Hello everyone,
I have a large set of potential proteins that I believe may or may not actually exist. I was looking for a way to query existing mass-spec databases to check for the existence of these proteins and see if there was a potential 'hit'. I have experience with Python + the Biopython library, but I am a relative novice when it comes to analyzing any sort of mass-spec data. I just downloaded MaxQuant but I have yet to choose/download a potential dataset, let alone figure out how to check if the novel peptides I have exist in a dataset.
I would appreciate any help!
Hi,
You could BLAST search the sequences of your alleged proteins against the protein database of your organism of interest (if the latter exists..), or download a proteomic dataset from an open-source repository (like that of journals such as Molecular and Cellular Proteomics or Journal of Proteome Research) and search that against a protein database (FASTA, Uniprot, ..) containing the sequences of your alleged proteins (that you've added to the database file yourself).
Hope this helps!
Hey Eef,
I don't think that would work because if the protein isn't annotated in the genome, you wouldn't be able BLAST against it!
Also @Pritam,
Thanks for the response but I didn't find a tool in the list you sent that includes anything like I was looking for unfortunately
Hi Yousuf Khan,
Peptide identification- http://caps.ncbs.res.in/peptidemine/peptidemine.html
http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=PMF
peptideatlas- http://www.peptideatlas.org/
Tandem mass spectrometry data based peptide search- https://www.ncbi.nlm.nih.gov/CBBResearch/qmbp/raid/raid.html
Hope this link useful,
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