Agilent Technologies G1701DA User manual

Agilent Technologies
Agilent G1701DA
MSD ChemStation
5973 MSD / ChemStation
Quick Reference
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What’s New in Revision D.01.00
• A new toolbar has been added to the Top view
and an expanded set of toolbars have been
added to Data Analysis. Moving the cursor of
the mouse over a toolbar will display tool tips
(quick descriptions) for each of the buttons.
• The sequence user interface or sample log
table has been transformed into a
spreadsheet user interface.
• During sequencing the ABORT button in the
status panel has been changed to Pause.
When this is selected, the sequence will pause
immediately. When thesequenceis started,it
will restart the sequence from where it was
paused.
• Long files names are supported. Data file and
method paths can be up to 100 characters
long. The names of individual data files and
methods can be up to 50 characters long.
• User Interfaces for selecting or saving files
and directories have been enhanced with
browse buttons.
• Support for 5973A and 6890A instruments
using GPIB has been restored.
• It is now possible to disable Method
Resolution for most changes in the 6890
configuration.
• The Manual Tune and Diagnostics / Vacuum
Control views have be merged into a single
view, Tune and Vacuum Control.
• A Tune Wizard has been provided to simplify
the modification of criteria (tune limits,
target ratios) used by the tuning algorithms.
• Loading data files in Data Analysis will now
preview the chromatogram.
• The method has been expanded to permit
printers other than the default printer to be
used for reports generated during Run
Method.
• Headers in Data Analysis reports are now
configurable for the reports generated by Run
Method.
• An improved BOOTP service has replaced the
previous BOOTP program. The new BOOTP
service will not interfere with shutting down or
logging off the computer.
• The SICL drivers have been updated to version
L.02.01 . Version M.01.01 is on the software
CD and is for GPIB support.
Use the online help to learn about these
new features as well as to learn about
instrumentcontrol,dataacquisition,data
analysis,methods,sequencing,tuning,and
how to use system commands and
variables. Troubleshooting the MSD is
included to help you diagnose problems.
Online Help
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Using Online Help
To access the online help, select Help
Topics from the Help menu in any
window, or click the Help button on any
dialog box.
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. Indicates a book containing more help topics.
To open a book, select it then double-click.
Indicates an open book of help topics. To close
an open book, select it then double-click.
Indicates a help topic. To jump to a help topic,
select it then double-click.
Help Icons
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5973 MSD with a 6890 GC
Column oven
5973 MSD
Status display
6890 GC
Keypad
Status board
ALS tower
On/off switch
Local control
panel
ALS tray
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GC Keypad
The MSD ChemStation software provides instrument control for the 6890 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.
Stop a run
Display column information Prepare a run (manual injection)
Start a run (manual injection)
Display the oven
temperature
Display the GC/MSD
interface temperature
(Thermal Aux 2)
Display the front injection
port temperature
Display the rear injection
port temperature
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Instrument Control View
Acquisition Status Lets you tell at a glance the status of the current
instrument or run (if any).
Start Button Lets you start a run. When a run is not in progress, the
arrow is green. To start a run, click the green arrow, fill in the Sample
Information, and click Start Run. When a run is in progress, the arrow
is gray.
This button also shows the current data file name, sample information
(if any), and the vial number (1 if no ALS).
See the online help for more details
on the menus, buttons, or windows
used in the software.
The Instrument Control view is displayed when you start up
the MSD ChemStation. This is where you set and monitor
instrument parameters. If you are in a different view, select
View / Instrument Control when you are ready to set up the
system for data acquisition.
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Run Time Clock Shows the elapsed time since the beginning of the
run if a run is in progress. The scheduled run time is shown below
the digital clock. When a run is not in progress, the Run Time clock
shows the elapsed time since the last run.
Stop Button Lets you stop the system when it is in Pre-Run,
Run, or Post-Run mode. The stop sign is red when a run is in
progress and gray when a run is not in progress.
Logbook Button Displays a menu where you can choose to view,
open, clear, save, or print a particular logbook.
Help Button Displays a menu where you can select an online help
topic for the Instrument Control view. Choose Help Topics to go to
the online help for the entire system.
Injector Button Lets you set parameters for the injector when
you have configured your system with an ALS.
