Hi, all,
I like to use Protein Prospector for searches by Mass. See the web site at
http://prospector.ucsf.edu/ucsfhtml3.2/msedman.htm
I simply pick the mass range--the narrower the better--and the
species--listing "All" for a search gives you a quick lesson in the sheer
number of proteins that are out there even when you specified a "narrow" mass
range--then under sequence I enter something like AAAAAA (this is protein
sequence data, not DNA sequence data) and ask for 5 amino acid mismatches in
the search--for sure your protein must have a sequence of 6 amino acids with
at least one A in it somewhere through the length of the protein!
For instance listing 24359 to 24459 as a mass range and looking under porcine
(that's Sus Scofra) yields three proteins m-calpain, titin and trypsin
precursor (it yields 38 MS-Edman searches involving these three proteins, but
these are all of the possible sequences fitting the AAAAAA search with 5 amino
acid mismatches.) If the search had been under All species more than 700
proteins would have been identified.
An even narrower mass range, say 24389 to 24429, and searching under porcine
yields only one protein, trypsin precursor. This is what I was centering this
exercise around, but normally you would not know apriori what you were going
to find--as usual the greater the mass accuracy, the better. Without
specifying the species (All species) and using this narrower mass range, 316
proteins were identified--clearly specifying the species will greatly narrow
down the search results.
Deb McMillen
Institute of Molecular Biology
University of Oregon
Eugene OR 97403
Len Packman wrote:
> Forwarded from sci.techniques.mass-spec......
>
> At NIH we are trying to get the NCBI, who run the National Library of
> Medicine's protein databases (e.g.Entrez, BLAST), to add the molecular
> weight of the protein as a searchable item. NCBI would like an estimate
> of how many people would make use of this feature i.e. would like to be
> able to identify a protein from its "accurate" molecular mass and some
> keywords. We have put up a trial system at
> http://sx102a.niddk.nih.gov/smass.html which you may look at and use.
> Warning... (1) it is a trial system only and no signal sequences are
> removed and (2) keywording is minimal. What we need is support from
> people to get this information added to the NCBI databases. Email to me
> will help but, better still, if you open the site above and do a search,
> these statistics are being kept and will be used to influence the
> decision. We will appreciate any encouragement as we think this
> information publically searchable in the database will extremely useful to
> many users, especially to the mass spectrometry community.
>
> Lewis Pannell, NIDDK, NIH.
> (ph. 301-402-2196, FAX 301-402-1967)
>
> *********************************************************************
> Dr Len C. Packman
> Assistant Director of Research
> Protein and Nucleic Acid Chemistry Facility
> Department of Biochemistry
> University of Cambridge
> 80 Tennis Court Road
> Old Addenbrookes Site
> Cambridge, CB2 1GA, UK
> Tel: +44 (1223) 333639
> FAX: +44 (1223) 766002
> e-mail: lcp2@mole.bio.cam.ac.uk
> Visit my WWW page at http://www.bio.cam.ac.uk/proj/adr/PNAC/pnac.html
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