Software Status Bulletin

GC/MS Translator     GC/MS Translator

Preface
-------------------------
This Software Status Bulletin (SSB) documents all known problems in the software
product designated above. The SSB is derived from Known Problem Reports (KPR)
which result from user problems that have been classified as documentation
problems or software defects. When a KPR is written, an identifying number is
assigned to it, and the KPR is added to the next edition of the SSB.

User inputs that have been classified as Enhancement Requests are not documented
in the SSB. User problems that have been submitted, but that have not been
classified by the time the SSB is generated are not included in the SSB.

How to use the SSB
-------------------------
When you experience a problem with a product, first check this SSB to see if the
problem has been reported already, and if there is a temporary workaround
available for the problem, or if the problem has already been fixed by a new
revision. If the problem is not listed in this SSB then you may wish to report
it to the Response Center or to your field support representative.

To determine if your problem is documented in this SSB, first look in the
Keyword Index section of the SSB. Under each keyword is a listing of one-line
descriptions of related KPRs. If any of these sound like yours, locate the KPR
# in the Known Problem Reports section of the SSB, and read the full KPR. The
KPRs in the Known Problem Reports section are sorted by KPR #.

There are two sections in the SSB:
Keyword Index: This index is categorized by keyword. For each KPR there is a
brief description and a KPR #. A KPR may be associated with more than one
keyword.

Known Problem Reports: This section contains KPRs, with all the available
information relevant to the problem. KPRs in this section are sorted by KPR #.

Keyword Glossary

Keyword Index

Keyword: 

One-line Description:

Using other than US Date Format will cause the GC and MSD Translator to crash

Problem:

Using other than US Date Format will cause the GC and MSD Translator to crash.

Temporary Solution:

1 - For older data files which were acquired with the day/month/year format then the patch file must be used.
2 - For current systems, user can either use step #1 or can change the date format to month/day/year.

Fix Information:

A point patch (new setup.exe file) is available for the user.  Please contact your software support representative for copy of the file, note file is 16 MBytes in size.

Fixed in B.05.00

Keyword: 

One-line Description:

Importing Files from CD and then output to hard drive results in program terminating terminates

Problem:

Importing the files from D:\gcms translator\data\msd data\gcms
output folder  c:\trans test; CD/DVD drive and then to a folder on the hard drive.

I get the error message of 
"Access to the path 'd:\gcms translator\data\msd data\gcms\cal_L12.d\data.ms' is denied

Looks like the program is trying to copy files initially to the drive and then move them.

Temporary Solution:

The source files must be on a read/writeable media location.  If the source files are located on a CD/DVD then the files must be copied onto the hard drive and then converted over.

Fix Information:

Fixed in B.04.01

Keyword: 

One-line Description:

Translated method crashes Quant when editing integrator or integrator parameters

Problem:

When a customer’s method is translated, then opened in Quant method editor and then an attempt to edit either the integrator or the integrator parameters is made Quant aborts.  Problem seen with Quant B.04.00 SP1 and SP2.

Temporary Solution:

Edit the translated method file (*.quantmethod.xml) and add the following  text :

  PeakAreaPctThreshold 
  0 

to each TargetCompound section.

Fix Information:

Fixed in B.05.01 however all integrators are set to Agile.

Keyword: 

One-line Description:

GC MSD Translator fails to convert GC signal if the type is OVEN TEMPERATURE

Problem:

If you try to convert the GC signal it fails with the error message
and does not translate the GC signal. See attached data file 
and screen dump of the 


Error message:
Specified argument was out of the range of valid values.
Parameter name: Ordinal number must be greater than 0

Temporary Solution:

None.

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

GC AIA-MS Translator fails reports error and Qual unable to read file

Problem:

When an attempt is made to translate an AIA file that contains GC signals the translator fails with error “File read error occurred (”.

Temporary Solution:

None

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

Translated compound names are corrupt

Problem:

When translating qdb.mth files the compound names can have extra characters which typically is seen as "|||" added at the end of the name.

Temporary Solution:

Edit compound names

Fix Information:

Fixed in B.05.01

Keyword: 

One-line Description:

Translator fails to translate GC ONLY AIA data files

Problem:

If an AIA file containing only GC data (no MS) is translated the translation software will create a MassHunter data file and no error message will be produced but the MassHunter data file cannot be read by Qual.

Temporary Solution:

None

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

SIM method translates with negative m/z and data type of SCAN

Problem:

When a SIM method file (qdb.mth) is translated the target masses all have a negative “MZ” and the “Scan” is Scan rather than SIM.