Inlets Button Lets you set parameters for the GC inlet (injection
port) that is configured on your system.
Columns Button Lets you configure columns and set up ramped
flow and pressure programs.
Oven Button Displays a menu that lets you edit GC oven
parameters or GC monitor parameters. When the GC is ready, the
small square in the upper right corner is green. When the GC is not
ready, the square is red.
Aux Button Lets you set the temperature of the GC/MSD
interface (usually Thermal Aux 2).
MS Button Displays a menu that lets you edit MS acquisition
parameters, select another tune file, or edit MS monitors.
Monitor Each monitor displays one instrument parameter. See
the online help for a description of the instrument monitors.
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Top Menus
Sequence
Run...
Load...
Save...
Edit Sample Log Table...
Load and Run Sequence...
Print Sequence...
1
2
3
4
Simulate Sequence
Position and Run...
View Sequence Log...
View Sequence Quality Log
Print Sequence Log
Import Sequence Information from CSV file...
Batch Mode...
More...
Method
Run...
Load...
Save...
Edit Entire Method...
Print
1
2
3
4
Set New Default Paths...
Exit
Secured Control
Enable Security...
Start Secured Control...
Select Methods for Secured Control...
Set/Change Startup Method <...>
Set Change Standby Method <...>
Assign Sample Names to Method...
Use Sample-centric Secured Control...
Report Manager password...
Edit Accounts...
View
Help
Help Topics
Using Help
View Revision Readme File
Review Revision History...
About
Top
Instrument Control
Data Analysis (offline)
Select View / Top to access
these menus.
The software menus shown on the following
pages are for an MSD ChemStation in
Enhanced Mode.
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Top Toolbar
Load Sequence Loads the selected sequence.
Save Sequence Saves the specified sequence.
Run Sequence Saves the specified sequence.
Edit Sequence Lets you set up or modify the sample log
table.
Print Sequence Prints the current sequence.
Simulate Sequence Simulates the current sequence.
Load Method Loads the selected method.
Save Method Saves the specified method.
Run Method Runs the current method. The Start Run
dialog box is displayed.
Edit Method Lets you modify the method parameters
for the current method.
Print Method Prints the current method.
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Instrument Control Menus
Method
Run...
Load...
Save...
Edit Entire Method...
Additional Method Information...
Print
1
2
3
4
Exit
Abort
Abort
View
Top
Instrument Control
Data Analysis (offline)
Tune and Vacuum Control...
Instrument
Inlet/Injection Types
GC Edit Parameters...
GC Plot...
GC Monitors...
Acquire RTLock Calibration Data...
Unlock Method...
Disable Method Resolution
Select MS Tune File...
MS SIM/Scan Parameters...
Change MSD Temperatures...
MS Monitors...
Edit MS Tune Parameters...
Perform MS Autotune...
EMF Utilities...
Select View / Instrument Control to
access these menus.
Window
Cascade
Tile Horizontal
Tile Vertical
Arrange Icons
Arrange Plots and Monitors
1
2
3
4
Qualify
Checkout Tune
Tune Evaluation
View Tunes...
Sensitivity Check
Software Validation
Installation Checklist
Familiarization Checklist
Help
Help Topics
Using Help
Review Revision History...
View Revision Readme File
About
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Tune and Vacuum Control Menus
File
Reset to Defaults
Load Tune Values...
Save Tune Values...
Trace on
View Trace...
Instrument Trace...
Print
Printer Orientation...
Generate Report...
View Tunes...
Set View Tunes Report Options...
Restore Previous Tune(s)...
Exit
Select View / Tune and Vacuum
Control from Instrument Control to
access these menus.
Status
MS Status
MS I/O Test
MS Temperature Controller Status
View Instrument Macro Log...
View Tune Log...
Clear Instrument Macro Log...
Clear Tune Log...
MS Error Codes...
Logbook/Sequence Log Error Codes...
Vacuum
Vacuum Status...
Pump Down...
Vent...
Purge Calibrant Valve
Power-on Temperatures
Initialize MS Interface
Parameters
Help
Help Topics
Troubleshooting
Using Help
About
Abort
Abort
View
Top
Instrument Control
Data Analysis (offline)
Manual Tune...
