NOTICE: This document contains references to Varian.
Please note that Varian, Inc. is now part of Agilent
Technologies. For more information, go to
www.agilent.com/chem.
Varian MS Workstation 6.9
Service Pack #2
The software contained in this kit is an add-on to the Varian MS Workstation 6.9 SP1
software (P/N 03-914982-01:17), containing a number of improvements and corrections.
Installing the MS Workstation 6.9 Service Pack #2 Software
Verify that Version 6.9 of the MS Workstation is installed on your computer. You can do
this by selecting “About...” under Help in the menu bar of any of the MS Workstation
applications and checking the version number, or right-click on an open area of the MS
Workstation Toolbar, select “About Workstation Toolbar” and check the displayed version
number. If ‘Service Pack 1’ is not displayed under ‘Version 6.9.0’, you must install MS
Workstation Version 6.9 with SP1 before you can install this Update.
If MS Workstation Version 6.9 SP1 is already installed, you may install the SP2 Update by
downloading it from http://www.varianinc.com/support/downloads/ and launching
MSWS690SP2.EXE.
2000 MS, 4000 MS, 500-MS
No changes
MS Data Handling/Reports
Id:
6359
Title:
Component:
Area:
Description:
Manual integration sometimes updates calibration replicates
incorrectly
MS Workstation Platform
MS DataRev – Quan, Review Results
When manual integration changes a compound result from Missing to
Identified or from Identified to Missing, the calibration data point replicates
sometimes can be updated incorrectly. If the modified calibration point was
an Internal Standard, the relative response factors in the data file for all of
the compounds that are calibrated with it will be updated incorrectly.
Id:
6366
Title:
Component:
Area:
Description:
Ion Time shown for Quad files!
MS Workstation Platform
MS DataRev - General
When Quad spectra are displayed, “N/A” should be displayed for Ion Time
values in spectrum Plot Titles.
Id:
6393
Title:
Component:
Area:
Description:
Long Sample ID name can crash Method Builder in Print Preview
MS Workstation Platform
DHMeth MS – Standard MS Reports
Method Builder can crash when Print Preview is selected if Sample ID is
selected as the Sort By key in the Standard MS Reports “Summary Report
Format” dialog, and the Sample ID string is very long.
Page 1
Core Workstation Platform
Id:
5927
Title:
Component:
Area:
Description:
Inject Single Sample makes two injections (& repeated sample list)
Core Workstation Platform
System Control - Automation
Under some conditions, a sample list or single sample injection ran twice
without any operator action. A potential cause of this problem was corrected
Id:
6386
Title:
Component:
Area:
Description:
212-LC: Method Printout broken
212-LC
Method Editor - Printing
Method printouts for the 212-LC did not show composition or flow. Run Log
printing/formatting was fine. The problem was corrected in the 212-LC driver.
Id:
6400
Title:
Component:
Area:
Description:
CPAL: Automix "Aspirate" command does not work
CombiPAL AutoSampler
System Control - Automation
The AutoMix "Aspirate" command moves the head to the specify vial, but the
needle does not go in the vial. The command was corrected to use the
penetration specified in the method.
Quadrupole MS (3X0-MS/1200/1200L)
Id:
6387
Title:
Component:
Area:
Description:
APCI Corona current resets on some Breakdown curves
1200
System Control - General
When running the API Capillary Breakdown in APCI mode in positive
mode, the corona current resets itself to 2.0 when the breakdown starts.
Id:
6360
Title:
Scan parameters changed during acquisition will not take effect if
probe is running
3X0-MS
ModWin - Acquistion
When performing an acquisition with the probe running and the Scan
Parameters (such as mass window) are changed, the message "Would
you like to Install the new method into the scan?" is displayed. Clicking on
Apply should cause the new parameters to be applied but they are not. If
the probe program is not active and the same changes are made, the
acquisition is updated correctly.
