Agilent Technologies G1701EA User manual

Agilent Technologies
Agilent G1701EA
MSD Productivity
ChemStation
Getting Started

2 MSD Productivity ChemStation Getting Started
Notices
© Agilent Technologies, Inc. 2012
No part of this manual may be reproduced in
any form or by any means (including elec-
tronic storage and retrieval or translation
into a foreign language) without prior agree-
ment and written consent from Agilent
Technologies, Inc. as governed by United
States and international copyright laws.
Manual Part Number
G1701-90069
Edition
Second edition, June 2012
Printed in USA
Warranty
The material contained in this docu-
ment is provided “as is,” and is sub-
ject to being changed, without notice,
in future editions. Further, to the max-
imum extent permitted by applicable
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either express or implied, with regard
to this manual and any information
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liable for errors or for incidental or
consequential damages in connec-
tion with the furnishing, use, or per-
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information contained herein. Should
Agilent and the user have a separate
written agreement with warranty
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document that conflict with these
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arate agreement shall control.
Safety Notices
CAUTION
A CAUTION notice denotes a haz-
ard. It calls attention to an operat-
ing procedure, practice, or the like
that, if not correctly performed or
adhered to, could result in damage
to the product or loss of important
data. Do not proceed beyond a
CAUTION notice until the indicated
conditions are fully understood and
met.
WARNING
A WARNING notice denotes a
hazard. It calls attention to an
operating procedure, practice, or
the like that, if not correctly per-
formed or adhered to, could result
in personal injury or death. Do not
proceed beyond a WARNING
notice until the indicated condi-
tions are fully understood and
met.
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard
Santa Clara, CA 95052

MSD Productivity ChemStation Getting Started 3
Contents
1 MSD Productivity ChemStation Quick Reference
In This Book 6
Where to Find Help 7
What’s New in This Revision 12
Hardware 13
ChemStation Views 21
Common ChemStation Tasks 33
Error Messages and Troubleshooting 49
2 Understanding Quantitation
Quantitation 56
Quantitation Database 59
Tutorial – Using AutoQuant Setup 66
3 Using Custom Reports
Custom Reports 82
Creating a Report Template 83
Customizing Reports 87
Printing Reports 92
Creating a Custom Reports Database 95
Selecting Multiple Data Files 98
Viewing and Printing Charts 100
Custom Reports Toolbar Buttons 101

4 MSD Productivity ChemStation Getting Started

5
Agilent G1701EA MSD Productivity ChemStation
Getting Started
Agilent Technologies
1
MSD Productivity ChemStation Quick
Reference
In This Book 6
Where to Find Help 7
What’s New in This Revision 12
Hardware 13
ChemStation Views 21
Common ChemStation Tasks 33
Error Messages and Troubleshooting 49

6 MSD Productivity ChemStation Getting Started
1 MSD Productivity ChemStation Quick Reference
In This Book
This document contains an overview of the items included with
your system. It is intended to help you get started using your
GC/MSD System.
In the following pages you will find:
•Details on where to find additional help
•Photos of your hardware with major parts identified
•Each toolbar found in the ChemStation software
•Procedures for common ChemStation operations
•A summarized maintenance schedule
•A brief section on operating tips, error messages, and
troubleshooting
•A review of how quantitation works with the ChemStation,
along with a tutorial to help you get started using the
time-saving AutoQuant feature
•A quick guide on how to use Custom Reports software
Please refer to your online help and the electronic manuals and
videos included on your supplied disk for detailed information.

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MSD Productivity ChemStation Getting Started 7
Where to Find Help
Your system comes with an extensive library of reference
material including printed manuals, online help files, and
electronic manuals on disk.
Each piece of hardware is accompanied by a disk which
contains hundreds of pages of in-depth reference material and
maintenance videos demonstrating how to operate, maintain,
and troubleshoot your equipment.
This hardware reference material includes detailed information
on:
•Operating the hardware
•Maintaining the hardware
•Troubleshooting the hardware
The online help files contain extensive software operating
instructions as well as tutorials on using the ChemStation
(Enhanced, Drug Analysis, Environmental, and Aromatics in
Gasoline) software. Included is task and reference information
on:
Data Analysis MSD System Configuration
•Analyzing Data •Configuring Instruments
•Commands and Functions •Typical PC Information in MSDCHEM.INI
•Using and Writing Macros
•Glossary of Terms
Instrument Control
•Using Instrument Control •Troubleshooting the MSD
•Using Methods •Secure Control
•Using Sequences •Report Manager
•Analyzing Data •Commands and Functions
•Using Batch Mode •Using and Writing Macros
•Tuning (Calibrating) the MSD •Glossary of Terms

