Agilent Technologies G1701EA User manual

Agilent Technologies
Agilent G1701EA MSD
Productivity
ChemStation
Familiarization Guide

Notices
© Agilent Technologies, Inc. 2012
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Manual Part Number
G1701-90070
Edition
Second edition, June 2012
Printed in USA
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Santa Clara, CA 95051 USA
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Agilent G1701EA MSD Productivity ChemStation Familiarization Guide 3
In This Guide
This guide contains a step-by-step exercise to help you become
familiar with your Agilent 7890A GC/5975 MSD with G1701EA
MSD Productivity ChemStation software.
To successfully use this book, you need the following:
Before operating your instruments, be sure to read all safety
and regulatory information included with your instruments.
1Start Up the System
Start up your system hardware and software for data
acquisition.
2Tune the MS
Determine whether the instrument is correctly tuned.
3Create a Method for Qualitative Analysis
Create a new qualitative analysis scan method from the system
default method.
4Run the Scan Method
Run the method created in Chapter 3to acquire sample data.
5Qualitative Data Analysis
Use the Enhanced Data Analysis program to analyze the data
generated in Chapter 4.
6Create a SIM Quantitation Method
Create a SIM method from the scan method created in
Chapter 3.
7Run a Sequence
Create and run a sequence using the method created in
Chapter 6.
•GC Inlet: Split/Splitless Inlet with EPC
(default inlet configuration)
•Column: HP-5ms 30 m x 250 µm x 0.25 µm
•Sample: 5975 MSD Sample (P/N 05970-60045) or
(P/N 5074-3025 Japan only)
•MSD Tuning
Calibrator:
PFTBA (perfluorotributylamine)

4 Agilent G1701EA MSD Productivity ChemStation
8Set Up a Quantitation Database
Set up a database with compounds and calibrators to identify
unknown samples.
9Generate a Report
Generate a report automatically after a run or at a later point
from previously acquired data.
10 Recalibrate and Quantitate Unknowns
Modify a sequence for recalibration and then use it to
quantitate an unknown sample.
11 Create a Cool Down Method
Create and store a maintenance method.
12 Shut Down the System
13 Frequently Asked Questions

Agilent G1701EA MSD Productivity ChemStation Familiarization Guide 5
Where to Find Information
Hardware
In addition to this document, Agilent provides several learning
products that document how to install, operate, maintain, and
troubleshoot the 7890A GC/5975 MSD. This information can be found
on the Agilent Technologies GC and GC/MS Hardware User
Information and Utilities DVDs that ship with your instrument.
The Agilent Technologies GC and GC/MS Hardware User Information
and Utilities DVDs that ship with your instrument provides an
extensive collection of online help, videos, and books for current
Agilent gas chromatographs, mass selective detectors, ion traps, and
GC samplers. 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
Software
For an introduction to, and where to find more information on,
the G1701EA MSD Productivity ChemStation see the Agilent
G1701EA GC/MSD ChemStation Getting Started manual.

6 Agilent G1701EA MSD Productivity ChemStation

Agilent G1701EA MSD Productivity ChemStation Familiarization Guide 7
Contents
1 Start Up the System
Start up the Hardware 12
Run the ChemStation Software 14
Select the Tune File 15
Load the Method 16
2 Tune the MS
Introduction 18
Run Autotune 19
Evaluate the Autotune Results 22
Tune History Trends 24
3 Create a Method for Qualitative Analysis
Introduction 26
Edit the Entire Method 27
Check the GC configuration 29
Set the GC readiness state 32
Set the GC oven parameters 33
Set the GC column parameters 35
Set the GC inlet parameters 36
Set the GC injector parameters 38
Set the GC Aux heaters parameters 40
Set the GC signals parameters 40
Edit the GC real time plots to display 42
Edit the MS parameters 42
Save the method 46
General Information for Editing the GC Parameters 47
Open the GC edit parameters window 47
Add a column to ChemStation local inventory 48
Select and configure a column 51
Upload parameters from the 7890A GC 53
Customize the status panel view 53

