantitative ratio with respect to the internal
standard compound.
2 Calculated by Select [Area] or [Height]. Normally, select [Area].
3 # of Calib. Levels Input the number of concentration levels of the calibration curve.
4 Unit Set the concentration unit used for reports.
5 Format of Set the number of digits used to indicate concentrations.
Concentration

6 Click on the [Compound Table] tab, and correct the compound table if necessary.
1 2
1 When performing quantitation using the internal standard method, change the ISTD setting from
[Type] to [ISTD]. For the [ISTD Group], make settings so that the number of target compounds is the
same as the number of internal standard substances to be used for correction as shown in the figure.
2 Enter the concentration of the standard sample to be used for the calibration curve.
To set the concentration at once, enter the concentration on the first line, select the cell that the
concentration has just been entered, select all the cells to set the concentration for, and then paste
the data. Enter "1" in the all concentration levels for the internal standard component.
7 Click [OK].
8 On the toolbar, click the (Save) icon to save (overwrite) the method file.
9 Measure the standard sample and unknown sample using the method file created.

2.5.3 Correct identification parameters.

When the concentration of the component targeted for measurement is low or there is an influence of
impurities, automatic identification of the component targeted for measurement may not be performed
smoothly. If the following messages are displayed even when the target compound has been detected,
correct the identification parameters so that automatic identification can be performed smoothly.
Message displayed when Message displayed when the

no peak is detected in the reference ion ratio of the detected
identification range component is out of the allowable
2
• Identification range
Set an allowable range for identification using the retention time. The range can be set by [Window] or
[Band]. Usually, select [Band] for programmed temperature analysis.
[Band]: The allowable time range for the peak top is set by the absolute time.
Allowable time range (min.) = ± band (min.) For example, when the standard retention time
is 5.0 min. and the band is 0.5 min., the allowable time range is 5.0 min. ± 0.5 min., which is
4.5 to 5.5 min.
• Allowable range for ion ratio
Set an allowable range for identification from the reference ion ratio. The range can be set by [Absolute
Allowable] or [Relative Allowable]. When [Relative Allowable] is selected, the allowable range is set
according to the ion ratio of each component.
When the reference ion ratio is low When the reference ion ratio is high
Example) Example)
Target Ion :100% Target Ion :100%
Reference Ion :20% Reference Ion :400%
Allowable Range of Ion Ratios :30% Allowable Range of Ion Ratios :30%
[Absolute Allowable] [Absolute Allowable]

20 ± 30% = 0 to 50 % 400 ± 30% = 370 to 430 %
Identification is performed even when the reference ion is Allowable range for ion ratio becomes narrow.
not detected.
[Relative Allowable] [Relative Allowable]

30　 %= 14 to 26 %
20 ± 20 × --------- 30
- 　-% = 280 to 520 %
400 ± 400 × ---------
100 100

1 Start the [GCMS Postrun Analysis] program, and click the

the [Postrun] assistant bar.
(Quantitative) icon on
2 Open measurement data of the standard sample or unknown sample.
3 On the [Quantitative] assistant bar, click the (Peak Integration) icon, change
the values in the black frames below to the desired values, and then click [OK].
4 Check the results. If necessary, perform the operation described in step 3 again and
change the identification parameters.

5 To change the identification parameters for each compound, click [Edit] in the upper
right corner of the compound table and change the allowable range for [Allowance] or
[Band] on each row.
2
If there is no [Band] item in the compound table, right-click the mouse on the compound table, select
[Table Style], and then add [Band] to the items to display.
6 Click [View] in the upper right corner of the compound table, select [Save Method As]
from the [File] menu, and save the method file.
Use the method file for routine analysis.

If you have performed maintenance on the analysis column (cutting or replacement), the retention
times in the compound table will need to be corrected. To correct the retention times, see "Appendix
C Correcting the Retention Times for Method Files Using AART" P.64.
If no retention index has been registered to the method file, measure the compound targeted for
measurement in Scan mode and create a method file again referring to "Appendix B Correcting
Retention Times Directly Without Using AART" P.62.