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Printed documents are intended to help you get up and running.
They include the:
•MSD Productivity ChemStation Getting Started (this
document)
•Site Preparation Checklist
•Hardware Installation Checklist
•Hardware Operation Manual
•Drug Analysis Getting Started

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MSD Productivity ChemStation Getting Started 9
Using ChemStation online help files
The online help files contain extensive information and
tutorials about instrument control, data acquisition, data
analysis, methods, sequencing, tuning, troubleshooting, and
how to use system commands and variables.
To access the online help, select Help topics from the Help menu
in any window, or click the help button on any dialog box.
Help Icons
Indicates a book containing more help
topics. To open a book, double-click it.
Indicates an open book of help topics. To close
an open book, double-click it.
Indicates a help topic. To jump to a help topic,
click it.
Item Description
Hide/Show Lets you turn on or
off the display of the
list of help topics.
Back Goes back to the
previous help topic.
Print Lets you print the
current book or help
topic.
Contents Displays the list of
help topics (shown
above).
Index Lets you use
keywords to search
the help index for a
particular topic.
Search Lets you type a word
or phrase and then
displays a list of all
the topics in the
online help that
contain those words.
Options Lets you change
various help options
such as the display
of tabs.

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To print a single help topic:
1Highlight the topic you want
to print (for example, Overview).
2Right-click, and select Print…
3Select Print the selected topic
and click OK.
4Verify the printer selected and
click Print.
5The information on that single
topic will print. The topics
linked to it will not print.
To print all subtopics in a heading at once:
1Highlight the topic you want
to print (for example, Print
Commands Quick Reference).
2Right-click, and select Print…
3Select Print the selected
heading and all subtopics, and
click OK.
4Verify the printer selected,
and click Print.
5The information for ALL
topics within the heading of
the selected topic will print. In
this case, all topics under Print
Commands Quick Reference
would print, which is about 26
pages of information.
NOTE Even if your cursor was on a single topic under this heading (say Tune
Commands) when you select Print all topics, you will still receive a copy
of all the topics under the heading, not just the topics below the one you
happened to be on in the list.

MSD Productivity ChemStation Quick Reference 1
MSD Productivity ChemStation Getting Started 11
Other User Information
Now your Agilent instrument documentation is in one place, at
your fingertips.
The software DVD that ships with your instrument provides an
extensive collection of online help, videos, and books for the
Agilent 7890A GC, 6890N GC, 5975 Series MSD, and the 7683B
ALS. Included are localized versions of the information you
need most, such as:
•Getting Familiar documentation
•Safety and Regulatory guides
•Site Preparation checklists
•Installation information
•Operating guides
•Maintenance information
•Troubleshooting details

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What’s New in This Revision
There are two ways to view a description of all the updates
made to this version of the software:
•Following your initial configuration, select “Yes” when
prompted “Do you want to view the Readme file now”.
•In either the Data Analysis, or Instrument Control view,
select Help/View Revisions Readme File.
A text file is displayed in a pop-up window. You may scroll
through this text and read it online, search it electronically, or
copy it, as desired.
Select File/Exit to return to the application when you are ready.

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MSD Productivity ChemStation Getting Started 13
Hardware
5975 Series MSD with an Agilent 7890A
7890A GC
ALS
5975 MSD
Local control panel
Source view window
MSD power switch
GC power switch

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Keypad for the 7890 GC
The ChemStation software provides instrument control for the
7890 and 6890 GCs. This allows you to use the software, instead
of the GC keypad, to program the instrument. However, there
are times when you may want to use the keypad to quickly
access the following functions.
The Run Keys
GC Component Keys
General Data Entry Keys
Method Storage and
Automation Keys
Supporting Keys

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MSD Productivity ChemStation Getting Started 15
Keypad for the 6890 GC
The 6890 keypad is similar to the 7890 keypad. It can be
controlled by software, as can the 7890, but the keypad is
convenient for frequently performed actions.
Display the back inlet information
Display the GC/MSD interface temperature
Display the front inlet information
Display the oven temperature
Display column information
Stop a run
Prepare a run (manual injection)
Start a run (manual injection)
(Thermal Aux 2)

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Keypad and display for the 6850 GC
The ChemStation software provides instrument control for the
6850 GC. This allows you to use the software, instead of the GC
keypad, to program the instrument. However, there are times
when you may want to use the keypad to quickly perform one of
the following tasks.
Depending on the configuration set by the control module or
ChemStation, during a run the scrolling display can show:
•Oven temperature
•Inlet pressure
•Column flow rate
•Raw detector signal
•Messages
•Sequence information
•Run time
Load
RunNot Ready Start
Stop
Prep Run
6850 Display
Scroll through a list
Load a method
Start a run, autoinjector, or sequence
when "Ready for..." appears
on the display
On during run,
blinks during post-run, autoinjector, sequence
On when not ready,
Set GC to Ready
conditions
Top line: Status
Bottom line: messages and scrolling list
blinks for error condition
Stop a run