Temporary Solution:

The method can be edited to work but requires edit of each target MZ value to make them positive and changing the “Scan” field to “SIM”.

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

MassHunter data files to AIA format will translate mass peaks as integer value

Problem:

When translating MassHunter data files to AIA format the m/z values are truncated to integer numbers.  Problem seen in B.05.00

For example 298.7 is translated to 298 and 299.2 is translated to 299

Temporary Solution:

None.

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

Sample types of 'Surrogate' and 'Matrix Spike' are not translated as such

Problem:

After translation, sample types of ‘Surrogate’ and ‘Matrix Spike’ appear in MassHunter Quantitative Analysis as ‘Target’s.

Temporary Solution:

After translation, change sample type to 'Surrogate' or 'Matrix Spike' for appropriate samples in MassHunter Quantitative Analysis.

Fix Information:

n/a

Keyword: 

One-line Description:

Quant gives wrong SCAN type for translated MSD SIM data

Problem:

In Quant, when using ‘create method from acquired SIM data’ on a translated MSD SIM file the scan type shows as MS2SIM and should instead be SIM.  The term MS2SIM is impossible for a single quad and inconsistent with the drop down menu in Quant MS of "SCAN" or "SIM".

Temporary Solution:

None

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

Qual unable to see all SIM ions in translated SIM file

Problem:

When a SIM file with multiple ion groups is translated only the 1 set of ions are extracted from the file by Qual B.04 when extracting SIM.   The other ions should be visible to Qual and extracted.  Ions do show in the TIC and EIC.

Temporary Solution:

None

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

GCMS MH AIA translator doesn't show translate button in Japanese PC

Problem:

When installed GC/MS translator software B.05.01, translate button doesn't show the screen in Japanese PC.
This issue has been seen in B.05.00, too.

Temporary Solution:

None

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

FID collected on MSD Chemstation B.01.00 fails

Problem:

FID collected on MSD Chemstation B.01.00 fails to translate and give error "Object reference not set to an instance of an object".

Temporary Solution:

None

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

SIM data file translated to scan data

Problem:

When the SIM only data file is translated it becomes scan data with all SIM ions placed in a single scan.  Quant must be set to extract from scan data.  When seen in Qual application doesn’t allow SIM signal extraction or give SIM mass dropdown list.

Temporary Solution:

None

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

Error message when attempting data translation on 64-bit OS

Problem:

Error message obtained when attempting data translation on Windows 7 Pro SP1 (64-bit), GC/MS Translator Build 080864.  Translation works on 32-bit Windows 7 SP1

Temporary Solution:

None

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

Data file fails with "Index was outside the bounds of the array" message

Problem:

MSD data file fails to translate and gives error message "Index was outside the bounds of the array" message.

Temporary Solution:

None

Fix Information:

Fixed in B.05.02

Keyword: 

One-line Description:

Translate Identification Reference Peak only when Internal Standard

Problem:

MH Quant does not allow you to specify a Time Reference Peak that is not an internal standard, so when the MSWS method is translated, it will only translate the Identification Reference Peak  if it is an internal standard.

Temporary Solution:

None

Fix Information:

No plans to address this in future releases.

Keyword: 

One-line Description:

SIM data file translates but is invalid

Problem:

The translator appears to run (no error message) but it runs to quickly and the resulting data file can’t be opened in Qual or Quant.  Qual error message indicates that the MSScanType is unspecified.  Sample Information window  in Quant displays "Failed to access sample data".  Data files were collected using SIMFIX algorithm in MSD ChemStation.

Temporary Solution:

None

Fix Information:

Fixed in B.05.02 - Jan 2012

Keyword: 

One-line Description:

GC MSD Translator fails with  "Object reference not set to an instance of an object." error

Problem:

Run the GC MSD Translator B.05.02 Build 1032 on data file which data collection started at zero minutes.  Example reported was on a GC 6890 Data File.  Program can not translate file and gives "Object reference not set to an instance of an object."

Temporary Solution:

None.

Fix Information:

Fixed in B.06.00

Keyword: 

One-line Description:

MSD SIM file translates with only some SIM signals seen

Problem:

When SIM data is translated the data appears to be complete and well formed in Quant but when viewed in Qual all of the SIM signals past the first SIM group (time segment) are not displayed when extracting by SIM in Qual.  TIC is complete and EIC of the SIM can be extracted only SIM chromatograms are missing.  The problem is that the translator relies on the acq.ms method file being stored with the data files to assign SIM signals to the correct time segments.  When the method is not found the software can only properly display the SIMs in the 1st time segment.

Temporary Solution:

Ensure acq.ms method file is being stored with the data files.