3 3 Registering Compound
Information in Smart Database
This chapter describes the procedures for registering compound information in Smart Database.
3.1 Steps for Registering Additional Compound

Information in Various Types of Smart Database
Files
Register new compound information as follows.
1. Create a quantitative method file for Q3Scan or Scan mode.
2. Register new compound information. (Registration of additional

information for Q3SIM and SIM completed)
3. Optimize transitions and collision energies (CEs).
4. Register new compound information. (Registration of additional

information for MRM completed)
3.2 Preparing for Analysis

Attach an analysis column appropriate for the Smart Database file in which to add new information. Then
configure the environmental settings and perform autotuning. Also create a folder for saving individual files.
^ Reference
For the procedures, refer to the GCMS Operation Guide - Basic Operation Guide.

3.3 Creating a Quantitative Method File for Scan Mode

Prepare a mixed standard sample (approximately 1 mg/L to 10 mg/L) of the additional compounds to be
registered (including the internal standard substance if quantitation is performed by the internal standard
method). Measure this solution in Scan mode.
3.3.1 Acquire data for the target compounds in Scan mode.

Acquire data of the mixed standard solution using a method file for Scan mode.
^ Reference
For the procedures, refer to “4. Qualitative Analysis” in the GCMS Operation Guide - Basic Operation Guide.
3.3.2 Create the compound table.

3
Create a compound table based on measurement data for the mix standard solution and save it in the
method file. For the procedure, refer to section 5.1.1 "Creating a Compound Table" in the GCMS Operation
Guide - Basic Operation Guide.
For the target and reference ions, set high-mass (high-selectivity) and high-intensity (high-sensitivity) ions
(m/z). Save (overwrite) the measurement data file.
3.3.3 Register the retention indices in the compound table.

Measure and identify n-alkanes and register the retention indices of the compounds targeted for
measurement in the compound table.
• If you want to create a new Smart Database file, follow the procedure below to create a method file for n-
alkane measurement and acquire the data
• To register additional information in an existing Smart Database file, perform operations described in step 8
and after, using the method file for measuring n-alkanes corresponding to the target Smart Database file.
• Perform operations described in "3.4 Registering Compound Information" P.34 and afte if you are not
registering retention indices to Smart Database.
1 Start up the [GCMS Real Time Analysis] program, and click the
Aqcuisition) icon on the [Real Time] assistant bar.
(Data
2 Copy "AART_SmartDatabase_default.qgm," which is saved in the

"C\GCMSsolution\SmartDatabase" folder. Paste it into the folder created in section "3.2
Preparing for Analysis" P.28, and open it.
3 On the [File] menu, select [Load Method Parameters].

The [Load Method] window is displayed.

3 Registering Compound Information in Smart Database
4 Select the method file for target compounds, which was used in section "3.3.1 Acquire
data for the target compounds in Scan mode." P.29. Then click [Open].
The [Select Method Parameters] window is displayed
5 In the [Data Acquisition] area, select all the checkboxes. Then click [OK].
6 In the MS parameter [Start m/z] and [End m/z] fields (measurement mass range), enter
"50" and "500," respectively.
7 Name and save the method file. (Example: "Alkane_AART.qgm")
8 Measure a mixed 5 μg/mL n-alkane standard sample.
Change the preparation concentration of n-alkane according to measurement conditions. The above
is an example of splitless analysis.

9 Click the (Create Compound Table) icon on the [Postrun] assistant bar in the
[GCMS Postrun Analysis]program, load the n-alkane data file.
10 Check and correct the identification results.

If the sample has been misidentified, perform either manual identification or manual peak integration to
identify it correctly.
Depending on the measurement conditions, the number of n-alkanes detected may differ from the
number registered in the compound table.
11 After the analysis, save (overwrite) the data file.