Edit Tune and Display Parameters...
Edit MS Temperatures...
Edit Ramp Parameters...
Edit Dynamically Ramped Parameters...
Tune
Tune MSD
QuickTune
Autotune (Atune.U)
Low Mass Autotune (Lomass.U)
Standard Spectra Tune (Stune.U)
DFTPP Tune (DFTPP.U)
BFB Tune (BFB.U)
Tune Wizard...
Air and Water Check
Tune Evaluation
Execute
MS ON
MS OFF
Profile scan
Repeat profile
Detailed profile
Ramp Lenses
Spectrum scan
Find mass...
Determine Mass Axis Correction Factors
Optimize Quadrupole Frequency
Calibrate
Mass axis
Mass #2 widths
Mass #3 widths
Peakwidth Linearity
Adjust Abundances
Ramp Repeller
Ramp Ion Focus
Ramp Entrance Lens
Ramp Entrance Lens Offset
Maximize Sensitivity
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Data Analysis Menus
Quantitate
Calibrate
Calculate
Generate Report
Use Classic Reports
Report Options...
Report Non Target Peaks...
Use Method Aligned GC trace
Trace Mode Quant...
Custom Reports...
Print Report
Update Database
Select Template/Database
Set Up Quantitation...
AutoQuant Setup
Edit Compounds...
Update...
List...
Clear...
Spectrum
Add
Subtract
Tabulate
Select Library...
Edit Strategy...
Edit Library...
Library Search Report
Change Spectral Display...
Find Mass Spectrum
Chromatogram
Chromatogram Scaling...
Draw Chromatogram - No Labels
Draw Chromatogram With Labels
Select Chromatogram Labels...
Extract Ion Chromatograms
Display Ion Chromatograms in Merged Format
Select Integrator
MS Signal Integration Parameters...
GC Signal Integration Parameters...
AutoIntegrate
Integrate
Integration Results...
Percent Report
Method
Run Method...
Run CustomAnalysis
Load Method...
Save Method...
Edit Method...
Edit CustomAnalysis...
Generate AutoSIM Method...
1
2
3
Batch Mode...
File
Load Data File...
Next Data File
List Header...
Edit File Info...
Take Snapshot
Subtract Background (BSB)
Select Signals...
Select Printer...
Printer Setup...
Print
Abort
Export Data to CSV File...
Export Data to AIA format...
Import AIA Raw Data Files...
1
2
3
Exit
Tools
DOLIST...
DOSCAN...
Process Scan List
Export 3-D Data...
Locate A Compound...
Locate All Compounds...
Set Overlay Parameters...
Overlay Chromatograms...
Signal to Noise check...
Change Data State...
Options...
Configure Report Headers...
Generate Screen Results for Current File
Generate Screen Report for Current File
Generate/Print Screen Report for Current File
Generate/Print Screen Report for Multiple Files...
Specify Method Screen Database...
Change Screen Database Parameters...
List Screen Database...
Exclude Zero Qualifiers
Copy Window...
Reset Windows...
View
EasyID
QEdit Quant Result
Edit Non Target Peaks
Parametric Retrieval
Align GC
Review Peak Purity
Results Screener
RTLock Setup
Help
Help Topics
Using Help
Review Revision History...
View Revision Readme file
About
Select View / Data Analysis (offline) to
access these menus.
The View menu in Data Analysis lets you
access other Data Analysis modes
(shown on the following pages).
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EasyID Menus
QEdit
View
Data Analysis
ChromEval
Evaluate Resolution
Evaluate Tailing
Evaluate Degradation
Spectrum
Draw Next
Draw Previous
Tabulate
Add
Subtract
Select Library...
Edit Strategy...
Edit Library...
Display Reference Spectra
Update Reference Spectrum
Select View / QEdit Quant Result in
Data Analysis to access these menus.
EasyID
Co Next Compound
Goto Compound #
Xpand Chromatographic Window +/- 2 minutes
Original Chromatographic Window
Graphics Report to the Printer
Restart Quick QEdit
Set Extract Window Start
Set Extract Window Stop
Abort Changes and Exit
Exit and Save Changes
Integrate
Integration Parameters
Save compound specific integration parameters
Remove compound specific integration parameters
Integrate
Select View / EasyID in Data
Analysis to access these menus.
