mass-spec data analysis pipeline

Question

[Himanshu Bhusan Samal]

Dear Community,

I need little help for processing mass-spec data. I would like to analyze two publicly available mass-spec datasets from PRIDE (PXD000134, PXD006271) to look for one protein sequence if it’s there or not.

It would be a great help if anyone could suggest me an easy/clear method and how to do the same. Thanks very much in advance!

Best, Himanshu

[Himanshu Bhusan Samal]

Dear Heriche,

Many thanks for your response. If I understood correctly, then in principle I couldn't expect the peptide sequence of my protein of interest to be there. Since it's not proved as a protein that means it should not be there in the list of identified peptides. Do they have some undetermined section ? Or, how should I proceed ?

I am sorry if this is too basic for you. But, I need little help. Thank you.

[Jean-Karim Heriche]

Please use the add comment button below the answer you want to reply to. This keeps the discussion organized and avoids creating answers that do not address the question.

[Himanshu Bhusan Samal]

Dear Heriche,

Sorry for that and many thanks for your response. If I understood correctly, then in principle I couldn't expect the peptide sequence of my protein of interest to be there. Since it's not proved as a protein that means it should not be there in the list of identified peptides. Do they have some undetermined section ? Or, how should I proceed ?

Thanks for your help!

[Jean-Karim Heriche]

I am not sure I understand your problem. Do you mean that your protein of interest is a predicted one ? If so, it could still be in the PRIDE peptide files if the sequence was in the database used to identify the peptides (or if the authors used a de novo identification approach which is not very common). Otherwise, you could take the spectra and reanalyze them using a database that contains the sequence you're interested in. Alternatively, you could also search the PeptideAtlas database if the data sets you're interested in have been re-analyzed there.

[Himanshu Bhusan Samal]

Thanks for the info. Yes, it's a predicted protein. I would try to do the same as you mentioned. Thank you!

Answer 1

[Jean-Karim Heriche]

The datasets in PRIDE have files that list identified peptides and associated proteins. You could simply scan them for the presence of peptides belonging to your protein of interest.