Fix Information:

n/a

Keyword: 

One-line Description:

NCI data file translates as PCI

Problem:

When translated both Qual and Quant see NCI data as positive data rather than negative.  In Quant this will appear as No Data Found and blank chromatograms.  In Qual the drop down on polarity is limited to positive (no negative signals found in file).

Temporary Solution:

Quant method must be switched from negative to positive for the data to become visible.

Fix Information:

Fixed in B.06.00

Keyword: 

One-line Description:

Acquisition Date-Time is incorrect for ChemStation data files that are acquired in one time zone and translated in a different time zone

Problem:

Data files acquired using ChemStation do not store the acquisition date-time in UTC format.  The GC/MS Translator assumes that the acquisition date-time for these data files is the same time zone as the PC used when the translation is performed.  So, translation on a PC in Pacific Time results in different Acq Date-Time values in the translated files when compared to translation on a PC in Eastern Time.   No issue exists if data acquisition and translation are done in the same time zone.

Temporary Solution:

Translate the files in the same time zone that the files were acquired in.

Fix Information:

Possibly addressed in a future version of MassHunter GCMS Data Acquisition

Keyword: 

One-line Description:

Translation of Profile data

Problem:

Profile (Raw) spectra from an GC/MSD are plotted as discrete mass peaks instead of a continuous line.

Temporary Solution:

None

Fix Information:

Fixed in B.07.00

Keyword: 

One-line Description:

Translated SIM/Scan data only displays 1st half of data in Qual

Problem:

SIM/Scan data file is translated from MSD ChemStation file format to MassHunter format by the GCMS Translator.  If opened in Qual only the 1st half of the file is displayed.  As an example a 20 minute runtime file only displays the 1st 10 minutes of data.  If opened in Quant the complete data file is displayed.

Problem seen in B.07.00 and earlier.

Temporary Solution:

None

Fix Information:

Fixed in B.07.00 SP2

Keyword: 

One-line Description:

'Object reference ...' message displayed when attempting to translate a data file

Problem:

The problem was seen in GC 6890 GC/FID data file where a  START TIME is reported as below zero milliseconds.  Such a state can occur and is not an error.

Temporary Solution:

None

Fix Information:

Fixed in B.07.00 SP2

Keyword: 

One-line Description:

Some Varian Triple Quad data files could not be translated, and error message refers to them as "methods"

Problem:

This was seen on older file versions. The Varian QQQ translator only supported data and methods acquired or developed on MS Workstation 6.9.2 and newer.

Temporary Solution:

None

Fix Information:

Fixed in B.07.00 SP2

Keyword: 

One-line Description:

Translated data file missing data in Qual but seen in Quant

Problem:

An example SIM/Scan file shows no SIM or Scan data in Qual past approximately 9 minute mark in an approximately 16 minute run.  However Quant shows both SIM and Scan data to the 16 minute mark.

Temporary Solution:

None

Fix Information:

Fixed in B.07.01

Keyword: 

One-line Description:

Incorrect version displayed in installed list of programs

Problem:

Version displayed in the Windows 'Add/Remove' programs is ‘1.00’.

Temporary Solution:

None

Fix Information:

Fixed in B.07.01

Keyword: 

One-line Description:

Warning messages are displayed during uninstallation of the GCMS Translator

Problem:

Messages say that shortcuts cannot be removed, but desktop shortcuts for Translator applications appear to be removed after clicking 'OK' in the message.  However, right-clicking in the desktop and selecting 'Refresh' displays the shortcuts although the shortcuts do not work.

This issue seems to be related to some Windows  configurations.

Temporary Solution:

Manually delete shortcuts.

Fix Information:

n/a

Keyword: 

One-line Description:

MRM Data from a Varian LCQQQ converted to MassHunter the data appear to be only SCAN data

Problem:

MRM Data from a Varian LCQQQ converted to MassHunter the data appear to be only SCAN data.  The Pre cursor Ions are not shown.

Temporary Solution:

None

Fix Information:

Fixed in B.07.00 SP2

Keyword: 

One-line Description:

Translator places conversion date rather than acquisition date in Contents.xml, Qual shows wrong date

Problem:

There are two places where acquisition date appears, Contents.xml and Sample_info.xml.  The translator places the correct acquisition date in the sample_info.xml but the conversion date in the contents.xml.  Quant reads the correct date from msample_info.xml while Qual reads the wrong (conversion) date from contents.xml.  Example data file is attached.