QEdit Menus
CO Next Compound
Goto Compound
Xpand Chromatographic Window
Original Chromatographic Window
Graphics Report to the Printer
QDEL Compound
Next File
Load Data File...
Restart Quick QEdit
Abort Changes and Exit
Exit and Save Changes
Spectrum
Draw Next
Draw Previous
Tabulate
Add
Subtract
Select Library...
Edit Strategy...
Edit Library...
Display Reference Spectra
ChromEval
Evaluate Resolution
Evaluate Tailing
Evaluate Degradation
View
Data Analysis
Display
Normal
Qualifiers
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Parametric Retrieval Menus
Structures
Retrieve
Select Structure Database...
Set Structure Parameters...
Set Parameters...
Select Library...
Continue Results
Spectrum
Draw Next
Draw Previous
Tabulate
Add
Normalized Subtract
Library
Select Library...
Edit Strategy...
Edit Library...
Library Search Report...
Read JCAMP File...
Write JCAMP File...
Subset Library...
Add Current Entry
File
Load...
List Header
Take Snapshot
Subtract Background (BSB)
Print Current View
Save Parameters
Abort
Exit
Options
Select Normalization Ion
Extend Database Headers...
Command Line
Stack
Manual Integration
Copy Window...
Reset Windows
View
Standard Menu
Library Entry Only
TIC and Library Entry
Unknown and Library Entry
Unknown, Library Entry, and Difference
Help
Help Topics
About
Select View / Parametric Retrieval in
Data Analysis to access these menus.
Align GC Menus
Alignment
Select View / Align GC in Data
Analysis to access these menus.
Show Current Method Alignment Points
Perform Alignment
Restore Alignment Chromatograms
Abort
Exit/Save
View
Data Analysis
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Review Peak Purity Menus
Quick Screener Menus
PkPurity
Select View / Review Peak Purity in
Data Analysis to access these menus.
Next Peak
Previous Peak
Select Peak...
Print Selected Window...
Return to DA
Spectrum
Add
Subtract
Tabulate
Help
Help Topics
Peak Purity
Using Help
RTLock Menus
Select View / RTLock Setup in
Data Analysis to access these menus.
RTLock
View Current Method Setpoints
Calculate New Curve from Selected Peaks
Restore Nominal Chromatogram
.
Report RTLock Calibration...
Print...
Relock Method...
Use AutoRelock
Unlock Method...
View
Data Analysis
Help
Help...
Select View / Results Screener in
Data Analysis to access these menus.
Screener
CO Next Compound
Goto Compound
Xpand Chromatographic Window
Original Chromatographic Window
Graphics Report to the Printer
QDEL Compound
Next File
Load Data File...
Restart Quick Screener
ReRun Screen
Abort Changes and Exit
Exit and Save Changes
Spectrum
Draw Next
Draw Previous
Tabulate
Add
Subtract
Select Library...
Edit Strategy...
Edit Library...
Display Reference Spectra
ChromEval
Evaluate Resolution
Evaluate Tailing
Evaluate Degradation
View
Data Analysis
Display
Normal
Qualifiers
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Data Analysis Toolbar Buttons
Load Data File Loads the selected data
(.D) file and displays the total ion
chromatogram (TIC) for that file.
Load Method Loads the selected method
(.M) file.
Save Method Saves any changes made to
the current method.
Take Snapshot Displays the data that
has been acquired up to the time the
snapshot is activated. GC/MS data only.
Print Lets you print the selected window,
the TIC and spectrum, or the current
method.
Copy Window Lets you copy the selected
window to the clipboard.
Reset Windows Rearranges the graphics
windows to their default positions.
Execute Command Executes the command
that is typed into the command line.
Abort Stops a command or macro.
Toggle Command Line Turns the display of
the command line on or off.
Edit Colors Lets you adjust the colors of
various display items in Data Analysis.
Toggle Graphics Lets you minimize or
maximize the displayed graphics.
Close Screen Reports Closes the currently
displayed screen reports.
EasyID Lets you update expected
retention times and ion ratios for MS data
in an existing quantitation database on a
compound-by-compound basis.
