De novo peptide analysis

[mfaleevs]

Hi there! I

 was wondering if it is possible to do some de novo peptide analysis peptideshaker? 

I have a list of peptides (gotten from genomic intergenic regions), that I would like to see if they are part of the mass-spec data I have downloaded from PRIDE. I was wondering whether its possible to somehow search for these? 

Any guidance would be greatly appreciated!

Many thanks,

Maria

[Harald Barsnes]

Hi Maria,

First of all, sorry for the late answer. I did not see your message until now.

As to your question, I guess it comes down to what you mean by novo peptide analysis. It sounds like what you want is to see whether a list peptide sequences can be found in a given PRIDE dataset and not research or reprocess the peptide/spectra? In that case, this is not something that is supported by our tools which are mainly focused on identifying peptides starting from a file of input spectra.

However, I think that there may be tools in PRIDE that you can use for your wanted task. But you'd be better of contacting the PRIDE team directly.

In any case, I guess you have most likely already found a way, given our very late answer.

Best regards,

Harald