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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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Export MGF with annotated fragment ions? #482

Open denisbeslic opened 2 years ago

denisbeslic commented 2 years ago

Hi!

Is it possible to export the mgf file with the identified fragment ions?

I run a database search via DeNovoGUI using MSGF+ & XTandem!, and want a mgf with the annotated b- and y-ions as a result.

For example:

Input MGF

BEGIN IONS
TITLE=test1
RTINSECONDS=562.54803
PEPMASS=479.76953
CHARGE=2+
211.9772644 1524.0 
226.1559906 10176.0 
305.6876221 1620.0
306.1850586 1068.0
317.1324158 1120.0 
331.1958008 1400.0 
...

Output MGF

BEGIN IONS
TITLE=test1
RTINSECONDS=562.54803
PEPMASS=479.76953
CHARGE=2+
211.9772644 1524.0 
226.1559906 10176.0 b1
305.6876221 1620.0
306.1850586 1068.0
317.1324158 1120.0 b2
331.1958008 1400.0 b3
...

Or is there another way to export the exact mass of the identified fragment ions?

hbarsnes commented 2 years ago

As far as I know, this is not something we support at the moment. It should not be too difficult to implement, but I'm afraid we do not have the resources that allows us to prioritize it right now. I will however put it on the request list and maybe we'll get to it at some point. No guarantees though.