Trans-Proteomic Pipeline
{{Short description|Data analysis software for proteomics}}
{{Infobox software
| name = TPP
| title =TPP
| logo =
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| screenshot =
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| developer = Institute for Systems Biology
| released = {{Start date and age|2004|12|10|df=yes}}
| latest release version = 5.0.0
| latest release date = {{Start date and age|2016|10|11|df=yes}}[https://groups.google.com/forum/#!topic/spctools-discuss/t3eucG5bgRc TPP 5.0.0 Release is Available]
| discontinued =
| programming language = C++, Perl, Java
| operating system = Linux, Windows, OS X
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| genre = Bioinformatics / Mass spectrometry software
| license = GPL v. 2.0 and LGPL
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| website = [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP 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,[http://tools.proteomecenter.org/wiki/index.php?title=Software:PeptideProphet Software:PeptideProphet - SPCTools] ProteinProphet,[http://tools.proteomecenter.org/wiki/index.php?title=Software:ProteinProphet Software:ProteinProphet - SPCTools] 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.{{cite journal | last1 = Keller | first1 = A | author-link4 = Ruedi Aebersold | last2 = Nesvizhskii | first2 = A | last3 = Kolker | first3 = E | last4 = Aebersold | first4 = R. | year = 2002 | title = Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search | journal = Anal Chem | volume = 74 | issue = 20| pages = 5383–5392 | doi=10.1021/ac025747h | pmid=12403597}} 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.{{cite journal|last1=Choi|first1=Hyungwon|last2=Ghosh|first2=Debashis|last3=Nesvizhskii|first3=Alexey I.|title=Statistical Validation of Peptide Identifications in Large-Scale Proteomics Using the Target-Decoy Database Search Strategy and Flexible Mixture Modeling|journal=Journal of Proteome Research|volume=7|issue=1|year=2008|pages=286–292|issn=1535-3893|doi=10.1021/pr7006818|pmid=18078310|url=http://www.stat.osu.edu/~statgen/joul_spr2011/Choi.pdf}} 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) "[http://www.proteomecenter.org/PDFs/Nesvi.stat.model.analchem.03.pdf 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.{{Cite journal | last1 = Reiter | first1 = L. | last2 = Claassen | first2 = M. | last3 = Schrimpf | first3 = SP. | last4 = Jovanovic | first4 = M. | last5 = Schmidt | first5 = A. | last6 = Buhmann | first6 = JM. | last7 = Hengartner | first7 = MO. | last8 = Aebersold | first8 = R. | title = Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. | journal = Mol Cell Proteomics | volume = 8 | issue = 11 | pages = 2405–17 |date=Nov 2009 | doi = 10.1074/mcp.M900317-MCP200 | doi-access = free | pmid = 19608599 | pmc=2773710}}
=== Spectral library handling ===
The SpectraST tool is able to generate spectral libraries and search datasets using these libraries.[http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST Software:SpectraST - SPCTools]