Wikiomics:Protein mass spectrometry: Difference between revisions
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Revision as of 21:00, 19 November 2007
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.
- 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
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