The identification results are saved.
12 Load the data file for the target compounds, saved in section "3.3.2 Create the
compound table." P.29."

The [Modify Compound Table] window is displayed.
(Wizard [Modify]) icon.

14 Select the [Modify Retention Index] checkbox, and click [Ret. Index Param.].
The [Qualitative Parameters] window is displayed.
15 Click [Load from Data File] and load the n-alkane data file saved in step 11).
The n-alkane identification results are loaded.
16 Click [OK] to close the window.

17 In the [Reference Ion] area, clear all the checkboxes. Click [Next] and then [Finish].
The retention indices are registered in the compound table.
3.3.4 Create a quantitative method file.

Save (overwrite) the compound table, with retention indices registered, in the method file for target
compounds of Scan mode. And also save (overwrite) the data file.
1 Save (overwrite) the data file.
2 On the [File] menu, select [Save Method As] to save the method file for target
compounds of Scan mode.

3.4 Registering Compound Information

Compound information can easily be registered in the database from the quantitative method file created.
• To create a new Smart Database file, open "SmartDatabase_Blank.xls" saved in
"C:\GCMSolution\SmartDatabase" and save it under a new name.
• To add compound information in an existing Smart Database file, open the existing Smart Database file.
1 Open the Smart Database file, and open the [Database] sheet.
2 To register additional information in an existing Smart Database file, open the [Ret.
Index for AART] drop-down list and then select "Ret Index" for the column used for
measurement.
3 Click [Import].
The method file selection window is displayed.

3.4 Registering Compound Information
4 Select the quantitative method file for Scan mode saved in section "3.3.4 Create a
quantitative method file." P.33 and click [Open].
The compound names, ions (m/z), retention indices, retention time and standard spectra are registered in
Smart Database.
If compound information is already registered, the following confirmation message is displayed.
Yes Overwrites the information about the compound shown in the message.
Yes to All Overwrites the information about all the compounds to be registered.
No Skips the information about the compound shown in the message without registering it.
Cancel Cancels the registration process.
• The software determines that compounds are the same when their names are identical.
• When the information is overwritten for registration, the retention indices are not overwritten.
• When m/z values for Scan and SIM modes are overwritten for registration, those already
registered in the Smart Database file are all cleared. MRM transitions are not cleared.

5 Save (overwrite) the Smart Database file.

Registration of compound information for Scan and SIM modes is now complete.
To create a method file for SIM mode, perform operations described in chapter "2 Creating Method Files"
P.7 and after.
• If there is already a quantitative method file for MRM mode, you can register additional
information for MRM mode by repeating the above-mentioned procedure from step 3) and
selecting the quantitative method file for MRM mode during the procedure. In this case, if the
compound names match, the additional information will be registered in the same rows as the
information for SIM mode that is already registered.
• For [User Field] and [Filtering], see P.50.

3.5 Optimizing Transitions and Collision Energies (CEs)
If you are measuring in MRM mode, better measurement sensitivity can be obtained by optimizing the
transitions and their collision energies (CEs). Additional optimal transitions and their CEs can be registered
in the Smart DB file created by the procedures described in section "3.4 Registering Compound
Information" P.34.
3.5.1 Create a method file for product ion scan mode.

Create a method file for product ion scan mode based on the data file of the standard sample acquired in
Q3Scan mode. 3
1 In the [GCMS Postrun Analysis] program, click the
icon on the [Postrun] assistant bar.
(Create Compound Table)
2 Open the data file saved in section "3.3.4 Create a quantitative method file." P.33.
The Q3Scan mode target ions and reference ions are configured to the precursor ions. If you are
investigating transitions utilizing multiple precursor ions simultaneously per compound, configure
three precursor ions or less.
In product ion scan mode, the absolute quantity of product ions generated by CID is small when the
measurement is performed. This may result in insufficient sensitivity if a large number of precursor
ions are configured.

