Protein grouping tool

Question

[pisiposo84]

Hi,

Does anyone know a tool that can compute the list of protein groups (following the occam' s rule) using as input a list of peptide sequences?

All the proteomics software I know do this only 'internally' on the list of peptides identified by MS analysis. I am looking for something that allows me to submit a list of peptides I want, regardless if they have been identified or not...

Thanks

[Jean-Karim Heriche]

I have this as part of an old perl script, using EnsEMBL proteins as reference. It would probably need adapting but I can dig it up if nobody comes with a ready to use solution.

[pisiposo84]

That would be great. I am currently basing my 'analysis' on UniProt entries, whereas the list of peptides is a two columns lists, with the column 1 containing the peptide sequence and column 2 the accession number of the protein the peptide belongs to... but I guess I can be very flexible with the input data.

[Joe]

What kind of 'groups' are you after? If you just want to group/cluster the proteins by sequence, you can do this with the CD-HIT suite of tools.

Answer 1

[prvst]

You can try ProteinProphet, it's part of the Trans-Proteomics Pipeline (TPP)