Building Agilent GC/MSD Deconvolution
Reporting Libraries for Any Application
Technical Overview
Authors
Xiaofei Ping
Agilent Technologies (Shanghai) Co Ltd
412 Yinglun Road, Shanghai, 200131
P.R. China
Chin-Kai Meng and Michael Szelewski
Agilent Technologies, Inc.
2850 Centerville Road
Wilmington, DE 19808-1610
USA
Abstract
This technical note describes the steps to build deconvo-
lution reporting software (DRS) libraries for any applica-
tion. The starting point is either the data file(s) for all the
chemical standards or a customer-built Agilent mass
spectral library (*.L). The DRS library-building process
would take 3–4 hours following the steps in this technical
note.
Introduction
Agilent Technologies developed methods and
libraries to screen for 567 pesticides and suspected
endocrine disrupters in a single gas
chromatography/mass spectrometry (GC/MS)
analysis using the techniques of retention time
locking (RTL) [1, 2] and spectral deconvolution [3].
Spectral deconvolution helps to identify compounds
even when they are buried under co-eluting matrix
compounds. The deconvolution process is fully
automated and only takes about 1 to 2 minutes for
a total ion chromatogram (TIC). The process not
only allows the analysts to get reliable and repro-
ducible results fast, false positives and false
negatives are also minimized.
However, not all compounds are included in a com-
mercial mass spectral library ready for deconvolu-
tion process, especially the unique compounds for
a special study. In this case, the analysts need to
build their own deconvolution libraries in order to
take advantages of DRS for the specific analyses in
their laboratories.
Prerequisites
• GC/MSD ChemStation (G1701DA) revision
D.02.00 or higher
• Microsoft Excel
• NIST05 Mass Spectral Library
• Automatic Mass Spectral Deconvolution and
Identification System (AMDIS, version 2.62)
from the National Institute of Standards and
Technology (NIST). This software is included on
the NIST05 CD.
• GC/MS data file(s) for all the chemical stan-
dards acquired using GC/MSD (gas
chromatography/mass selective detector)
This article describes the steps required to con-
struct the needed files and libraries for DRS.
(Note: “oxymix” is just an example used in this
article to be substituted with a name relevant to
your application. The operating system may affect
the graphics shown.) Here is an outline for the
process:
Create a *.tab file (for example, oxy_original.tab) using
Microsoft Excel, see reference 4.
File Locations (Files types: *.d, *.tab, *.L,
*.SCD, *.MSP, *.MSL, and *.CAL)
• Data files (*.d) in C:\MSDChem\1\DATA
• *.TAB, *.SCD and *.L in C:\Database
• *.MSP in C:\NIST05\MSSEARCH
• *.MSL and *.CAL in C:\NIST05\AMDIS32\LIB

Build a Mass Spectral Library (MSL) (for example,

oxymix.L)

Convert oxymix.L to oxymix.MSP (Simple Mass

Spectrum)

Create oxymix.MSL from oxymix.MSP

Create oxymix.CSL (Calibrated Spectral Library) from

oxymix.MSL

Create oxymix.CAL (Retention Time Calibration File) for

RTL applications

Use MSD-DRS Configuration program to associate

oxymix.MSL and oxymix.CAL with oxyquant.m

Please refer to Technical Note “Building and Editing

RTL Screener/Quant Database and Libraries” [4] for
further information.

2
Procedure for Building Databases and
Libraries*
Create the *.TAB File
1. Load a data file (for this example, oxymix_2.d,
see Figure below) which consists of the peaks
(spectra) of standard compounds for the library
entries. Make sure no peaks were overlapped in
the data file causing contaminated spectra. In
situations where clean spectra of target com-
pounds cannot be obtained (for example, over-
lapping peaks), refer to the DRS User
Information section “Adding Compounds to
Existing AMDIS_32 Libraries” for instructions
to deconvolute the spectra before adding them
to the library.

Load the default.m, turn off library searching and

reporting, and save the method under a unique
name. When you complete the steps in this section,
refer to Appendix A to build a quant database for
this new method.