Component:
Area:
Description:
Id:
6361
Id:
6364
Title:
Component:
Area:
Description:
Open Current Error if running Probe with automatic adjust to signal
strength
3X0-MS
ModWin - General
If the Probe is running in “feedback” mode (aka Changes temperature
ramp to reach target ion signal strength), an "Open Current Error" occurs
shortly after initiating the program with a starting current of 10.
Title:
Exposure Probe maximum current is wrong
Page 2
6364
Component:
Area:
Description:
3X0-MS
System Control - Automation
When typing a number greater than 450 into the current program (or
constant current) for an Exposure Probe method and clicking on Apply, the
value is automatically changed to 450. The Exposure Probe max current
should be 1500mA.
Id:
6365
Title:
If using all masses in Probe feedback mode evaluates incorrect mass
range
3X0-MS
ModWin - General
If the “Intensity of ions scanned” Ion signal type is selected in Probe
“feedback” mode (Changes temperature ramp to reach target ion signal
strength), an incorrect mass range is evaluated.
Component:
Area:
Description:
Id:
6391
Title:
Component:
Area:
Description:
Probe Status in Instrument Status screen gets truncated
3X0-MS
System Control - General
If there are more than 2 numerical digits for the probe current/temperature,
the text box in the instrument status screen gets cut off, so that the values
are not visible.
Id:
6402
Title:
Component:
Area:
Description:
Low end limiting of the RF is too restrictive
3X0-MS
System Control - General
When scanning from mass 10, some systems will sometimes exhibit a
ghost peak as a result of variances in Mass Calibration.
Id:
6407
Title:
Component:
Area:
Description:
There is no 'EFC/EPC Check' Log
3X0-MS
System Control - General
It would be desirable to have an 'EFC/EPC Check' Log that would
document the steps taken.
Id:
6443
Title:
Component:
Area:
Description:
Inlet interlock cable disconnected should behave as open cap
3X0-MS
System Control - General
When the Inlet interlock cable is disconnected, it should disable the
filament, detector, and quad voltages as it does when the spray chamber
is open.
Id:
6457
Title:
Instrument status says 'Calibrating Methane' when it’s actually
Flushing.
3X0-MS
System Control - General
When the system is switched from EI to CI the status says 'Calibrating
Methane' instead of 'Flushing'.
Component:
Area:
Description:
Id:
6477
Title:
Component:
Area:
Description:
Air/Water Check runs even when masses 18 & 28 are not tuned.
3X0-MS
System Control - General
Currently, when the system is Autotuned with masses 18 & 28 unchecked
and the 'Air Water' check is run, although the system is unable to adjust
Page 3
resolution on these masses, the check still completes and gives a report.
The user should be warned to Tune the system at 18 & 28 before running
the test.
Id:
6334
Title:
Component:
Area:
Description:
System Control Crash/Blue Screen of Death when syntax error
occurs in Advanced Options PML command line
Quad (General)
System Control - General
In the Advanced Options window of the Scan Table (in Manual Control), if
a PML with incorrect syntax is entered, there is an error message
displayed, but System Control hangs without allowing the error to be
resolved.
Id:
6344
Title:
Component:
Area:
Description:
EDR Calibration Error
Quad (General)
ModWin – Auto Tune
The EDR calibration error currently tells the user that the calibration was
aborted: "Curve - ion signal too large".
There should be an additional comment telling the user to try the
calibration again after 1 - 7 days if a new multiplier was just installed.
Id:
6385
Title:
Component:
Area:
Description:
Acquisition hangs on Waiting for Injection
Quad (General)
System Control - Automation
When running a Sample List without an autosampler, after a number of
injections, the acquisition/automation will get stuck on Waiting for Injection.
If automation is suspended and restarted, it will start again, but will
eventually happen again.
Id:
6388
Title:
Component:
Area:
Description:
RunLog and Detector Overrides
Quad (General)
System Control - General
Currently, the detector behaves in such a way that if there is an override in
one segment, the detector does not revert back to the original global value
when it goes to the next segment and that segment has no override
checked.
The RunLog shows the detector reverting back to the global value, while
System Control shows the overriden value in a segment where the value is
not overridden. The runlog should match what the detector actually does
during the run.
