Wikiomics:Protein mass spectrometry

Reviews

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

• Hernandez et al. 2006 (HTML)

• Palagi et al. 2006 (PDF)

• Shadforth et al. 2005 (PDF)

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.

• MASPIC [9]

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

• ProteinProspector [11]

• ProFound [12]

• Aldente [13]

• Sonar [14]

de novo sequence determination algorithms

• PepNovo: (PDF)
• Sherenga (PDF)
• Peaks (PDF)
• Lutefisk web

to be verified

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

Comercial Programs

• Sequest [15]
• Mascot [16]
• Spectrum Mill [17]

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