The [Select Method File] window is displayed.
(Create MS Table) icon.
4 Name the file so that it can be identified as a method file for product ion scan mode, and
click [Open]. (Example: "TargetComp_ProductionScan.qgm")
The [Creation of Automatic MRM or SIM Table] window is displayed.

5 In the [Select Data Acquisition Mode] area, select [Product Ion Scan].
6 Correct the table if necessary.
To obtain sufficient sensitivity, the number of m/z values set for a single group (= row) should be four
or less. If necessary, split groups, or divide the method file.
To split groups, use the following procedure. (Example: Splitting Group 3 into two groups)
1. Click the third row of the SIM table.
2. Right-click on the table and select [Insert Row].
3. Click the inserted row and drag the mouse on the chromatogram to specify and enlarge the
desired area.
4. Click near the center of peaks labeled with compound names.
Group 3 is divided into two groups.
7 Click [OK].
A method file for product ion scan mode is created.
In product ion scan mode, the settings are automatically configured so that all the product ions from
"m/z 50" to "precursor ion m/z +15" are collected.

3.5.2 Acquire data in product ion scan mode.

This section describes the procedures for automatically creating a batch file and multiple method files
(product ion scan mode) with the CE configured in 3 V increments, using the MRM optimization tool
("MRM_Optimization_Tool.xlsm").
1 Copy "MRM_Optimization_Tool.xlsm," which is saved in the

"C\GCMSsolution\SmartDatabase" folder. Paste it into the folder created in section "3.2
Preparing for Analysis" P.28.
2 Open the copy of the MRM optimization tool, and open the [Create_MethodBatch] sheet.
3 In the [Method File] area, click the

The [Select Method File] window is displayed.
(Load) button.

4 Open the method file for product ion scan mode created in section "3.5.1 Create a
method file for product ion scan mode." P.37.
5 Enter the CE optimization parameters.
[CE Range]: The configurable range is 0 V to 60 V. Normally, enter "3" V and "45" V for the range.
[CE Interval]: Multiple method files are created with the V increment configured here.
For example, if the CE range is set from 3 V to 45 V, and the CE interval is set to 3 V:
15 investigatory method files with CE values of 3 V, 6 V, 9 V,...42 V, and 45 V will be created
automatically.

6 Enter the batch file creation parameters.
[Inj. Count]: Set how many times to acquire the sample from a single vial.
3
When acquiring the sample from a single vial, the syringe can be inserted about ten times.
If the number of cycles of syringe rinsing by the sample is set to one, then the analysis can
be repeated about five times.
[Inj. Volume]: Set the injection volume.
[Vial#]: Set the starting vial number for the sample vials. For the ending vial number, the number of
vials required for the injection cycles is automatically calculated and displayed, based on
the required number of method files calculated from the CE settings in step 5).
[Sample Name]:Set a sample name if necessary.
7 Click the [Create Batch File] button.

The [Save Batch File] window is displayed.

8 Name and save the file.

The path name for the batch file created is displayed in the [Batch File Path] area.
A new folder (named with the date) is created in the folder in which the method file loaded in step 4) is
saved. A batch file and method files for individual CE setting values are saved in the new folder.
9 The new folder opens. Check the contents.
10 Using the batch file created, measure the mixed standard sample (1 mg/L to 10 mg/L).
Names are automatically assigned to the data files so that the CE setting values are evident.
3.5.3 Determine the transitions and their optimal CE values.

Using the MRM optimization tool, determine the transitions and their optimal CE values based on the
multiple data files acquired in section "3.5.2 Acquire data in product ion scan mode." P.39.
1 Open the [MRM Optimization] sheet in the MRM optimization tool copied in section
"3.5.2 Acquire data in product ion scan mode." P.39.
2 Click the [Select Data File] button.

The [Select Data File] window is displayed.