Defect reported in B.07.00 SP2 but confirmed in B.07.01 Build 1767

Temporary Solution:

None

Fix Information:

Fixed in B.07.02

Keyword: 

One-line Description:

Non English Installs - Help icon is not working for GCMS Translator, MSD ChemStation Data Translator, Quant Method Translator and MS WorkStation Data Translator

Problem:

For installs with language selected other than English the Help icon is not working for GCMS Translator, MSD ChemStation Data Translator, Quant Method Translator and MS WorkStation Data Translator.

When clicked no Help is launched.

Temporary Solution:

None

Fix Information:

Fixed in B.07.03

Keyword: 

One-line Description:

CompoundType  appears in “CompoundGroup” column instead of “CompoundType”

Problem:

Transfer of ChemStation "CompoundType" appears in MassHunter "CompoundType" rather than setting the “CompoundType” to either Surrogate or MatrixSpike.

Temporary Solution:

None

Fix Information:

Fixed in B.07.03

Keyword: 

One-line Description:

'Comment' is not getting translated for GC ChemStation data files.

Problem:

Misc. Info in GC ChemStation data files is not getting translated into the 'Comment' of MassHunter Quant

Temporary Solution:

None

Fix Information:

Fixed in B.07.03

Keyword: 

One-line Description:

GCMS data file translator is not accurately transferring four sample information fields to MH Quant

Problem:

1.      OperatorName (set to “MassHunter GC/MSTranslator” instead of actual value)
2.      Vial Number (Missing)
3.      Acquisition MethodName (Says “MS Translator” instead of actual value)
4.      Instrument Name (Says "7890" instead of "SVGC30")

problem fixed for 5890, 6890, and 7890 GC signal files

Temporary Solution:

None

Fix Information:

Fixed in B.07.03

Keyword: 

One-line Description:

Copy ChemStation "Index" identifier into MassHunter Quant's new TargetCompound/ID (integer) field

Problem:

The Index compound from ChemStation data was not translated into the Quant method.

Temporary Solution:

None

Fix Information:

Fixed in B.07.03 (and requires Quant B.07.01 or greater)

Keyword: 

One-line Description:

Export Error in GCMS translator tool B.07.02 - Duplicate names

Problem:

If the translator encounters duplicate compound names in MSD ChemStation Quant Database it will display an error message indicating duplicates and abort translation into MassHunter format.

Problem seen in B.07.01, B.07.02 and B.07.03.  

Not seen in B.07.00.

B.07.04 will ask for permission to add a suffix of (-1,-2,etc) to compound names.

Temporary Solution:

Try using B.07.00 version.

Fix Information:

Fixed in B.07.04

Keyword: 

One-line Description:

Translated method assigned signal type as 'MS' in MH Quant for ECD data

Problem:

When translating a GC method (qdb.mth) file the signals are defined as MS rather than GC.  Signal type of 'MS' gives Quant method validation error:  Invalid product ion MZ

Temporary Solution:

Load Method using the GC Mode of Quant and manually assign GC signal information to GC compounds.  Method editor in MS version of Quant may not be used.

Fix Information:

n/a

Keyword: 

One-line Description:

AIA Export fails on GC signal

Problem:

Seen when one tries to export a file with only FID data (no MS) to AIA.  B.07.02 gives error message attached.  B.07.03 fails to translate but runs without message.

Temporary Solution:

None

Fix Information:

Fixed in B.07.04

Keyword: 

One-line Description:

GCMS Translator fails on GC signals and reports missing device_example.xml file in error message

Problem:

The GCMS Translator fails when translating GC signal, but not GCMS signals, reports missing device_example.xml file in error message.  Problem was traced to a specific version of the "Agilent MassHunter Acquisition Offline Utilities version 5.0.269.  Reported in B.07.03 and B.07.04 but likely seen in any version.

Temporary Solution:

Place a copy of the devices_example.xml file at the path location in the error message creating any folders as needed.

Fix Information:

This is not a defect in the GCMS Translator but an issue with the specific version of the "Agilent MassHunter Acquisition Offline Utilities version 5.0.269.

Keyword: 

One-line Description:

Microsoft Redistributable says it fails on MSWS PC.

Problem:

Installing the B.07.04 Translator on a PC which has MSWS installed, the Microsoft 2012 C++ resdistributable tries to install.  A message pops up asking if you would like continue Translator installation even though Redistributable installation failed. If you click Yes, translator installs.  If I go into the Control Panel, it seems that the redistributable did install.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

After translation of GC FID data collected on GC 5890 with signal data files of Type 108 the  Devices.xml is not present

Problem:

Data files collected on GC 5890 with signal data files of Type 108 will cause a problem and after translation the files lack the Devices.xml file.

Temporary Solution:

None

Fix Information:

Fixed in B.07.05