Import TSQ files

[Damaris Bausch, IMSB]

Dear all,

I tried to import a mzXML file from a thermo TSQ machine into the
TIQAM viewer. Unfortunately I got a parsing error. I have read the
earlier posts on this subject and installed the newest TIQAM viewer
release (1.2.0). The .raw files were converted with ReAdW.exe 4.0.2

I uploaded part of the mzXML file.

Best Regards,
Damaris

[Mi-Youn Brusniak]

Dear Damaris,

Would you tell us the error message?

Mi-Youn

Mi-Youn Brusniak, Ph.D.
Computational Biology
Seattle Proteome Center
mbru...@systemsbiology.org
Tel: (206) 732-1327

[Damaris Bausch, IMSB]

Dear Mi-Youn,

This is the error message:
--------------
java.io.IOException: Missing scan information or invalid scan type:
org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor
$Scan@830ed5
at
org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor.parse
(MzXmlFileProcessor.java:319)
at
org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor.access
$2(MzXmlFileProcessor.java:232)
at org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor
$1.run(MzXmlFileProcessor.java:209)
at
org.systemsbiology.aebersoldlab.core.db.HibernateUtil.runInTransaction
(HibernateUtil.java:461)
at
org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor.process
(MzXmlFileProcessor.java:205)
at org.systemsbiology.aebersoldlab.tiqam.importdata.ImportTask.run
(ImportTask.java:75)
at org.eclipse.jface.operation.ModalContext$ModalContextThread.run
(ModalContext.java:113)
--------------

Damaris

[Mi-Youn Brusniak]

Dear Damaris,

Do you have scanType="SRM" in your mzXML file?
What version of converter did you use?
The error message basically tells me that the file did not contain scanType="SRM" or scanType="MRM".

Mi-Youn

--

[Damaris Bausch, IMSB]

Dear Mi-Youn,

I you take a look at the example file I uploaded (tsq_example.mzXML),
you can see that there is scan Type="SRM" in it.
I used the ReAdW.exe converter 4.0.2.

What might be the problem is, that we have a not officially released
new beta-version of Xcalibur on the tsq-computer. But nevertheless, I
could convert the file.

Damaris