Trans-Proteomic Pipeline
| Developer(s) | Institute for Systems Biology |
|---|---|
| Initial release | 10 December 2004 |
| Stable release | 4.6.2 / 15 February 2013[1] |
| Written in | C++, Perl, Java |
| Operating system | Linux, Windows, OS X |
| Type | Bioinformatics / Mass spectrometry software |
| License | GPL v. 2.0 and LGPL |
| Website | TPP Wiki |
The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet,[2] ProteinProphet, [3] ASAPRatio, XPRESS and Libra.
Contents
Software Components
Probability Assignment and Validation
PeptideProphet performs statistical validation of peptide-spectra-matches (PSM) using the results of search engines by estimating an false discovery rate (FDR) on PSM level.[4] The initial PeptideProphet used a fit of a Gaussian distribution for the correct identifications and a fit of a gamma distribution for the incorrect identification. A later modification of the program allowed the usage of a target-decoy approach, using either a variable component mixture model or a semi-parametric mixture model.[5] In the PeptideProphet, specifying a decoy tag will use the variable component mixture model while selecting a non-parametric model will use the semi-parametric mixture model.
ProteinProphet identifies proteins based on the results of PeptideProphet.[6]
Mayu performs statistical validation of protein identification by estimating an False Discovery Rate (FDR) on protein level.[7]
Spectral library handling
The SpectraST tool is able to generate spectral libraries and search datasets using these libraries.[8]
See also
References
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<references />, or <references group="..." />- ↑ TPP 4.6.2 Release is Available
- ↑ Software:PeptideProphet - SPCTools
- ↑ Software:ProteinProphet - SPCTools
- ↑ Keller A, Nesvizhskii A, Kolker E, and Aebersold R. (2002) "Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search." Anal Chem 74:5383–5392.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Nesvizhskii AI, Keller A, Kolker E, Aebersold R. (2003) "A statistical model for identifying proteins by tandem mass spectrometry." Anal Chem 75:4646-58
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Software:SpectraST - SPCTools