Id:
6403
Title:
Component:
Area:
Description:
Manifold heater should be shut off if fuse F3 is blown
Quad (General)
System Control - General
Currently the software maintains power to the manifold heater as long as
the line voltage is not greater than 140V. However, if the instrument is set
up for 220V operation and fuse F3 is blown or missing the line voltage will
continue to be powered but the current to it will be doubled.
Id:
6404
Title:
Q1ms and Q3ms switching isn’t always immediately reflected in the
status
Quad (General)
ModWin - General
After typing Q1ms in the command line and then switching to Q3ms,
Component:
Area:
Description:
Page 4
although scanning does change as it should to Q3ms, the status screen
reflecting this isn’t always updated until some other action is taken in the
system.
Id:
6406
Title:
Component:
Area:
Description:
Need to clarify Air/Water Check Criteria
Quad (General)
ModWin - General
The AutoTune process currently reports the following conditions if they are
detected:
"Mass 18 is at least as large as Mass 69"
"Mass 28 is at least as large as Mass 69"
However, this situation does not necessarily imply a leak and we should
eliminate these messages to stop leading users to this invalid conclusion.
On the other hand, we need to encourage regular use of the Air/Water
check to explicitly check for leaks. To that end:
1) Eliminate the above checks and messages from the Auto Tune
process - They should not affect the results.
2) Unconditionally and automatically run the Air/Water Check at the end
of each Auto Tune [Tune and Calibrate, Calibrate] when operating in
EI mode.
Id:
6426
Title:
Component:
Area:
Description:
CID Pressure Calibration
Quad (General)
ModWin - Diagnostics
Change the way that CID and source pressure calibration results are
reported.
If there is too much noise or pressure drift, report the resulting error with a
message like "Warning!, CID calibration is only within 1.2mTorr"
If there is no pressure or any other error not allowing the creation of a
calibration curve, report the following: "CID calibration failed, no new
calibration was generated" or "CID calibration failed, default calibration
table was installed"
Id:
6431
Title:
Component:
Area:
Description:
Uninitialized EEPROM on new power PCB should be initialized
Quad (General)
System Control - General
When a new Power PCB is installed in a Quad the EEPROM on it has not
yet been initialized. If there is a valid config.cub on the system then the
EEPROM should be initialized automatically. Correcting this should
resolve spurious “Model Definition” errors.
Id:
6432
Title:
Component:
Area:
Description:
Analyzer Connections test questionable
Quad (General)
System Control - General
Eliminate the “dirt test” from the Analyzer Connections test.
Id:
6454
Title:
Component:
Area:
Description:
EDR Calibration Problems
Quad (General)
ModWin – Auto Tune
Periodically, especially with new detectors, there are discontinuities in the
EDR calibration due to the broad range of voltages included in the curve.
Limiting the curve to the range of calibrated values eliminates the problem.
Page 5
Id:
6478
Title:
Component:
Area:
Description:
Autotune vs. Report Only flags are inconsistent
Quad (General)
ModWin – Auto Tune
The Autotune report will flag ions that were not used in the tune as “report
only, not tuned.” However, if a report is generated without re-tuning the
instrument, the tune report shows warning flags for mass shifting and peak
resolution on these unused ions. These flags should match the Autotune
report so as not to confuse and unduly concern the user.
Id:
6489
Title:
Component:
Area:
Description:
Mass shift on Q1
Quad (General)
System Control (General)
When doing Full Scan: If the collision cell energy listed in the Scan Table
is 0.00, rather than a blank cell, the masses are shifted on Q1 (M-1), but
OK on Q3. In Full Scan, if 0.00 is the collision cell energy, it should
behave the same as if there was no energy entered.
Note:
The following change to the Tune Report was implemented in MSWS 6.90 for Quadrupole
MS systems:
If a problem is encountered with a mass that is specified to be included in the report but not
tuned, the message “Reported only, not tuned” will appear in the report under that
particular mass. If the mass is reported only and no problem is encountered, no message
will appear.
Page 6