QEdit Quant Result Lets you review and
edit quantitation results once a data file
has been quantitated.
Generate Signal-to-Noise Report Lets
you perform a signal-to-noise check and
then display or print the report.
Review Peak Purity Helps you detect
overlapping peaks (multiple-component
peaks) in your chromatogram.
Retention Time Locking Accesses the
RTLock Setup view which is used for
retention time locking tasks.
CUSTOMTOOL1 Lets you run a
user-created macro. This macro must first
be created and then named CUSTOMTOOL1.
See the online help for Using and Writing
Macros, and Data Analysis Commands.
CUSTOMTOOL2 Lets you run a
user-created macro. This macro must first
be created and then named CUSTOMTOOL2.
See the online help for Using and Writing
Macros, and Data Analysis Commands.
CUSTOMTOOL3 Lets you run a
user-created macro. This macro must first
be created and then named CUSTOMTOOL3.
See the online help for Using and Writing
Macros, and Data Analysis Commands.
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Draw Chromatogram Redraws the original
chromatogram of the current data file
without labels or integration marks.
Scale Chromatogram Scales the selected
chromatogram by the specified scale
factors.
Extract Ion Chromatogram Extracts and
displays extracted ion chromatograms
(EICs) from the total ion chromatogram
(TIC) of the current data file.
Merged Format Causes extracted ion
chromatograms to be displayed overlaid on
each other.
Overlay Chromatograms Lets you select
multiple chromatograms to be displayed
superimposed on each other.
AutoIntegrate Tries to find the best
integration parameters for the current
chromatogram and then integrates the
chromatogram.
Integrate Integrates the current
chromatogram using parameters set for
the current integrator.
Subtract Spectrum Subtracts one
spectrum from another and displays the
difference.
Select Library Lets you select the libraries
that will be used for PBM searches of the
currently selected spectrum.
Library Search Report Integrates the
current TIC, searches the current library,
and generates a report.
Set Up Quantitation Lets you set up a
quantitation database by specifying
quantitation database globals and entering
compounds into the database.
AutoQuant Setup Provides a semi-
automated way to create a quantitation
database.
Edit Compounds Lets you review and edit
information in the quantitation database
compound-by-compound.
Update Calibration Lets you add, delete,
or update a calibration level in the current
quantitation database.
Calculate Quant Report Quantitates the
current file and generates a quantitation
report.
Generate Quant Report Generates a
quantitation report for a file that has
already been quantitated.
Print Quant Report Prints the
quantitation report.
Custom Reports Starts the Custom
Reports software. If the method does not
have a quantitation database, or no data
file is loaded, you can use default values.
Print Custom Report Prints the custom
report template specified by the method
using the current data file.
Online Help Displays the MSD
ChemStation online help.
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To vent (shut down) the MSD
1If your system is equipped with a gauge
controller, switch off the triode gauge
controller.
2Before venting a CI MSD, press the Gas Off
button (turns off the reagent gas flow and
closes the isolation valve.)
3From the Tune and Vacuum Control view,
select Vent from the Vacuum menu in the
software. Follow the instructions presented.
4Set the GC/MSD interface heater and the GC
oven temperatures to ambient (25°C).
5When prompted, turn off the MSD power
switch.
6Unplug the MSD power cord.
7Remove the analyzer cover.
8Turn the vent valve knob counterclockwise only
3/4 turns or until you hear the hissing sound
of air flowing into the analyzer chamber.
WARNING
On a CI MSD, the Gas Off light must be on when the
MSD is venting.
WARNING
If you are using hydrogen as a carrier gas, the carrier
gas flow must be off before turning off the MSD
power. If the foreline pump is off, hydrogen will
accumulate in the MSD and an explosion may occur.
Read the Hydrogen Carrier Gas Safety Guide
(5955-5398) before operating the MSD with
hydrogen carrier gas.
CAUTION
BesuretheGCovenandGC/MSDinterfacearecool
before turning off carrier gas flow.
CAUTION
Do not turn the knob too far, or the O-ring may fall
out of its groove. Be sure to retighten the knob
before pumping down.
WARNING
Allow the analyzer to cool to near room temperature
before touching it.
