Substitutions (point mutations ) are not supported by the parser API

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Currently the API does not make a distinction between normal modifications and 
substitution modifications, although this difference is clear in the X!Tandem 
output. 

Now everything gets into the fixed or variable modification Maps (accessible 
via XTandemFile.getModificationMap() ). For the substitution cases it is not 
possible to get the new Amino Acid letter information using the current API. 

I have attached an example X!Tandem output file which has an example of the 
peptide ADNTPANAVVPLEK having a P substituted by an S. This is recorded with an 
extra attribute called "pm" in the modification tag:

<aa type="P" at="54" modified="-10.0207" pm="S" />

Regards,

Pieter

Original issue reported on code.google.com by pieterlu...@gmail.com on 25 Jul 2012 at 8:35

Attachments:

• 55merge_tandem_WITH_SUBSTITUTIONS.xml

[GoogleCodeExporter]

Hi Pieter.

Thanks for making us aware of this shortcoming. It has now been fixed and the 
fix will be included in the next release. Two new methods have been added to 
the Modification interface isSubstitution() and getSubstitutedAminoAcid(). The 
first one simply tells you if the modification is a substitution or not, while 
the second gives you the original amino acid (or null if not a substitution).

I've tested the new methods on your example file. The file is parsed without 
issues and the information regarding the original amino acid now appears in the 
X!Tandem Viewer.

Harald

Original comment by harald.b...@gmail.com on 13 Aug 2012 at 5:03

• Changed state: Fixed

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Original comment by harald.b...@gmail.com on 13 Aug 2012 at 6:14

[GoogleCodeExporter]

I checked the fix, and it seems to be working fine now.

Original comment by pieterlu...@gmail.com on 1 Oct 2012 at 3:19