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 and view the source code, design documents, or content of the product. The open source model is a decentrali ...
data analysis software for
proteomics
Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replicatio ...
developed at the
Institute for Systems Biology
Institute for Systems Biology (ISB) is a non-profit research institution located in Seattle, Washington, United States. ISB concentrates on systems biology, the study of relationships and interactions between various parts of biological systems, ...
(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
In statistics, the false discovery rate (FDR) is a method of conceptualizing the rate of type I errors in null hypothesis testing when conducting multiple comparisons. FDR-controlling procedures are designed to control the FDR, which is the exp ...
(FDR) on PSM level.
The initial PeptideProphet used a fit of a
Gaussian distribution
In probability theory and statistics, a normal distribution or Gaussian distribution is a type of continuous probability distribution for a real number, real-valued random variable. The general form of its probability density function is
f(x ...
for the correct identifications and a fit of a
gamma distribution
In probability theory and statistics, the gamma distribution is a versatile two-parameter family of continuous probability distributions. The exponential distribution, Erlang distribution, and chi-squared distribution are special cases of the g ...
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
In statistics, the false discovery rate (FDR) is a method of conceptualizing the rate of type I errors in null hypothesis testing when conducting multiple comparisons. FDR-controlling procedures are designed to control the FDR, which is the exp ...
(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
/ref>
See also
* OpenMS
* ProteoWizard
* Mass spectrometry software
Mass spectrometry software is used for data acquisition, analysis, or representation in mass spectrometry.
Proteomics software
In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS2) experiments are used for protein/ ...
References
{{reflist
Free science software
Bioinformatics software
Mass spectrometry software
Proteomics
Chromatography software