3 Using the mouse, select all the data files acquired in section "3.5.2 Acquire data in
product ion scan mode." P.39, and click [Open].
The compound information is loaded.
If the loaded data includes data for which quantitative peak integration has not been performed or an
unidentified compound is included in all data, the message below is displayed. In this case, perform
quantitative peak integration on all data to identify all compounds and then load the data again.
4 Enter the optimization parameters.
[Number of MRM Transition]: Up to 10 transitions can be registered in Smart Database.
[Product Ion Range]: Enter the mass range (start m/z and end m/z) for analyzing the product
ions. The end m/z is specified in the form of "precursor ion (m/z) - setting
value."
Low-mass product ions have low selectivity, so normally set the start m/z to
"50," and the end m/z to the precursor ion (m/z) - "2."
5 Click the [MRM Optimization] button.

The same number of transitions is selected as configured for the number of MRM transitions, in
descending order of intensity, within the mass range set for the product ion scan range.

6 Open the [Result of Optimization (Graph)] sheet, and check the graphs.
The compounds are displayed in descending order of transition intensity. You can select the
transitions to be registered by deleting unnecessary transitions.
Deleting unnecessary transition by

[Delete] key
To delete an unnecessary transition graph display as well, click the graph to delete and then select
[Delete] from the menu displayed by right-clicking the mouse.

■Procedure for Correcting Graph Shape Problems

Depending on the precursor ions selected, sufficient sensitivity may not be obtained in product ion scan
mode. Accordingly, there may be a problem with the shape of the transition optimization graph. This
section describes how to use the acquired data files in order to correct the graphs for the target compounds
with shape problems.
1 Double-click the
program.
(GCMS Browser) icon to start up the [GCMS Browser]
3
2 On the [Browser] assistant bar, click the
The [Quant Browser] window is displayed.
(Quant Browser) icon.

3 Load all the data files acquired in section "3.5.2 Acquire data in product ion scan mode."
P.39 by dragging and dropping them from [Data Explorer].
4 Click the rows in the compound table in which precursor ions for target compounds
with shape problems are configured.

5 Perform manual peak integration on the total ion current chromatogram (TIC).
In order to extract spectra at the retention times indicated in the identification results from all the data and
optimize the CEs, confirm that the compounds listed in all the data files are identified properly, and then
perform manual peak integration as needed.
6 Click the (Save) icon on the toolbar.
7 Repeat the procedure from step 5 of section "3.5.3 Determine the transitions and their
optimal CE values." P.42.

3.6 Registering Additional Information for MRM Mode

Register additional information for MRM mode in the rows for the same compounds in the Smart Database
file saved in section "3.4 Registering Compound Information" P.34.
1 Click [Register with Smart Database].

The [Select Smart Database] window is displayed.
Alternatively, clicking the [Register with Smart Database] button on the [Result of Optimization
(Table)] sheet registers the information in the Smart DB file. If there are unnecessary transitions or
compounds, delete them using the [Delete] key on the [Result of Optimization (Table)] sheet and
select transitions and compounds to register.
Deleting
unnecessary
The compound names are registered in the [Compound Name] column currently displayed in Smart
Database. To register compound names in a different [Compound Name] column, set [Lang.] -
[Compound Name Lang.] in Smart Database, and save the file before registering the compound
names.

3.6 Registering Additional Information for MRM Mode
2 Open the Smart Database file in which to add information.

The transitions, their CE values, and the ion ratio information are registered using the MRM optimization
tool.
To create a method file for MRM mode, perform operations described in chapter "2 Creating Method
Files" P.7 and after.
If compound information for Scan or SIM mode is already registered, the following confirmation
message is displayed. Select [Yes to All]
Yes Overwrites the information about the compound shown in the message.
Yes to All Overwrites the information about all the compounds to be registered.
No The compound information displayed in the message will be registered on the new
bottommost row without overwriting the information.
Cancel Cancels the registration process.
• The software determines that compounds are the same when their names are identical.
• When the information is overwritten for registration, the retention indices are not overwritten.
• When the compounds are overwritten for registration, MRM transitions already registered in the
Smart Database file are all cleared. The m/z values for Scan and SIM modes are not cleared.

