The Trans-Proteomic Pipeline (TPP) is an
open-source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...
data analysis software for
proteomics
Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...
developed at the
Institute for Systems Biology (ISB) by the
Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, ProteinProphet, 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.
The initial PeptideProphet used a fit of a
Gaussian distribution for the correct identifications and a fit of a
gamma distribution
In probability theory and statistics, the gamma distribution is a two-parameter family of continuous probability distributions. The exponential distribution, Erlang distribution, and chi-square distribution are special cases of the gamma distri ...
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.
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.
[Nesvizhskii AI, Keller A, Kolker E, Aebersold R. (2003)]
A statistical model for identifying proteins by tandem mass spectrometry.
Anal Chem 75:4646-58
Mayu performs statistical validation of protein identification by estimating a
False Discovery Rate (FDR) on protein level.
Spectral library handling
The SpectraST tool is able to generate spectral libraries and search datasets using these libraries.
Software:SpectraST - SPCTools
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See also
* OpenMS
* ProteoWizard
* Mass spectrometry software
References
{{reflist
Free science software
Bioinformatics software
Mass spectrometry software
Proteomics