Trans-Proteomic Pipeline
Template:Short description Script error: No such module "Infobox".Template:Template other Script error: No such module "Check for unknown parameters".Script error: No such module "Check for conflicting parameters".
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,[1] ProteinProphet,[2] ASAPRatio, XPRESS and Libra.
Software Components
Probability Assignment and Validation
PeptideProphet performs statistical validation of peptide-spectra-matches (PSM) using the results of search engines by estimating a false discovery rate (FDR) on PSM level.[3] 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.[4] 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.[5]
Mayu performs statistical validation of protein identification by estimating a false discovery rate (FDR) on protein level.[6]
Spectral library handling
The SpectraST tool is able to generate spectral libraries and search datasets using these libraries.[7]
See also
References
<templatestyles src="Reflist/styles.css" />
- ↑ Software:PeptideProphet - SPCTools
- ↑ Software:ProteinProphet - SPCTools
- ↑ Script error: No such module "Citation/CS1".
- ↑ Script error: No such module "Citation/CS1".
- ↑ Nesvizhskii AI, Keller A, Kolker E, Aebersold R. (2003) "A statistical model for identifying proteins by tandem mass spectrometry." Anal Chem 75:4646-58
- ↑ Script error: No such module "Citation/CS1".
- ↑ Software:SpectraST - SPCTools
Script error: No such module "Check for unknown parameters".