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HP 5973 MSD System

with PCI/NCI

Quick Reference
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Learning About Your System
HP 5973 MSD
PCI/NCI Reference Collection
This CD-ROM
includes CI theory
of operation and
useful application
tips.
Use this book to learn
HP 5973 MSD how to operate and
Hardware Manual maintain your HP 5973
MSD hardware.
Use this book to learn
HP 6890 Series GC
how to maintain your
Maintenance and GC. Troubleshooting is
Troubleshooting included to help you
Manual diagnose problems.
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Online Help
Use the online help to learn about
instrument control, data acquisition, data
analysis, methods, sequencing, tuning, and
how to use system commands and
variables. Troubleshooting the MSD is
included to help you diagnose problems.
Use this book to learn
HP 5973 MSD how to operate and
PCI/NCI Hardware maintain the CI
Manual (chemical ionization)
hardware.
HP 6890 Series GC Use this book to learn
Operating Manual how to operate your
HP 6890 Series GC.
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Using Online Help

When you jump to a help topic, it

is displayed in another help
To access the online help, select
window. Click the Contents
Contents from the Help menu in any
button in that window to return
window, or click the Help button on any
to this list of help topics.
dialog box.

Item Description
Contents Displays the list of help topics
(shown to the right).
Index Lets you use keywords to
search the help index for a
particular topic.
Find Lets you type a word or phrase
and then displays a list of all
the topics in the online help
that contain those words.
Open Opens the selected book or help
topic. When you open a book or
select a book that is already
open, this button changes to Help Icons
Close.
Print Prints the selected book or help Indicates a book containing more help topics.
topic for future reference. If you To open a book, select it then double-click or
select a book, then all the help click the Open button.
topics contained in the book are
Indicates an open book of help topics. To close
printed. To print a popup, click
an open book, select it then double-click or
on it with the right mouse
click the Close button.
button and select Print from
the menu. Indicates a help topic. To jump to a help topic,
Cancel Closes the Help Topics window. select it then double-click or click the Open
button.

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HP 5973 MSD System with PCI/NCI

ALS
Bar code reader Injection port

GC status display

GC status board

GC keypad

Flow control display

HP 5973 MSD HP 6890 Series GC

On/off switch On/off switch

for MSD for GC

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Reagent Gas Flow Control Module

Isolation valve Rear flow module cover

Reagent gas inlet lines
Control panel

CI calibration valve Mass flow controller

Reagent gas select valve
EI/CI GC/MSD interface

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CI Ion Source

CI filament CI ion source body

Entrance lens
CI source
heater assembly

CI ion focus

Sensor cables

Heater cables

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CI Source - Exploded View

CI lens insulator Entrance lens

CI drawout plate

CI ion source body

CI repeller insulator
CI filament

CI ion focus
lens

CI drawout
cylinder

CI lens insulator

CI interface tip seal

CI repeller

CI source
heater assembly

Dummy filament

Heater cables Sensor cables

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Instrument Control View

The Instrument Control view is displayed when you start up

the MSD ChemStation. This is where you set and monitor See the online help for more details
instrument parameters. If you are in a different view, select on the menus, buttons, or windows
View / Instrument Control when you are ready to set up the used in the software.
system for data acquisition.

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).

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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 Contents 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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MS Top Menus

Method Sequence View SecuredControl Help

Run... Run... Top Enable Security... Help Topics
Instrument Control Using Help
Load... Load... Data Analysis (offline) Start Secured Control...
Save... Save... Review Revision History...
Select Methods for Secured Control... About
Edit Entire Method... Edit Sample Log Table... Set/Change Startup Method <None>...
Print Set/Change Standby Method <None>...
Load and Run Sequence...
1 Print Sequence... Report Manager Password...
2 Edit Accounts...
3 Simulate Sequence
4 Position and Run...
View Sequence Log...
Set New Default Paths... View Sequence Quality Log
Print Sequence Log
Exit
More...

Select View / Top to access

these menus.

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Instrument Control Menus

Method Instrument View Abort

Run... Inlet/Injection Types Top Abort

Instrument Control
Load... GC Edit Parameters... Data Analysis (offline)
Save... GC Plot...
GC Monitors... Diagnostics/Vacuum Control...
Edit Entire Method... Manual Tune...
Print Select MS Tune File...
MS SIM/Scan...
1 MS Monitors...
2
3 Edit MS Tune Parameters...
4 Perform MS Autotune...

Exit

Window Qualify Help

Cascade Checkout Tune Help Topics
Tile Horizontal Tune Evaluation Using Help
Tile Vertical View Tunes...
Arrange Icons Sensitivity Check Review Revision History...
Arrange Plots and Monitors Installation Checklist About
Familiarization Checklist
1
2
3
4

Select View / Instrument Control to

access these menus.