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MSD Productivity ChemStation Getting Started 17
Maintenance schedule
Detailed maintenance tasks are described in the hardware
manuals supplied with your system. How often you need to
perform system maintenance may vary for your system. Keep a
maintenance record.
Every day
Check, and if necessary, replace the septum.
Check the tightness of the inlet liners.
Check the tightness of the column nuts.
Every week
Check the foreline pump fluid level, if applicable.
Change the inlet liners and O-rings.
Every month
Clean the split/splitless inlet vent line trap.
Check for leaks (inlet, column connections).
Every 3 months
Replace gas cylinders (when below 500 psig).
Every 6 months
Replace the foreline pump fluid, if applicable.
Check, and if necessary, refill the calibration vial(s).
Every year
Check, and if necessary, replace the diffusion pump fluid.
Recondition or replace internal and external traps and
chemical filters on the GC.

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As needed
Tune the MSD.
Clean the ion source.
Replace the carrier gas trap.
Replace worn out parts (filaments, EM, etc.).
Replace the column.
Lubricate seals.
Safety warnings
WARNING Do not perform maintenance with the MSD on or connected to its
power source unless specifically instructed to by documentation
supplied with the MSD.
The GC/MSD interface can be on and at a dangerously high
temperature even though the MSD is off. After it is turned off, the
GC/MSD interface cools very slowly. Make sure all parts have
cooled before handling them.
Be careful when working behind the GC. During cool-down cycles,
the GC will emit hot exhaust that could cause burns.
If you are analyzing toxic chemicals or using toxic solvents, use a
hose to route the pump exhaust out of your laboratory. Note that the
oil trap provided with standard foreline pumps stops foreline pump
oil only, it does not trap or filter out toxic chemicals.
Use chemical-resistant gloves and safety glasses when replacing
pump fluid. Avoid all contact with the fluid.
The insulation around the inlets, detectors, valve box, and insulation
cups is made of refractory ceramic fibers (RCF). Avoid inhalation of
RCF particles. Ventilate your work area, wear long sleeves, gloves,
safety glasses, and a disposable respirator. Dispose of insulation in a
sealed plastic bag. Wash your hands with soap and cold water after
handling RCFs.

MSD Productivity ChemStation Quick Reference 1
MSD Productivity ChemStation Getting Started 19
Operating tips
Back up your data and methods regularly.
Make sure the tune file you are using is appropriate for
your samples.
Save Tune reports in a notebook for future reference.
Perform system maintenance as indicated by the
maintenance schedule in the GC and MSD hardware
documentation. Keep a record of all maintenance
performed.
When venting the MSD, take advantage of the cool GC to
do maintenance such as replacing inlet liners, septa, etc.
After pumpdown, wait at least 2 hours for the MSD to
reach thermal equilibrium before tuning or acquiring
data.
Optimum sensitivity generally occurs at column flow
rates of 1.2 mL/min or less.
When injecting volumes greater than one microliter, use
the pulsed splitless mode and increase the initial oven
temperature 10–20°C.
For splitless injections, pulsed splitless mode gives more
quantitative sample transfer onto the column. A pulse
pressure of twice the initial inlet pressure is typical.
Selecting Constant Flow mode will provide the most
efficient separation in most cases.
For a new column, check that the column nuts are still
tight after the first few oven temperature cycles.
Use the [Config] [Status] buttons on the Agilent 7890A
and 6890 GC keypads to set the three display items most
important to you (for example, time remaining, oven temp,
etc.). These are then always visible regardless of which
GC/MSD ChemStation view is on top.
Rinse and refill ALS wash vials. Do not add more solvent
to a partially full vial.

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Use the following table as a guide to using the SIM and/or
Scan acquisition modes.
When choosing masses for SIM, use the exact mass
printed in the Tabulation report, not the nominal mass
annotated on the spectrum display. This provides more
accurate data.
When doing SIM analysis, use low resolution mode unless
you are trying to determine the ratios of masses one amu
apart. Low resolution provides maximum sensitivity and
repeatability.
Choose the narrowest scan range that still produces good
library search results. This allows more spectra across
the peak and better quantitation.
Task Mode
Analyze a mixture with unknown components. Scan, or
SIM/Scan
Analyze a mixture with known components in
unknown amounts (quantitate).
Scan, or
SIM, or
SIM/Scan
Identify the presence of a few known
compounds at low levels within a mixture.
SIM