Tiqam viewer trouble

[MartinH]

HI,

I have tried to load the mzXML files into TIQAM viewer and it failed.
The mzXML were converted by mywiff.exe from the original wiff file
that contained more than 1 run. The conversion looked good to me, at
least in viewr I can read the data. Do you have the same experience
with such convereted files?

Martin

This is the error I am getting:
org.hibernate.exception.DataException: could not insert:
[org.systemsbiology.aebersoldlab.tiqam.model.MassSpectrum2]
at org.hibernate.exception.SQLStateConverter.convert
(SQLStateConverter.java:77)
at org.hibernate.exception.JDBCExceptionHelper.convert
(JDBCExceptionHelper.java:43)
at org.hibernate.persister.entity.AbstractEntityPersister.insert
(AbstractEntityPersister.java:2272)
at org.hibernate.persister.entity.AbstractEntityPersister.insert
(AbstractEntityPersister.java:2665)
at org.hibernate.action.EntityInsertAction.execute
(EntityInsertAction.java:60)
at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:
263)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:
167)
at
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions
(AbstractFlushingEventListener.java:298)
at org.hibernate.event.def.DefaultAutoFlushEventListener.onAutoFlush
(DefaultAutoFlushEventListener.java:41)
at org.hibernate.impl.SessionImpl.autoFlushIfRequired
(SessionImpl.java:969)
at org.hibernate.impl.SessionImpl.executeUpdate(SessionImpl.java:
1136)
at org.hibernate.impl.QueryImpl.executeUpdate(QueryImpl.java:94)
at
org.systemsbiology.aebersoldlab.tiqam.model.TransitionDao.updateMaxTraceIntensity
(TransitionDao.java:147)
at
org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor.handleMRMScans
(MzXmlFileProcessor.java:426)
at
org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor.parse
(MzXmlFileProcessor.java:355)
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)
Caused by: java.sql.BatchUpdateException: Data truncation: Data too
long for column 'peakBytes' at row 1
at com.mysql.jdbc.PreparedStatement.executeBatchSerially
(PreparedStatement.java:1269)
at com.mysql.jdbc.PreparedStatement.executeBatch
(PreparedStatement.java:955)
at com.mysql.jdbc.jdbc2.optional.StatementWrapper.executeBatch
(StatementWrapper.java:681)
at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch
(BatchingBatcher.java:48)
at org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:
34)
at org.hibernate.persister.entity.AbstractEntityPersister.insert
(AbstractEntityPersister.java:2252)
... 19 more

[Simon Letarte]

Hi Martin,

I don't know mywiff.exe. But I would guess that this does not produces
mzXML that is valid for TIQAM. Try using mzWiff, the latest version. I
have used wiff files that contained multiple runs succesfully before,
so that should not be the issue.

Good Luck,

--
Simon Letarte, Ph. D.
Senior Research Scientist
Institute for Systems Biology
1441 North 34th Street
Seattle, WA 98103-8904

office: 206-732-1331
mobile: 206-859-0370
fax: 206-732-1299
slet...@systemsbiology.org

[Martin Hubalek]

Hi Simon,

sorry, that was a typo. I am using mzwiff 4.0.2. But thanks for the info that os not related to the multiple runs in one file. In the mean time I have tried different file with multiple runs and it worked OK. I am not sure what is wrong witho those files. Is anyone able to guess based in the error message?

Martin


> ------------ Původní zpráva ------------
> Od: Simon Letarte <slet...@systemsbiology.org>
> Předmět: Re: Tiqam viewer trouble
> Datum: 06.2.2009 16:38:39
> ----------------------------------------

[Simon Letarte]

Hi Martin,

I have to admit that it happened to me too. Certain files just don't
work. We investigated that at some point. Not sure what was the
conclusion...

Natalie, do you remember?

Thanks

--
Simon Letarte, Ph. D.
Senior Research Scientist
Institute for Systems Biology
1441 North 34th Street
Seattle, WA 98103-8904

office: 206-732-1331
mobile: 206-859-0370
fax: 206-732-1299
slet...@systemsbiology.org

[Mi-Youn Brusniak]

Dear Martin,

There are two things to look for.

1. possibility of mzwiff converter
Simon described earlier with mzwiff converter. I would like to clarify
little more.
We had mzwiff converter problem. More specifically, there were a case that
Simon verified that raw data contains precursor ion using XCalibur but the
converted mzXML file from raw data doesn't contain precursorMZ. It's not
happening all the time. Only certain files that we don't know why. In turn,
TIQAM doesn't show any transitions when <precursorMZ> fields are not existed
in the converted mzXML. Simon notified group
(spctools-...@googlegroups.com) with his raw files and log files from
mzwiff converter. To the best of my knowledge, it is still pending and
doesn't address the issue.
If you have this issue after examining your mzXML file and raw data, please
directly post the issue to spctools-discussion group.

2. more likely of your problem
Based on your error messages, it's more like your database setup is not
correct.
Either your database is not running or mrm database setup was not correct.
Please try the following two steps (1) select tools -> drop/create database
and (2) load the example data posted in the TIQAM website.

If you have no problem seeing transitions of the example data, your file is
the problem.
If you have trouble with example dataset, you need reinstall and follow
installation instruction carefully to setup the database.

Have a great day!

Mi-Youn

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