Re: [Open-ms-general] X!Tandem Adapter node - Conversion of X!Tandem ouptut to idMXL

[Straube,Werner <wer...@im...>]

Hi Hendrik,

Thank you very much for your response. 

I was asking this for the following reason:

When converting X!Tandem output tandem.xml-files into pepXML-files using the TPP tool "tandem2pepXML", an error message (warning) occurred. This seems to happen due to the fact, that pepXML-format has a limitation, if 2 modifications can occur at a single amino acid.

This happens for example with peptide N-terminal cyclization:
- if deamidation on Gln is allowed and also formation of pyro-Glu at the peptide N-terminus
- if carbamidomethylation on Cys is applied as fixed modification (from iodoacetamide) and formation of Pyro-carbamidomethyl at the peptide N-terminus is allowed

Therefore, I hope during conversion of tandem.xml files into idXML-files the occurrence of such cases are considered, as they (at least in my hands) are found quite often.

With best regards,

Werner



-----Original Message-----
From: Hendrik Weisser [mailto:hw...@sa...] 
Sent: 27 May 2014 10:30
To: General OpenMS discussion
Subject: Re: [Open-ms-general] X!Tandem Adapter node - Conversion of X!Tandem ouptut to idMXL

Hi!

> I have a question regarding the conversion of the X!Tandem output  by the X!Tandem adapter node. Are the tandem.xml result files directly converted into idXML by an OpenMS proprietary tool ? Or is a converter tool such as tandem2pepXML.exe (from TPP ?) applied during the conversion ?

They are read directly in OpenMS, using the "XTandemXMLFile" class. This is done internally in the XTandemAdapter, i.e. there is no extra conversion tool. (It would however be trivial to make one based on the XTandemAdapter code.)


Cheers

Hendrik


--
 The Wellcome Trust Sanger Institute is operated by Genome Research  Limited, a charity registered in England with number 1021457 and a  company registered in England with number 2742969, whose registered  office is 215 Euston Road, London, NW1 2BE. 

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