8 Agilent G1701EA MSD Productivity ChemStation Familiarization Guide
4 Run the Scan Method
Prepare the Sample 56
Load the Method 57
Run the Method 58
Take a Snapshot 61
View the Logbook 62
5 Qualitative Data Analysis
Integrate Peaks 66
Edit the integration events 69
Save the integration events to the method 70
Manually integrate peaks 71
View the integration results in a table 72
Edit the Method to Generate a Report 74
Display Extracted Ion Chromatograms (EIC)s 76
Enable or Disable the Right Mouse Click Context Menu 78
Analyze Data 79
Subtract the baseline noise from the spectra 81
Select target and qualifier ions 82
Search the Spectral Library 83
Generate an automated library search report 84
Print a Window, TIC, Spectrum, or Method 86
Select a printer 86
Select an item to print 87
Save the Data Analysis Method 87
Exit the Data Analysis Program 88
6 Create a SIM Quantitation Method
Introduction 90
Create a SIM Method 91
Simultaneously Acquire Scan and SIM Data (SIM/Scan Mode) 96
SIM/Scan Mode Cycle Frequency 98
7 Run a Sequence
Prepare the Samples 100
Create the Sequence 101

Agilent G1701EA MSD Productivity ChemStation Familiarization Guide 9
Save the Sequence 103
Load the Sequence 104
Run the Sequence 105
Print the Sequence Log 106
8 Set Up a Quantitation Database
Add Compound Entries for the Database 108
Identify compounds 112
Add the Calibration Curve 115
Add calibrator level 1 115
Add calibrator levels 5, 10, 25, and 50 to the calibration curve 117
Save the database 119
View or Edit an Existing Database 120
9 Generate a Report
Generate a Report Automatically After the Run 124
Load the method 124
Edit the method to generate a report 124
Run the method and generate the report 127
Generate a Detailed Report for Previously Acquired Data 129
Load the method 129
Load the data file 129
Generate a detailed quantitation report 129
10 Recalibrate and Quantitate Unknowns
Create a Recalibration Sequence 132
Save the Sequence 134
Run the Sequence 135
11 Create a Cool Down Method
Create the Cool Down Method 138
Use the Cool Down Method 139
12 Shut Down the System
Shut Down the MS 142
Shut Down the GC 143
13 Frequently Asked Questions

10 Agilent G1701EA MSD Productivity ChemStation Familiarization Guide

11
Agilent G1701EA MSD Productivity ChemStation
Familiarization Guide
Agilent Technologies
1
Start Up the System
Start up the Hardware 12
Run the ChemStation Software 14
Select the Tune File 15
Load the Method 16
In this chapter, the startup checklist is reviewed for instrument
readiness. If necessary, changes are made to the instrument
hardware configuration to handle the data acquisition of the
samples that are run in this manual. With the instruments off
and the G1701EA MSD Productivity ChemStation not running,
the instruments are started and the MSD is pumped down.
Finally, a method is loaded in preparation for bringing all
instrument parameters to settings required for data acquisition.

12 Agilent G1701EA MSD Productivity ChemStation Familiarization Guide
1Start Up the System
Start up the Hardware
1Review the Agilent 7890A Gas Chromatograph Operating
Guide (P/N G3430-90011) and the Agilent 5975 Series MSD
Operation Manual (P/N G3170-90036) for important safety
information and start up details before powering on your
instruments.
2Verify that the split/splitless (S/SL) inlet septum, liner, and
O-ring are clean, properly installed, and in good condition.
3Install a conditioned (HP-5ms 30 m x 250 µm x 0.25 µm)
column in the GC. Attach the column inlet to the S/SL inlet
and its outlet to the MSD transfer line. See the Agilent 5975
Series MSD Operation Manual for details.
4Verify the EI ion source is installed.
5Verify 99.9995% purity helium is attached to the carrier gas
supply of the S/SL inlet.
6Power on the 7890A GC.
7From the GC keypad, turn off the oven, Aux 2 heated zone
(GC/MSD transfer line), and inlet heater. If equipped, turn
off any GC detectors.
8Before you turn on or attempt to operate the MSD verify the
following:
•The vent valve must be closed (the knob turned all the
way clockwise).
•All other vacuum seals and fittings must be in place and
fastened correctly.
•The front side plate screw should not be tightened.
•The MSD is connected to a grounded power source.
•The GC/MSD interface extends into the GC oven.
•A conditioned capillary column is installed in the GC
inlet and in the GC/MSD interface.
•The GC is on, but the heated zones for the GC/MSD
interface, the GC inlet, and the oven are off.
•Carrier gas of at least 99.9995% purity is plumbed to the
GC with the recommended traps.
•The foreline pump exhaust is properly vented.
9Open the MSD analyzer top cover.
10 Close the MSD vent valve.
11 Press the Power button on the front of the MSD to power it
on. The foreline pump will make a gurgling noise.

