Difference between revisions of "Wikiomics:Protein mass spectrometry"

From OpenWetWare
Jump to: navigation, search
m (credits)
m (Web sites: +GenePattern)
Line 72: Line 72:
* [http://proteome.gs.washington.edu/ U. of Washington (MacCoss)]
* [http://proteome.gs.washington.edu/ U. of Washington (MacCoss)]
* [http://www.proteomecommons.org/tools.jsp Proteome Commons] collection of tools & links
* [http://www.proteomecommons.org/tools.jsp Proteome Commons] collection of tools & links
* [http://www.broad.mit.edu/cancer/software/genepattern/desc/proteomics.html GenePattern] proteomics modules from Broad Inst.

Revision as of 12:11, 23 November 2007

Protein mass spectrometry can be divided into:

  • identification of proteins/peptides
  • quantification

Protein/peptide identification

Peptide Mass Fingerprinting (PMF) or (MS)

Old method, superseded by MS/MS

  • algorithms:
  • caveats
    • no sequence information
    • journals started to require that at least one peptide of a protein identified by PMF should be confirmed by MS/MS

Peptide fragment fingerprinting (PFF) or (MS/MS)

  • algorithms (most commonly used):
  • algorithms (other/new/experimental):
    • Spectrum Mill $$$
    • MASPIC
      • this paper claims 5-15% more confident hits than Sequest: [1]
    • InsPecT A new variable mods search from Pevzner & Tanner @UCSD (free?)

  • filtering of the results
    • Trans Proteomic Pipeline [2] (free?)
    • DTASelect it seems to be in a semi-frozen state (free for nonprofit but requires signed MTA)


Use (if possible):

  • IPI International Protein Index
  • always use target-decoy database (i.e. concatenated: human_IPI + reversed_human_IPI)
  • decoy databases creation methods:
    • protein reversal (simple)
    • peptide pseudo-reversal (used in Sorcerer by Sage-N Research)
      • MEGGAYGAGKAGGAFDPYTL => (trypsin digest, used Ms-Digest) MEGGAYGAGK AGGAFDPYTL => GAGYAGGEMK-ALTYPDFAGG (each peptide reversed, but trypsin digestion site preserved -> guessed from the Elias 2007 paper)
    • shuffled
      • MEGGAYGAGKAGGAFDPYTL => FYAGADEAGMGTYKGGAGLP (used SMS, results differ each time)
    • random (i.e. creating database of random proteins based on frequency of AA in source fasta file)
  • to create decoy database use DBToolkit free java standalone

de novo sequence determination algorithms

Spectral matching

  • P3 (server) from Global Proteomics Machine (free)
  • SpectraST from ISB, Seattle (not as many species/options as P3)
  • BiblioSpec from MacCoss lab. (free for non-profit, online licence)
    • command line only

Web sites


For a good review of programs and aspects of protein identification by mass spectrometry see:

Other tools to be sorted out

  • massSorter [3]
  • ProteinProspector [4]
  • Sonar [5]
  • DeNovoID web
  • SPIDER (PDF) de novo + homology search in other species
  • OpenSea (HTML) Java program available from authors
  • MSQuant MSQuant Parser for Mascot results for quantitation.
  • ModifiComb (HTML) (available from authors?)
  • MODi [6] web server for PTMs discovery
  • UNIMOD [7] database of PTMs
  • SILVER view your spectra with LOD scores