The Trans-Proteomic Pipeline (TPP) is a complete, free, and widely-adopted suite of tools for the analysis of tandem mass spectrometry (MS/MS) proteomics data ("shotgun proteomics"). The TPP is used for analyzing raw MS/MS data to identify and quantify proteins and their abundance levels in cells and tissues, allowing investigation of research questions surrounding the identification of causes of disease, the production of diagnostic techniques, and the development of treatments. The TPP is already in use by a community of hundreds of researchers, and is of fundamental importance to many ongoing research projects. This grant will allow us to continue to maintain current functionality, support the community, and adapt to changing proteomics technology and techniques.

Public Health Relevance

Mass spectrometry based proteomics has become key to the study of many aspects of human health, it allows for the study of disease pathology, the identification of diagnostic markers and the development of treatments. The Trans Proteomics Pipeline software suite has become the cornerstone for numerous research groups who undertake mass spectrometry based experiments. This grant will enable the maintenance and evolution of this invaluable software, and enable its continued usage and expansion of its relevance throughout research institutions, hospitals, university departments and commercial organizations.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Biodata Management and Analysis Study Section (BDMA)
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Lyster, Peter
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Institute for Systems Biology
United States
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Farrah, Terry; Deutsch, Eric W; Omenn, Gilbert S et al. (2014) State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J Proteome Res 13:60-75
Bundgaard, Louise; Jacobsen, Stine; Sørensen, Mette A et al. (2014) The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research. Proteomics 14:763-73
Vizcaíno, Juan A; Deutsch, Eric W; Wang, Rui et al. (2014) ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 32:223-6
Mayer, Gerhard; Jones, Andrew R; Binz, Pierre-Alain et al. (2014) Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochim Biophys Acta 1844:98-107
Lane, Lydie; Bairoch, Amos; Beavis, Ronald C et al. (2014) Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J Proteome Res 13:15-20
Sangar, Vineet; Funk, Cory C; Kusebauch, Ulrike et al. (2014) Quantitative proteomic analysis reveals effects of epidermal growth factor receptor (EGFR) on invasion-promoting proteins secreted by glioblastoma cells. Mol Cell Proteomics 13:2618-31
Seymour, Sean L; Farrah, Terry; Binz, Pierre-Alain et al. (2014) A standardized framing for reporting protein identifications in mzIdentML 1.2. Proteomics 14:2389-99
Kusebauch, Ulrike; Deutsch, Eric W; Campbell, David S et al. (2014) Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Curr Protoc Bioinformatics 46:13.25.1-13.25.28
Vialas, Vital; Sun, Zhi; Loureiro y Penha, Carla Veronica et al. (2014) A Candida albicans PeptideAtlas. J Proteomics 97:62-8
Mayer, Gerhard; Montecchi-Palazzi, Luisa; Ovelleiro, David et al. (2013) The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford) 2013:bat009

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