Question: mass-spec data analysis pipeline
0
gravatar for Himanshu Bhusan Samal
10 months ago by
Germany/Berlin/Max Delbruck Center for Molecular Medicine
Himanshu Bhusan Samal20 wrote:

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

mass-spec • 414 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by Himanshu Bhusan Samal20

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.

ADD REPLYlink written 10 months ago by Himanshu Bhusan Samal20

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.

ADD REPLYlink written 10 months ago by Jean-Karim Heriche20k

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!

ADD REPLYlink written 10 months ago by Himanshu Bhusan Samal20

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.

ADD REPLYlink written 10 months ago by Jean-Karim Heriche20k

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

ADD REPLYlink written 10 months ago by Himanshu Bhusan Samal20
2
gravatar for Jean-Karim Heriche
10 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

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.

ADD COMMENTlink modified 10 months ago • written 10 months ago by Jean-Karim Heriche20k
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