3 Save (overwrite) the Smart Database file in which the additional information for MRM
mode has been registered.
[User Field]:
You can enter any information in the user field. You can also change the title name.
[Filtering]:
By using the filtering function when creating a method file from the Smart Database file with
additional information registered, you can easily select the target compounds.
Enter a lower-case "x" in the cells for the compounds to select collectively, and then change the title
name to suit the category.
4 To save analysis results, name and save the MRM optimization tool.

A
Appendix A Creating Method Files for
Other Measurement Modes
Section "A.1 Creating Method Files for Scan Mode" P.51 describes how to create method files to
measure target compounds in Scan mode.
Section "A.2 Creating Method Files Combining Multiple Measurement Modes" P.53 describes how to
A
create method files to measure target compounds in multiple measurement modes simultaneously.
A
A.1 Creating Method Files for Scan Mode
A
1 Set all compounds set to "Target" in the [Type] column to "Scan" in the [Acq. Mode]
column. A
A
A
A
2 Check the settings for target ions and reference ions listed in the [m/z for SIM or Scan]
table.
To change or add ions, make your selection on the drop-down menu in the [Type] cell. A
A
A
A
A
A
A
A
A Creating Method Files for Other Measurement Modes
3 After checking the settings in the [Parameter] area, click [Create Method File].

Set the parameters for Scan measurement.
Enter "0.3" seconds in the [Event Time of Scan] field. Consider the molecular weights of the target
compounds. Then set the start m/z and end m/z for the measurement mass range. Measure the sample
once, and correct the settings if necessary.
^ Reference
For details on Scan parameters, see step 5 in "Appendix A.2.1 Creating Method Files for
Simultaneous Scan/MRM Measurement" P.53.

A.2 Creating Method Files Combining Multiple Measurement Modes
4 Click [OK].
The [Save As] window is displayed. Enter a name that will identify it as a method file for Scan mode, and
then click [Save].
If you create a method file for Scan mode, the measurement range is not output on the
A
[MSTableView] sheet.
A.2 Creating Method Files Combining Multiple

Measurement Modes
The following sections describe how to create method files to measure target compounds in multiple
modes.
Section "A.2.1 Creating Method Files for Simultaneous Scan/MRM Measurement" P.53 describes
how to create method files to measure target compounds in Scan and MRM modes simultaneously.
Section "A.2.2 Creating Method Files for Simultaneous Scan/SIM Measurement" P.56 describes how
to create method files to measure such compounds in Scan and SIM modes simultaneously.
Section "A.2.3 Creating Method Files for Mixed SIM/MRM Measurement" P.59 describes how to
create method files to measure any compound in SIM mode, and other compounds in MRM mode.
A.2.1 Creating Method Files for Simultaneous Scan/MRM Measurement
1 Set all compounds set to "Target" in the [Type] column to "MRM" in the [Acq. Mode]
column.

2 Check the settings for target ions and reference ions listed in the [MRM Transition]
table.
To change or add ions, make your selection on the drop-down menu in the [Type] cell.
4 Select [ON] in the [Scan Mode] area.

5 Set the parameters for MRM measurement, and the parameters for Scan measurement.
([Loop Time(MRM,SIM)], [Required Processing Time], and in the [Scan Parameter] area, [Event Time of
Scan], [Scan Range], and [Acquisition Time])
A
Scan Parameters
[Event Time of Scan]: Set the event time for Scan measurement.
For simultaneous Scan/MRM measurement and simultaneous Scan/SIM
measurement, the total of [Event Time of Scan] and [Loop Time(MRM,SIM)] will be
the total loop time. The value will be displayed in the [Total Loop Time] field. When
measurements are performed in Scan mode only, the value set here will be the
loop time.
Recommended values
Scan/MRM or Scan/SIM : 0.1 sec
Scan : 0.3 sec
[Scan Range]: Set the m/z range for Scan measurement.
[Acquisition Time]: Set the measurement start time and end time.
^ Reference
For details on MRM and SIM parameters, see step 2) in section "2.4.6 Create the MS table." P.17.
6 Click [OK].
The [Save As] window is displayed. Enter a name for the method file, and then click [Save].
The [MSTableView] sheet will be displayed automatically.