CAUTION
Always wear clean gloves while handling any parts
that go inside the analyzer chamber.
WARNING
WhentheMSDisvented,donotputtheChemStation
into the Top view. Doing so will turn on the interface
heater.
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To pump down (start up) the MSD
1Make sure your system meets all of the
following conditions before you pump down:
oThe vent valve is closed (the knob is turned
all the way clockwise.)
oAll other vacuum seals and fittings are in
place and fastened correctly. (The front
side plate screw should not be tightened
unless hazardous carrier or reagent
gases are being used.)
oThe MSD is connected to a grounded power
source.
oThe GC/MSD interface extends into the
GC oven.
oA conditioned capillary column is installed in
the GC inlet and in the GC/MSD interface.
oThe GC is on, but the heated zones for the
GC/MSD interface, the injection port, and
the oven are off.
oCarrier gas of at least 99.999% purity is
plumbed to the GC with the recommended
traps.
oIf hydrogen is used as carrier gas, carrier
gas flow is off and the front sideplate
thumbscrew is loosely fastened.
oThe foreline pump exhaust is properly
vented.
2Select Tune and Vacuum Control from the
View menu.
3Select Pump Down from the Vacuum menu.
4When prompted, switch on the MSD.
WARNING
MakesureyourMSD meetsALLtheconditions listed
above. Failure to do so can result in personal injury.
5Press lightly on the side board to ensure a
correct seal.
The rough pump will make a gurgling noise.
This noise should stop within a minute. If the
noise continues, there is a large air leak in
your system, probably at the side plate seal,
the interface column nut, or the vent valve.
6Once communication with the PC is
established, click OK. Within 10 to 15 minutes
the diffusion pump should behot, or the turbo
pump speed up to 80%. The turbo pump
should eventually reach 95%.
7When prompted, turn on the GC/MSD
interface heater and GC oven. Click OK when
you have done so. The software will turn on
theionsourceandmassfilter(quad)heaters.
The temperature setpoints are stored in the
current autotune (*.u) file.
8After the message Ok to run appears, wait
two hours for the MSD to reach thermal
equilibrium.
CAUTION
If these conditions are not met, the foreline pump
willbeshutoff. YoumustthenpowercycletheMSD.
If the MSD does not pump down correctly, see the
online help for information on troubleshooting air
leaks and other vacuum problems.
CAUTION
Do not turn on any GC heated zones until carrier
gasflowison. Heatingacolumnwithnocarriergas
flow will damage the column.
CAUTION
DataacquiredbeforetheMSDhasreachedthermal
equilibrium might not be reproducible.
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To tune your MSD
You should tune the MSD periodically to maintain
its optimum performance. Tuning is the process
of adjusting MSD parameters so the instrument
meets certain performance criteria. How often
you should tune is determined by the number and
type of samples you are running, as well as the
overall condition of your system.
Note Always tune the MSD with the same GC
oven temperature and column flow, and the same
analyzer temperature that will be used for data
acquisition.
Keep the Tune reports in a notebook so that
successive reports can be easily compared.
To use Autotune
1From the Instrument Control view, select
Perform MS Autotune from the Instrument
menu.
2Select one of the following options, depending
on the instrument performance required by
your application, then click OK.
oAutotune
Results in maximum sensitivity over the full
scan range.
oLow Mass Autotune
Tunes for the low-mass range.
oStandard Spectra Tune
Results in a standard response over the
full scan range. This option may reduce
sensitivity.
oQuickTune
Adjusts the peak width, mass assignment,
and abundance without changing ion ratios.
3Review the Tune report.
4To view the history of tune results, select View
Tunes from the Qualify menu.
To use Manual Tune
Manual tuning lets you interactively set the MSD
parameters, such as lens voltages and tuning
masses, to values that meet the needs of your
particular analysis. You can often obtain greater
sensitivity than you can with autotune.
Manual tuning allows you to ramp individual
parameters and to specify the range and step
size for the ramp. The results of the ramp are
displayed visually with the optimum value for the
parameter clearly marked on the plot.
You can acquire two types of data in manual
tune: profile scans (plots the abundance and
peak shape of the tune masses) and spectrum
scans (scans plot response across the entire
mass range).
See the online help for more details about manual
tuning.
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