Conversion of mascot dat files takes wrong DeltaMono from .dat file

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Import .dat file
2. Look at PTM section of converter

What is the expected output? What do you see instead?
MonoDelta values are incorrectly rounded values of the delta values listed in 
the mascot dat file.

For instance, in .dat file:

FixedMod1=304.205360,iTRAQ8plex (K)
FixedModResidues1=K

Is parsed as (in .dat-report.xml):
<ModMonoDelta>304.0</ModMonoDelta>

This is problem in rounding is a fatal error since the converter does not 
permit the selection of the appropriate modification because of too large 
differences between the listed MonoDelta values.    

What version of the product are you using? On what operating system?
2.10 on Linux 64bit

Original issue reported on code.google.com by p...@japps.nl on 8 Jul 2014 at 12:59

[GoogleCodeExporter]

Dear  pim@japps.nl,

Sorry about this error you've encountered when trying to convert your dat file. 
We will try and look into this issue, but in the mean time would you be able to 
generate mzIdentML (and related peak files) with Mascot in order to still make 
a 'complete' submission?
http://www.ebi.ac.uk/pride/help/archive/submission/mzidentml
http://www.ebi.ac.uk/pride/help/archive/faq#complete-PX

Else if that's not possible, could you make a 'partial' submission using your 
.dat files as 'search' files?
http://www.ebi.ac.uk/pride/help/archive/faq#partial-PX

If you have any further questions about making a submission, please email us 
using: pride-support@ebi.ac.uk

Best regards,
Tobias Ternent
Bioinformatician
PRIDE Team

Original comment by tob...@ebi.ac.uk on 8 Jul 2014 at 1:15

[GoogleCodeExporter]

Sorry my version is:

2.0.20 (build 20131031-1454)

Original comment by p...@japps.nl on 8 Jul 2014 at 1:18

[GoogleCodeExporter]

And relating to your suggestions about mxIdentML or a partial release, these 
are both no option for me now. We do not own Mascot version 2.4 needed to 
export MXIdentML v1.1 (we have v 2.3) and we publish in MCP that does not allow 
partial submissions. 

Original comment by p...@japps.nl on 8 Jul 2014 at 1:21

[GoogleCodeExporter]

Don't supposed you can contact Mascot to get some sort of free upgrade to v 2.4 
so you can export mzIdentML, which is needed for your manuscript?

Ah, the MCP requirements are a little complicated.
As I understand it, MCP require the data to be visualized in a free tool:
http://www.ebi.ac.uk/pride/help/archive/faq#journal-MCP
And any 'complete' submission would satisfy this because 'result' files can be 
viewed in PRIDE Inspector.

Technically there is a free open-source .msf viewer available (not developed or 
maintained by PRIDE):
https://code.google.com/p/thermo-msf-parser/
Which may/may not satisfy the requirements for MCP's validator. Would you be 
able to ask MCP if that would be OK for your dataset, to have .msf files which 
reviewers can view using that free Java tool?

Original comment by tob...@ebi.ac.uk on 8 Jul 2014 at 3:15

[GoogleCodeExporter]

Hello, I have been able to work around this bug in Pride converter by
performing an inline replace of the incorrect values with the correct ones
in the dat-report.xml files. I'll be all right, it does not hold be away
from submitting my results. Just fix the bug at your leasure :)

Bye, Pim

2014-07-08 17:15 GMT+02:00 <pride-converter-2@googlecode.com>:

Original comment by p...@japps.nl on 9 Jul 2014 at 7:25

[GoogleCodeExporter]

Hi Pim,

Sorry about my last message - I confused you with another of our users who has 
been trying to convert .msf files, so ignore that part about the MSF viewer.

Original comment by tob...@ebi.ac.uk on 9 Jul 2014 at 7:31

[GoogleCodeExporter]

Strange, the .dat files that I used and that gave the wrongly rounded MonoDelta 
numbers are all swissprot searches. I am working on ncbi nr searches now and 
these seem to take the correct values (same modifications). Very strange 
because there does not seem to be a format difference between the DeltaMono 
format listed in the dat files. 

Original comment by p...@japps.nl on 10 Jul 2014 at 8:37