*A manual procedure for building the library is also available; please refer to applica-
tion note “Retention Time Locking: Creating Custom Retention Time Locked
Screener Libraries” [5] for further information.

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2. Create a *.tab file using Microsoft Excel. Refer
to Table 1 for explanation of columns in the
*.tab file [4]. For column F, sort all entries in
*.tab file into ascending retention time (RT)
order before saving, this is especially important
if the library is to be created from multiple
datafiles. See the Figure below.

Table 1. Explanation of Columns in *.tab File

Column Header
A Open (column A is used in GC for RT, not used in MSD)
B Name (compound name, for example isobutanol)
C CAS (CAS number without dashes, for example, 12345, not 00012-34-5)
D Molecular formula (for example, C6H14N2O, no commas, dashes, quotes, etc., must use
capital letters) (Note: for chlorine, use Cl, not CL)
E Molecular weight (for example, 32.04)
F RT (GC/MSD, in minutes, for example, 3.33)
G Open (not used)
H Company ID (an unique identifier, for example, cmpd01 - more explanation on this later)
I File name (complete file path for *.d acquired such as: C:\MSDChem\1\data\oxymix_2.d)

The first two lines of the spreadsheet are ignored in

the library-building process; however, they cannot
be left blank. All information used for building
libraries will start from the third line.

The columns B, C, D, E, F and I are required; column H is

optional but recommended. All other columns are left blank.
Use one compound per row. The formula is case sensitive, only
capital letters can be used.

Note : Sort all entries in .tab file into ascending RT order before saving – especially
important if the library is to be created from multiple datafiles

Only capital letters could be used for Molecular Formula

Use single sheet template only

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3. Save the file in *.tab type in C:\database.
Go to File | Save as | and choose Text (Tab
delimited) (*.txt). The file name must be
enclosed in “ as shown.

Path C:\DATABASE

Type in “oxy_original.tab”

We recommend adding the word “original” in the

tab file name so the file won’t get overwritten in
the future.

4. Click Yes to keep the format.

5
5. Close Excel, otherwise you will get an error
message (Could not open file
C:\database\oxy_original.tab) from MSD
ChemStation.
6. Click No.

Build the Library and SCD

1. Go to Enhanced Data Analysis. Load the proper
method and data file. Click the “Data Analysis
Options” icon to toggle/display the command
line. On the command line type rtl_import and
then click Execute.

2. Select Library and SCD and then click OK.

6
3. Select oxy_original.tab in C:\database, click
Open.

4. Type in the Library name (such as “oxymix.L” -

the library name is limited to eight characters)
and SAV folder name (for example
C:\DATABASE\oxymix.SAV), click OK. Make
sure your library name is different from your
tab-file name.

Type in oxymix.L

Type in C:\DATABASE\oxymix.SAV

Enhanced DA will call each of the files in Column I

of your *.tab file. It will then go to the RT you speci-
fied in Column F and create a Library entry using
that spectrum and the information from Columns B,
D, and E. You should see flashing chromatograms. If
you fill in column H of the *.tab file, you will get a
*.SAV directory when the library is built.

7
The figure below shows the new library, oxymix.L,
oxymix.scd, oxy_original.tab files and the *.sav
directory.

The *.sav is a folder created in Database folder

when you create a Library from a *.tab. The *.sav
folder contains one *.sav file for each entry in the
Library you just created as shown in the Figure
below. Each *.sav file contains the spectrum of the
Library entry. The *.sav file name is taken from
Column H. If Column H is left blank you will get no
usable *.sav files. You can rebuild the Library using
the *.sav files if you lost the original data files. In
the dialogue box where you entered the library
name when you first created it, there is a “more”
button. Clicking “more” gives you a field to specify
whether you are using original data or *.sav files.

8
The *.scd file, found in the database folder, could
be used to create Calibration Table (quantitation
database) automatically; refer to Appendix A for
further information.

Use these steps to confirm the MSL was built

successfully:

1. Type listlib on the command line and then click

Execute.

2. Select the library name you just created (that is,

oxymix.L), then click OK.

9
3. Click No to the detailed graphics question, as
shown below.