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Manual Tune - CI Menus

File Setup Tune Execute Calibrate

Reset to Defaults Select CI Gas... CI Autotune MS ON Mass axis
Load Tune Values... Set Tune Limits... MS OFF
Save Tune Values... Select Masses... Mass #2 widths
Profile scan Mass #3 widths
Trace on Methane Flow Setup Repeat profile PW linearity
View Trace... Methane Pre-Tune Detailed profile
Print Methane Flow Adjust Adjust abundances
Printer Setup... PFDTD Spectrum scan
Generate Report Full Spectrum scan
Find mass...
Exit

RampParam AdjParam Status View Abort

Ramp Repeller Edit MS Params... MS Status Top Abort
Ramp Ion Focus Edit Acq Params... MS I/O Test Instrument Control
Ramp Ent. Lens Offset Edit MS Temps... MS Interface Error Data Analysis
Select Data Filter... MS Temp Ctlr Status
Maximize Sensitivity Diagnostics/Vacuum Control
Purge Cal Valve Vacuum/Temp Status Manual Tune - CI
Edit Ramp Params...

Select View / Manual Tune to

access these menus.

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Diagnostics / Vacuum Control Menus

File Status Vacuum Diagnostics

Reset to Defaults MS Status Vacuum Status... MS ON
Load Tune Values... MS I/O Test MS OFF
Save Tune Values... MS Interface Error Pump Down...
MS Temp Ctlr Status Vent... Set RFPA...
Trace on Set a Parameter...
View Trace... MS Error Codes Purge Cal Valve
Print Initialize MS Interface
Printer Setup... MS Temp
Air and Water Check
Exit
Edit MS Params...

Power-on Temps

Logs View Stop/Abort Help

View Instrument Macro Log... Top Stop [Use when instructed] Help Topics
Instrument Control Abort [Use at anytime] Troubleshooting
Clear Instrument Macro Log Data Analysis (offline) Using Help

Diagnostics/Vacuum Control About

Manual Tune

Select View / Diagnostics/Vacuum

Control to access these menus.

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Data Analysis Menus

File Method Chromatogram Spectrum

Load Data File... Run Method... Chromatogram Scaling... Add

Next Data File Draw Chromatogram - No Labels Subtract
List Header... Load Method... Draw Chromatogram With Labels Tabulate
Edit File Info... Save Method... Select Chromatogram Labels...
Take Snapshot Select Library...
Subtract Background (BSB) Edit Method... Extract Ion Chromatograms Edit Strategy...
Display Ion Chromatograms in Merged Format Edit Library...
Select Signals... 1
2 Select Integrator Library Search Report
Printer Setup... 3 MS Signal Integration Parameters...
Print GC Signal Integration Parameters... NIST Output
Abort AutoIntegrate
Integrate Change Spectral Display...
Export Data to CSV File... Integration Results...
Export Data to AIA format... Percent Report
Import AIA Raw Data Files...

1
2
3

Exit

Calibrate Quantitate Tools View Help

Set Up Quantitation... Calculate
Edit Compounds... Generate Report
Update... Report Options...
List... Report Non Target Peaks...
Clear... Use Method Aligned GC trace
Trace Mode Quant...
DOLIST... EasyID Help Topics
DOSCAN... QEdit Quant Result Using Help
Process Scan List Edit Non Target Peaks Review Revision History...
Parametric Retrieval
Locate A Compound... Align GC About
Locate All Compounds... Review Peak Purity

Custom Reports... Set Overlay Parameters...

Print Report Overlay Chromatograms...
Update Database
Change Data State...
Select Template/Database Options...

Copy Window...
Reset Windows...

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

EasyID Spectrum Integrate

Co Next Compound Draw Next Integration Parameters

Goto Compound # Draw Previous Save compound specific integration parameters
Xpand Chromatographic Window +/- 2 minutes Tabulate Remove compound specific integration parameters
Original Chromatographic Window
Graphics Report to the Printer Add Integrate
Subtract
Restart Quick QEdit
Select Library...
Set Extract Window Start Edit Strategy... ChromEval View
Set Extract Window Stop Edit Library...
Evaluate Resolution Data Analysis
Abort Changes and Exit Display Reference Spectra Evaluate Tailing
Exit and Save Changes Evaluate Degradation
Update Reference Spectrum

Select View / EasyID in Data

Analysis to access these menus.

QEdit Menus

QEdit Spectrum ChromEval Display View

CO Next Compound Draw Next Evaluate Resolution Normal Data Analysis

Goto Compound Draw Previous Evaluate Tailing Qualifiers
Xpand Chromatographic Window Tabulate Evaluate Degradation
Original Chromatographic Window
Graphics Report to the Printer Add
Subtract
QDEL Compound
Select Library...
Next File Edit Strategy...
Load Data File... Edit Library...
Restart Quick QEdit
Display Reference Spectra
Abort Changes and Exit
Exit and Save Changes

Select View / QEdit Quant Result in

Data Analysis to access these menus.