Here, you can check the measurement range for compounds targeted for measurement in MRM mode.
A.2.2 Creating Method Files for Simultaneous Scan/SIM Measurement
1 Set all compounds set to "Target" in the [Type] column to "SIM" in the [Acq. Mode]
column.
2 Check the settings for target ions and reference ions listed in the [m/z for SIM or Scan]
table.

4 Select [ON] in the [Scan Mode] area.

5 Set the parameters for SIM measurement, and the parameters for Scan measurement.
([Loop Time(MRM,SIM)], [Required Processing Time], and in the [Scan Parameter] area, [Event Time of
Scan], [Scan Range], and [Acquisition Time])
^ Reference
For details on MRM and SIM parameters, see step 2) in section "2.4.6 Create the MS table." P.17.
For details on Scan parameters, see step 5) in "Appendix A.2.1 Creating Method Files for
Simultaneous Scan/MRM Measurement" P.53.
6 Click [OK].
The [MSTableView] sheet will be displayed automatically. Here, you can check the measurement range
for target compounds in SIM mode.

A.2.3 Creating Method Files for Mixed SIM/MRM Measurement
1 Set all compounds set to "Target" in the [Type] column to "SIM" in the [Acq. Mode]
column.
A
2 For compounds to be measured in MRM mode, check the settings for target ions and
reference ions listed in the [MRM Transition] table.
For compounds to be measured in SIM mode, check the settings for target ions and reference
ions listed in the [m/z for SIM or Scan] table.

4 Set the parameters for MRM and SIM measurements. ([Loop Time (MRM,SIM)] and
[Required Processing Time])
^ Reference
For details on MRM and SIM parameters, see step 2 in section "2.4.6 Create the MS table." P.17.

5 Click [OK].
The [MSTableView] sheet will be displayed automatically. Here, you can check the measurement range
for target compounds in MRM mode and SIM mode.
A

B Correcting Retention Times
Appendix B
Directly Without Using AART
Before following the procedure below, you need to create a method file for Scan mode, as shown in
"Appendix A.1 Creating Method Files for Scan Mode" P.51".
In the procedure, you measure the target compounds in Scan mode, and then set the retention times
based on the identification results.
The retention times are set directly without using the retention indices, so the target compounds must be
identified correctly.
1 Follow the steps in section "2.4.1 Open Smart Database." P.10.
2 On the [Ret. Index for AART] drop-down menu, select "Not Use AART"
3 In the [Template Method File] area, click the

file for Scan mode created earlier.
(Load File) button. Select the method

4 Copy the retention times from the identification results indicated in the compound table.
Then paste them into the [Ret. Time] column in Smart Database.
When pasting the data, be sure that rows on the compoud table and [Database] sheet are aligned in the
same order.
Copy the data using the [Ctrl] + [c] keys.
Paste the data using the [Ctrl] + [v] keys.
5 Follow the steps from section "2.4.3 Select the target compounds." P.13.

C
Appendix C Correcting the Retention
Times for Method Files
Using AART
C.1 Measuring the Mixed n-Alkane Standard sample
Measure the mixed n-alkane standard sample in order to correct the retention times.
^ Reference
For the procedure, see section "2.3.1 Measure the mixed n-alkane standard sample." P.8.
C.2 Identifying the n-Alkanes

Open the acquired n-alkane data file, and identify the compounds.
^ Reference
For the procedure, see section "2.3.2 Identify the n-alkanes." P.8.
C.3 Correcting the Retention Times for Method Files

Using AART
1 On the [Create Compound Table] assistant bar, click the (AART) icon.
2 Select the method file with retention times to correct, and then click [Open].