If all went well, you will see a list of your library

entry, compound name, MW, CAS, etc as shown in
the Figure below. If you see only a few lines of text
at the top, the library was not built properly. Go
back to repeat steps 1 to 6 (starting on page 3)
carefully, especially entering the correct data file
name and the data path in column I of the *.tab
file.

10
Create *.MSP from *.L
1. Go to Windows Start, Programs, NIST Mass Spectral
Database and click Lib2NIST Converter.

2. Choose the *.L library you created from previ-

ous steps (that is, “oxymix.L”), select HP
Lib[*.L], Text[*.SDF, *.MSP], NIST Lib[*.*]
type, then click Open.

11
3. Select folder “C:\NIST05\MSSEARCH” for NIST
Library and Output, select Text File [.MSP] for
Output Format, highlight the library in the left
panel, then click Convert.

4. The oxymix.MSP file will be created in

C:\NIST05\MSSEARCH, click Exit.

The .MSP file will be created even though it is not

displayed in the above graphic.

12
Convert *.MSP to *.MSL
1. As shown below, go to Windows Start,
Programs, NIST Mass Spectral Database and
then click AMDIS_32.

While in AMDIS, pay special attention to the file

extensions, that is, *.msp, *.msl, and *.csl.

2. Click File and Open… to open a data file (for

example, oxymix_2.d).

3. Click Library and then click Library

Transfer… .

13
4. You will be prompted with a Transfer from
Library to Library window, click Files. A
subsequent Files window will display.

14
5. In Files window,
click Load Library… ,
change the file type to *.MSP,
select OXYMIX.MSP in C:\NIST05\MSSEARCH,
then click Open.
Back to Files window,
click Create New Library… ,
select folder C:\NIST05\AMDIS32\LIB,
save files as type Target Library(*.MSL),
type in oxymix.MSL for File name,
click OK.

Path
C:\NIST05\MSSEARCH

Type in proper file name

Select oxymix.MSP

Path
C:\NIST05\AMDIS32\LIB

6. Click Close.

15
7. Highlight all compounds on left and click
Transfer->. The *.MSL file is saved in
C:\NIST05\AMDIS32\LIB.

Highlight all compounds

Convert *.MSL to *.CSL

1. Continue from previous step, click Files.

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2. In Files window,
click Load Library…,
select “oxymix.MSL in C:\NIST05\AMDIS32\LIB,
then click Open.
Back to Files window,
click Create New Library…,
select folder C:\NIST05\AMDIS32\LIB,
save files as type RI Calib Library(*.CSL),
type in oxymix.CSL for File name,
click OK.

Path
C:\NIST05\AMDIS32\LIB

Type in proper file name

Select oxymix.MSL

Path
C:\NIST05\AMDIS32\LIB

3. Click Close.

17
4. Highlight all compounds on left and click
Transfer->.

Highlight all compounds

5. Click Exit. The *.CSL file is saved in

C:\NIST05\AMDIS32\LIB.

So far, all libraries and files required by DRS were

saved in C:\NIST05\AMDIS32\LIB.

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Using AMDIS Interactively
1. Open AMDIS, click Analyze and then
Settings… shown below.

2. Click the Libraries tab, highlight Target

Compound Library, and then click Select New.

19
 Select oxymix.MSL in
C:\NIST05\AMDIS32\LIB and then click Open.

Path
C:\NIST05\AMDIS32\LIB

Confirm the proper *.MSL is selected

20
3. Highlight RI Calibration Library and then click
Select New.

Select oxymix.CSL in C:\NIST05\AMDIS32\LIB

and then click Open.

Path
C:\NIST05\AMDIS32\LIB

21
 Confirm the proper *.CSL is selected

4. Highlight RI Calibration Data, and then click

Select New.

22
Do not pick one of the existing file names. Type in
a unique name for a *.cal file to be created.

Type in oxymix.cal as filename, then click

Open.

Path
C:\NIST05\AMDIS32\LIB

Type in proper file name

Confirm the proper *.CAL is selected

23
5. Click the “Identif.” tab, type in Minimum Match
Factor suitable for your analysis (for example,
60) and highlight RI Calibration/Performance
in Type of analysis. This setting is used to
create the *.CAL file.

