Wikiomics:Protein mass spectrometry

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Contents

Reviews

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

Programs used in protein mass spectrometry

TPP

Trans Proteomic Pipeline [1] and its comercial offshot IPP There is also a new wiki devoted to TPP [2] as well as a dynamic newsgroup: [3]

GPM & XTandem

An open source effort from Canada: [4]

InterAct

A new variable mods search from Pevzner & Tanner @UCSD [5]

Other tools

  • massSorter [6]
  • Open Mass Spectrometry Search Algorithm (OMSSA) [7]
  • DTASelect [8]

it seems to be in a semi-frozen state.

this paper claims 5-15% more confident hits than Sequest: [10]

  • ProteinProspector [11]

de novo sequence determination algorithms

to be verified

  • DeNovoID web
  • SPIDER (PDF) de novo + homology search in other species
  • OpenSea (HTML) Java program available from authors

Comercial Programs

New additions

  • MSQuant MSQuant Parser for Mascot results for quantitation.
  • ModifiComb (HTML) (available from authors?)
  • MODi [18] web server for PTMs discovery
  • UNIMOD [19] database of PTMs
  • SILVER view your spectra with LOD scores


Personal tools