C.3 Correcting the Retention Times for Method Files Using AART
3 Check the n-alkane identification results, and then click [Next].
C
4 Check the corrected retention times, and then click [Finish].
If you select the [Modify the time of MS Instrument parameters] checkbox, the parameter settings
(such as for grouping) for the MS instruments included in the method file for MRM or SIM mode will
also be corrected automatically.

C Correcting the Retention Times for Method Files Using AART
5 In the [Save Modified Method File] window, name the corrected method file and then
click [Sve].
The retention times for the method file have been corrected using AART. The setting times corrected via
AART are as follows.
Compound Table
[Ret.Time], [Proc.From], [Proc.To], and [Program]
Parameters for MS Instruments (Optional)
[Start Time], [End Time], and [MS Program]
Corrected Method File
The AART function may modify the MS instrument [Start Time] parameter setting, resulting in the
start time being earlier than the [Solvent Cut Time]. In such a case, open the [Acquisition] window in
the [GCMS Real Time Analysis] program, open the method file modified by the AART function, and
then change the [Solvent Cut Time] setting to be 0.5 minutes earlier than the [Start Time] setting.

GCMSOperationGuide (Ver4 4) MethodDevelopment PDF

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

GCMSOperationGuide (Ver4 4) MethodDevelopment PDF

Uploaded by

Copyright:

Available Formats

225-28480

Gas Chromatograph Mass Spectrometer

Read this Instruction Manual thoroughly before using the product.

Also, keep this manual for future reference.

Method Development Guide i

ii Method Development Guide

Shimadzu Corporation provides the following warranty for this product.

Method Development Guide iii

^ Reference Indicates the location of related information.

iv Method Development Guide

 Installation Site Precautions

Method Development Guide v

• Legal authorization is required to use cylinders with a capacity of 300 m3 or greater.

vi Method Development Guide

 Emergency Shutdown Procedure

2 Turn OFF all accessories.

4 Disconnect the power supply.

Method Development Guide vii

viii Method Development Guide

1.2 Overview of Smart Database...............................................................................3

2 Creating Method Files 7

2.2 Preparing for Analysis..........................................................................................7

2.3 Measuring and Identifying n-Alkanes...................................................................8

2.4 Creating a Compound Table and MS Table ......................................................10

2.5 Correcting Method Files.....................................................................................20

3 Registering Compound Information in Smart Database 28

3.2 Preparing for Analysis........................................................................................28

Method Development Guide

3.3 Creating a Quantitative Method File for Scan Mode.......................................... 29

3.4 Registering Compound Information................................................................... 34

3.5 Optimizing Transitions and Collision Energies (CEs) ................................. 37

3.6 Registering Additional Information for MRM Mode ..................................... 48

Appendix A Creating Method Files for Other Measurement Modes 51

Appendix B Correcting Retention Times Directly Without Using AART 62

C.1 Measuring the Mixed n-Alkane Standard sample ............................................. 64

x Method Development Guide

1 Measure the standard sample by scan mode

2 Create compound table

3 Measure the standard sample by product ion scan mode

4 Find optimal transitions and collision energy

"2 Creating Method Files"

Method Creation Function

Method Development Guide xi

1 Measure the standard sample by scan mode

2 Create compound table

3 Create method file of MRM mode

Method file of SIM mode

"2 Creating Method Files"

Method Creation Function

xii Method Development Guide

Smart Database is a file in Microsoft Excel format.

1.1.1 Measurement Modes for the GCMS-QP Series

1.1.2 Measurement Modes for the GCMS-TQ Series

Analysis Mode Q1 Collision Cell Q3

Analysis Mode Q1 Collision Cell Q3

MRM (Multiple Reaction Monitoring):

Product Ion Scan:

2 Method Development Guide

1.2 Overview of Smart Database

Under default conditions, no compound information is registered in Smart Database

1.2.2 Operating Environment

OS Microsoft Windows 7 Professional

1.2.3 Compatible Equipment