6. Click Save.

Refer to the User Information section of DRS for

selecting all the proper settings.

24
7. Click Yes.

8. Close AMDIS.

In order to perform DRS using the libraries just

built, you need to associate the libraries (that is,
oxymix.MSL and oxymix.CAL) with the
quantitative method (that is, oxyquant.M). The CSL
is only needed for building the CAL file.
1. Go to Windows Start, Programs, MSD Decon-
volution Reporting Software, and Configura-
tion Utility, launch the Compound
Identification Configuration program.

25
2. Click Method Associate Settings, and then
New Method Associate Settings ….

3. Type in the MSD ChemStation quantitative

method name (that is, oxyquant) and then click
the “…” icon. Do not add “.m” after the method
name!

Type in proper method name

26
4. Select oxymix.MSL as AMDIS target library,
and click Open.

5. Check Use RI Calibration Data, and then click

the … icon.

27
6. Select oxymix.CAL” as RI Calibration Data,
and click Open.

7. Check Open Report and Print Report, and

then click … icon.

28
8. Select onsite.ini as AMDIS Initialization
Settings File.

Select this file

9. Click Add to complete the configuration.

29
10.Click Exit, and then Exit and Save.

Note : AMDIS only recognizes and uses the onsite.ini settings file when it runs automatically. The DRS software copies
the settings file specified here to onsite.ini before it deconvolutes the chromatogram

Now you can use the new DRS libraries to generate

reports as shown in reference 3 for your own
applications.

References
1. V. Giarocco, B. Quimby, and M. Klee, “Retention
Time Locking: Concepts and Applications”,
Agilent Technologies, publication 5966–2469E,
www.agilent.com/chem
2. H. Prest, P. Wylie, K. Weiner, and D. Agnew,
“Efficient Screening for Pesticides and
Endocrine Disrupters Using the 6890/5973
GC/MSD System”, Agilent Technologies,
publication 5968–4884E, www.agilent.com/chem
3. P. Wylie, M. Szelewski, and C.K. Meng, “Compre-
hensive Pesticide Screening by GC/MSD Using
Deconvolution Reporting Software”, Agilent
Technologies, publication 5989–1157EN,
www.agilent.com/chem
4. Michael J. Szelewski, Kenneth R. Weiner, and
Chin-Kai Meng, “Building and Editing
RTL/Screener/Quant Databases and Libraries”,
Agilent Technologies, publication 5989–0916EN,
www.agilent.com/chem
5. Kenneth R. Weiner and Harry F. Prest, “Reten-
tion Time Locking: Creating Custom Retention
Time Locked Screener Libraries”, Agilent
Technologies, publication 5968–8657E,
www.agilent.com/chem

30
Appendix A

Creating Quantitation Database

Automatically Using a *.SCD File
The information in *.SCD file could be used to build
a quantitative method automatically following steps
1 to 4.

1. Find qdb.mth in relevant *.M directory (for

example, oxyquant.M).

2. Rename qdb.mth to qdb.mth.ori.

31
 www.agilent.com/chem
3. Copy oxymix.SCD from the C:\database
directory into relevant *.M (oxyquant.M)
directory.

4. Rename oxymix.scd to qdb.mth.

For More Information

For more information on our products and services,
visit our Web site at www.agilent.com/chem.

The resulting calibration table in the method has

the Quant Ion set to the m/z of the most abundant
ion in the target peak spectrum. The three Qualify-
ing ions were set to the next three most abundant
ions from the target peak spectrum. Ion ratio
Agilent shall not be liable for errors contained herein or for incidental or consequential
damages in connection with the furnishing, performance, or use of this material.
Information, descriptions, and specifications in this publication are subject to change
without notice.

criteria were also set automatically. © Agilent Technologies, Inc. 2005

Reload the method from MSD DataAnalysis pro- Printed in the USA
gram to review the calibration table. Make sure October 3, 2005
5989-2249EN
that the CAS number is entered on page 2 for each
compound - no leading zeroes, no dashes, etc.