Trouble while loading Mascot DAT file

[GoogleCodeExporter]

> What steps will reproduce the problem?
Loading a Mascot Dat file in peptide-shaker

> What is the expected output? What do you see instead?
Expect identifications from the Mascot.dat file

> What version of the product are you using? On what operating system?
Peptide-shaker 0.18.3
searchGUI 1.10.4
Mascot 2.2
Windows XP sp3 32bits

> Please provide any additional information below.
Hi everybody,
I'm using peptide shaker for month and it use to work
well with X!Tandem and OMSSA (SearchGUI's results), however I'm having issues 
with importing my Mascot results.  I have read about parsing rules and mascot 
configuration (no decoy, same database, rule to parse accession 
">..|\([^|]*\)", parse description ">[^ ]* \(.*\)", but even with this good 
advices, when I add a Mascot.dat file the report say:

Mon Oct 15 13:03:34 CEST 2012   Parsing F002981.dat.
Mon Oct 15 13:03:36 CEST 2012   An error occured while loading the identification 
files:
Mon Oct 15 13:03:36 CEST 2012   For input string: "M"

Mon Oct 15 13:03:36 CEST 2012   Importing Data Canceled!

Log say: 

Mon Oct 15 13:38:46 CEST 2012: PeptideShaker version 0.18.3.

1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.7.0_07
os.name: Windows XP
memory: 26.1/129.8
processors available: 2
useCommandThread: false
No Decoy section found!!
java.lang.NumberFormatException: For input string: "M"
    at java.lang.NumberFormatException.forInputString(Unknown Source)
    at java.lang.Integer.parseInt(Unknown Source)
    at java.lang.Integer.valueOf(Unknown Source)
    at com.compomics.mascotdatfile.util.io.MascotIdfileReader.getAllSpectrumMatches(MascotIdfileReader.java:172)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:714)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:605)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

Do you have any helpful idea or suggestion?

> If the reported issue resulted in the tool crashing, please
> also upload the file called PeptideShaker.log (found in the
> PeptideShaker-X.Y.Z\conf folder).

Original issue reported on code.google.com by georges....@gmail.com on 15 Oct 2012 at 11:46

[GoogleCodeExporter]

Thanks for telling us about this issue. Using Mascot data in PeptideShaker can 
be a bit more tricky than using results from SearchGUI. But with the right 
settings it should work.

Can you send me the dat file you are trying to open in PeptideShaker? And 
perhaps also the mgf file used for the search? And finally the database, unless 
this is just a default UniProt database.

I'll then try to reproduce the error on my side and see if I can find the 
source of the problem.

Original comment by harald.b...@gmail.com on 15 Oct 2012 at 12:24

[GoogleCodeExporter]

Ok, I have shared you the requested files with my google Drive 
Thank you

Original comment by georges....@gmail.com on 15 Oct 2012 at 1:21

[GoogleCodeExporter]

Ok, I've been able to reproduce the problem. It turns out that some of the 
peptide charges in the mgf file are set as 'Mr' instead of '2+' or similar. And 
given that we assumed that this value would be an integer our code fails and 
PeptideShaker stops working. Should be possible to fix though. But I've also 
found some other issues when using this file in the next release of 
PeptideShaker, so we'll try to fix those as well before releasing a new version.

In the mean time you could perhaps try repeating the search in Mascot after 
first removing the 'CHARGE=Mr' lines from the MGF file. There are only two of 
these. The charge will then be "selected" by the search engine.

I'll let you know as soon as we have a new version that fixes this issue.

Original comment by harald.b...@gmail.com on 15 Oct 2012 at 2:56

• Changed state: Started

[GoogleCodeExporter]

BTW, which tool did you use to convert your instrument vendor file to mgf? We 
recommend using msConvert from ProteoWizard 
(http://proteowizard.sourceforge.net) has this should make sure that all mgf 
files are in a standard format.

Original comment by harald.b...@gmail.com on 15 Oct 2012 at 3:11

[GoogleCodeExporter]

Comment #3: Ok, I'm going to modify it and then try and let you know

Comment #4: I use an ESI-Trap HCT-ultra (Bruker�).To extract peptides and
spectra, I use DataAnalysis and ProteinScape. I've ever try to convert my
raw files (*.yep) with MSConvert, but it often crash (maybe because of
Bruker raw files). I'll try it again to compare

I thank you again

-- 
Georges PALAZON RUIZ
Interne en M�decine
Master 2 Biologie mol�culaire et cellulaire

6, bd de l'h�pital
75005 PARIS
FRANCE
tel: +33761171449
mail: georges.palazon@gmail.com <georges.palazon@gmail.com>

Original comment by georges....@gmail.com on 15 Oct 2012 at 4:12

[GoogleCodeExporter]

about comment #3: I try to change the value of "Mr" or to delete it but it 
didn't works

News : 
Happily, I've resolved this issue thanks to your advices. I think it's Bruker 
converter that fails to generate the right mgf files.

I detail it, maybe somebody have had the same problem, it could be usefull.

1- I convert *.yep (RAW file) to *.mzML with compassXport (-mode 2, -raw 0).
2- I convert *.mzML to *.mgf with MSconvert v3.0.4008 (64bits, TPP on, index 
on, other options off)
3- I generate OMX and XML with searchGUI(with an in-house decoy dB generated 
with dbtoolkit 4.1.15, and MS2 parameters)
4- I use Mascot Server to generate the dat file (with the same decoy dB, decoy 
option off,and the same parameters)
5- For the first time in many month, NO ISSUE appear with Peptide-Shaker by 
combining OMX XML & DAT

Thanks a lot

Original comment by georges....@gmail.com on 17 Oct 2012 at 12:45

[GoogleCodeExporter]

Just wanted to let you that I've now fixed the remaining issues with your old 
mgf file for the upcoming release of PeptideShaker. So in the next release you 
should be able to load it without issues. But it might still be recommended to 
use your new conversion pipeline as this removes the "Mr" values completely, 
while my solution simply ignores them.

BTW, if you change the content of an mgf file you also have to re-index the 
file. To do so simply delete the corresponding .cui file for the given mgf 
file. It is located in the same folder as the mgf file. The index file will 
then be re-created the next time you load it in PeptideShaker.

Original comment by harald.b...@gmail.com on 24 Oct 2012 at 5:02

• Changed state: Fixed