Start Up the System 1
Agilent G1701EA MSD Productivity ChemStation Familiarization Guide 13
Press lightly on the metal box mounted on the MSD side
board until the air noise stops to ensure a correct seal.
12 Close the MSD analyzer top cover.
13 On the MSD local control panel:
aPress Menu repeatedly until Maintenance appears.
bPress Item repeatedly until Pumpdown appears.
cPress Yes/Select to start the pumpdown.
The pumpdown is completely automatic and does not require
operator actions.
After the turbo pump starts and the ion gauge value reaches
100 mTorr, allow the MSD to operate for a minimum of 2 hours
before acquiring sample data.

14 Agilent G1701EA MSD Productivity ChemStation Familiarization Guide
1Start Up the System
Run the ChemStation Software
The GC and MSD must both be running before starting an online
session of the ChemStation product. If reports are to be printed,
a printer must be installed on the computer.
1Power on the PC.
2From the PC desktop, select the ChemStation Instrument
Control shortcut icon, to display the Enhanced ChemStation
Instrument Control window.
3If the Actual MS temperatures have not reached their
Setpoints, the MS Temperatures dialog box will appear. Enter
new setpoints if needed and click OK. The screen will appear
repeatedly until the temperatures are reached.
4Set the default printer to PDF Printer, if a PDF writer like
Adobe Acrobat is installed on the computer.

Start Up the System 1
Agilent G1701EA MSD Productivity ChemStation Familiarization Guide 15
Select the Tune File
1From the Enhanced ChemStation main control window, select
View > Tune and Vacuum Control…. to display the Tune and
Vacuum Control window.
2Select File > Load Tune Parameters. The Select Tune File dialog
box opens.
3From the Files list, select atune.u. The atune.u file contains the
optimal MSD parameter settings determined during the last
autotune run.
4Select OK. The atune.u tune file is loaded and the dialog box
closes.

16 Agilent G1701EA MSD Productivity ChemStation Familiarization Guide
1Start Up the System
Load the Method
1Select View > Instrument Control to close the Tune and Vacuum
Control…. and display the Enhanced ChemStation Instrument
Control window.
2Select the Load Method button, . The Load Method
dialog box opens.
3Navigate to and select default.m in the msdchem/1/methods
directory.
4Select OK.

17
Agilent G1701EA MSD Productivity ChemStation
Familiarization Guide
Agilent Technologies
2
Tune the MS
Introduction 18
Run Autotune 19
Evaluate the Autotune Results 22
Tune History Trends 24
This chapter provides a brief introduction to tuning and
explains how to run an autotune on the instrument. An
autotune report is generated as well as a report to evaluate the
autotune results. This report is reviewed to see which items
pass or fail the evaluation. Finally, we look at how we can
graphically view the variation in tuned parameters that are
plotted over a number of recent autotune runs.

18 Agilent G1701EA MSD Productivity ChemStation Familiarization Guide
2Tune the MS
Introduction
Tuning is the process that adjusts the MS for good performance
over the entire mass range. Using a known compound as a
calibrator, the tune parameters are set to achieve sensitivity,
resolution, and mass assignments for the known calibration
ions.
Tuning is performed using either the autotune or manual tune
features.
Manual tune allows you to adjust an MS tune parameter while
viewing the results easily in profile scans and spectra.
Manual tuning is used:
•To achieve maximum sensitivity by sacrificing some
resolution
•To tune specifically for the very low end of the mass range
(< 150 amu)
•To tune with a compound other than the standard calibrator
To access manual tune parameters select Parameters > Manual
Tune from the Tune and Vacuum Control window or select Instrument
> Edit MS Tune Parameters from the Instrument Control window.
Please see the ChemStation online help for details on using
manual tune.
The autotune program described in this section adjusts the MS
for good performance over the entire mass range and is
recommended for most applications.

Tune the MS 2
Agilent G1701EA MSD Productivity ChemStation Familiarization Guide 19
Run Autotune
1From the Instrument Control window select Instrument > Tune
MSD... to display the Select Tune Type dialog box.
2Select Tune MSD and click OK to close the dialog box and
start the autotune procedure.
The system uses the PFTBA (perfluorotributylamine)
calibrator to tune the instrument. When the tune is
complete, the mass 69, 219, and 502 profile scans are
displayed with abundance and peak widths noted. See
Figure 1. The tune report is also generated as shown in
Figure 2on page 21.

20 Agilent G1701EA MSD Productivity ChemStation Familiarization Guide
2Tune the MS
Figure 1 Profile scan results for mass 69, 219, and 502