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Parametric Retrieval Menus

File Spectrum Library Retrieve

Load... Draw Next Select Library... Set Parameters...
List Header Draw Previous Edit Strategy... Select Library...
Take Snapshot Edit Library...
Subtract Background (BSB) Tabulate Continue Results
Library Search Report...
Print Current View Add
Normalized Subtract Read JCAMP File...
Save Parameters Write JCAMP File...
Abort
Exit Subset Library...
Add Current Entry

Structures Options View Help

Select Structure Database... Select Normalization Ion
Set Structure Parameters... Command Line
Stack
Manual Integration
Copy Window...
Reset Windows
Standard Menu Help Topics
Library Entry Only About
TIC and Library Entry
Unknown and Library Entry
Unknown, Library Entry, and Difference

Select View / Parametric Retrieval in

Data Analysis to access these menus.

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Align GC Menus

Alignment View

Show Current Method Alignment Points Data Analysis

Perform Alignment
Restore Alignment Chromatograms

Abort
Exit/Save

Select View / Align GC in Data

Analysis to access these menus.

Review Peak Purity

PkPurity Spectrum Help

Next Peak Add Help Topics
Previous Peak Subtract Peak Purity
Select Peak... Tabulate Using Help
Return to DA

Select View / Review Peak Purity in

Data Analysis to access these menus.

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Troubleshooting Tips

No reagent gas peaks – PCI High vacuum pressure (> 5 x 10-4 Torr) with
reagent gas flow
1 Wrong tune file loaded or tune file corrupted
2 Wrong ion polarity 1 Reagent gas flow rate too high
3 No reagent gas flow 2 Air leak
4 Wrong reagent gas selected for tune file 3 Interface tip not sealed
5 Large air leak
6 Dirty ion source Pressure unchanged when reagent flow is
7 Poor vacuum (pump problem) changed
1 Reagent gas regulator is closed
No PFDTD peaks – PCI 2 Reagent gas regulator set to wrong pressure
1 Running wrong reagent gas (there are no PCI 3 Valve on reagent gas bottle closed
PFDTD peaks with isobutane or ammonia). 4 Reagent gas supply empty
Switch to methane. 5 Reagent lines bent, pinched, or disconnected
2 Analyzer not sealed (air leak) 6 GC/MSD interface clogged
3 No calibrant in vial
4 Defective calibration valve
5 Air leak in carrier or reagent gas path
No or low reagent gas signal
6 Reagent gas flow too low 1 Reagent gas is set too low
7 Dirty ion source 2 Dirty ion source
3 Clogged interface
No PFDTD peaks – NCI 4 Reagent lines bent, pinched, or disconnected
5 Problem with filament
1 Look for background ions 6 Too much air and water in system
2 Verify tune parameters 7 Electron inlet hole is blocked
3 Go back to methane PCI 8 Source wires are not connected properly

Pressure > 5 x 10-5 Torr without reagent

gas flow
1 Excess water in background
2 Air leak
3 Foreline pump not working properly
4 Turbo pump not working properly

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No or low PFDTD signal
1 No PFDTD in calibration vial
2 Calibration not purged after refill
3 Calibration vial was overfilled
4 Pressure of methane into flow controller too
high
5 Dirty ion source
6 Reagent gas pressure too low in ion source
Excessive noise/low signal-to-noise ratio
1 GC injection port needs maintenance
2 Dirty ion source
3 Reagent gas pressure/flow too high (PCI)
Large peak at m/z 19 (water in system)
1 System not baked out after venting
2 Moisture in reagent gas supply lines
3 Contaminated reagent gas supply
Large peak at m/z 32 (air in system)
1 Residual air from recent venting
2 New or dirty reagent gas supply lines
3 Air leak
4 Contaminated reagent gas supply
5 Capillary column is broken or disconnected
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CI ion ratio is difficult to adjust or unstable
1 Residual air and water in MSD or reagent gas
supply lines
2 Air leak
3 Incorrect reagent gas supply pressure setting
4 Leak in reagent gas delivery path
5 Improper analyzer operating temperature or
unstable ion source temperature
6 Dirty ion source
7 Bad source or interface seals
8 Flow control valve out of adjustment or
incorrectly installed
High electron multiplier voltage
1 Improper analyzer operating temperature
2 Dirty ion source
3 Electron multiplier (detector) is failing
Peak widths are unstable
1 Dirty ion source
2 Air leak
Refer to the following manuals for more detailed
troubleshooting information:
• HP 5973 MSD PCI/NCI Hardware Manual
• HP 5973 MSD Hardware Manual
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H


What’s in this Book

Learning About Your System, 2

Using Online Help, 3
HP 5973 MSD System with PCI/NCI, 4
Reagent Gas Flow Control Module, 5
CI Ion Source, 6
CI Source - Exploded View, 7
Instrument Control View, 8
Software Menus, 10
Troubleshooting Tips, 18

Document History

First Edition, 1/98

HP 5973 MSD System with PCI/NCI,
HP G1701BA Software, Enhanced Mode,
Rev. B.00.00 and later until superseded

*G1999-90003*
*G1999-90003*
Copyright © 1998
Manual Part Number Hewlett-Packard Company
G1999-90003 Printed in U.S.A. 1/98