Convert mascot format to fasta ??

Question

[Leandro de Mattos]

Dear colleagues of bioinformatics,

Anyone know some way to convert mascote format (mass) to Fasta.

Thanks,
Leandro.

[Pierre Lindenbaum]

give us an example of mascot file please.

Answer 1

[Leandro de Mattos]

Hi Peter. the Mascot generic format is a plain text (ASCII) file containing peak list information and contain a list of peptide mass values, one per line, optionally followed by white space and a peak area or intensity value.

###FS:    #m/z: 339.500011 #charge   3
###MaxRes:#m/z: 0.000000 #charge-128
###MS: 1610/1612/1615/
###MSMS: 1611/1613/1616/

BEGIN IONS
TITLE= Cmpd 2, +MSn(339.500000), 18.68 min
PEPMASS=339.5000114    8486
CHARGE=3+
267.1157527    136    
388.2284896    64    
489.2795900    158    
600.3089972    76    
618.3214060    218

END IONS

I think that I should discover how the program Maxquant (www.maxquant.org) or Mascot software works (www.matrixscience.com/). If anyone has any view.

Thanks for your attention!

[Jean-Karim Heriche]

FASTA is a format designed for sequences. The Mascot file you describe doesn't have sequences. If what you want is a FASTA file of the peptides produced by Mascot, Mascot can output theses in XML or CSV. It's then just a matter of parsing one of these to FASTA.

Maybe this can help: http://www.matrixscience.com/help/export_help.html

[Leandro de Mattos]

Thanks Jean-Karim. ;D