title: Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.
abstract: Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include MS to define protein sequence, protein:protein interactions, and protein PTMs. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative MS proteomics. It supports all major operating systems and instrument vendors via open data formats. Here, we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of MS/MS datasets, as well as some major upcoming features.
authors: Institute for Systems Biology, Seattle, WA, USA.
authors: Eric W
authors: EW
authors: Deutsch
authors: Institute for Systems Biology, Seattle, WA, USA.
authors: Luis
authors: L
authors: Mendoza
authors: Institute for Systems Biology, Seattle, WA, USA.
authors: David
authors: D
authors: Shteynberg
authors: Institute for Systems Biology, Seattle, WA, USA.
authors: Joseph
authors: J
authors: Slagel
authors: Institute for Systems Biology, Seattle, WA, USA.
authors: Zhi
authors: Z
authors: Sun
authors: Institute for Systems Biology, Seattle, WA, USA.
authors: Robert L
authors: RL
authors: Moritz
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006801:Humans; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D013223:Statistics as Topic
chemical_list: D020543:Proteome
keywords: Bioinformatics; Mass spectrometry
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