Peptide sequence column in result contains modification mass

[sudarshan kumar]

Dear members,

I want to use peptide sequences from the result after the peptide prophet search. But the sequences also contains modification mass in it.

P.GSM[147.04]GLPGPKGSSGDPGKPGEAGNA.G   

How can we remove it. so that the column of sequences can be converted into fasta files.

Reg,

[AZIZ ALNAKLI]

Hi Sud, 

I think you can do that with excel. Select the cells that have the modified peptides. Use the find and replace option to find" [147.04] " and replace it with nothing, i.e. just leave the replace box empty. 

That should be enough to take out the modification from the peptide sequence.

I hope this is not a too late response and that the answer is actually helpful.

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Aziz Alnakli

Master of Research Candidate (Bioinformatics Research Group)

Faculty of Science and Engineering |   Level 1 Room 120, F7B Building (4 Wally's Walk)
Macquarie University, NSW 2109, Australia

M: + 61 424375954 | aziz.a...@students.mq.edu.au