[Bioperl-l] protein identification program for proteomics

Peter J Ulintz pulintz@umich.edu
Thu, 14 Sep 2000 08:30:13 -0400 (EDT)

There are other packages that have been written that do similar,
MOWSE-type things, such as Protein Prospector
(http://prospector.ucsf.edu/) and PeptideSearch

These programs are also a bit more specific to the results of sequence
generated by MS/MS experiments, and are more geared to peptide mass
mapping data than simply N or C term sequence data.  Prospector has an
"MS-Edman" program that can be used without peptide masses, in which you
can enter a regular expression of the sequence and search for matches in

In my experience you can usually get a pretty good match with a normal 10
residues of N-term Edman sequence and a MW, at least for smaller genomes.  
I'd say a routine could be written to do this using the existing objects
in BioPerl, although how well it would work would depend on the data.



On Thu, 14 Sep 2000, Val Curwen wrote:

> >>>> 
> >>>> I am looking for a stand alone protein identification program for
> >>>> proteomics written in Perl to run on my Linux box.  This program will
> >>>> identify proteins based on their molecular weight, and their N-terminal,
> >>>> or C-terminal sequence (a short one that you get from micro sequencing).
> >>>> The program will search flat files of amino acids sequences from the
> >>>> generic databases.
> >>>
> >>>I think Alan Bleasbly once wrote something like this, so there might be
> >>>something in EMBOSS...
> It isn't in perl, but this does sound rather like mowse (EMBOSS version 
> is emowse), that uses peptide mass fingerprints following protease 
> digestion to identify proteins - proteins can be identified by a 
> very few experimentally determined fragment masses. Whether a 
> single N/C terminal peptide with sequence information and whole 
> sequence MW will be sufficient I don't know - I've forwarded the 
> message on to Alan but he's in a meeting right now.
> We have a mowse server at HGMP (you don't need to be registered to 
> use it):
> http://www.hgmp.mrc.ac.uk/Bioinformatics/Webapp/mowse/
> At the moment that only searches a database of fragments derived from
> OWL sequences. The version Alan has just checked into EMBOSS may well
> be able to search others - but I'll have to check with him. EMBOSS is 
> happy under Linux.
> Hope this helps,
> Val
> Val Curwen
> Bioinformatics, MRC HGMP-Resource Centre, 
> Hinxton, Cambridge, CB10 1SB
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