title: Software pipeline and data analysis for MS/MS proteomics: the trans-proteomic pipeline.
abstract: The LC-MS/MS shotgun proteomics workflow is widely used to identify and quantify sample peptides and proteins. The technique, however, presents a number of challenges for large-scale use, including the diverse raw data file formats output by mass spectrometers, the large false positive rate among peptide assignments to MS/MS spectra, and the loss of connectivity between identified peptides and the sample proteins that gave rise to them. Here we describe the Trans-Proteomic Pipeline, a freely available open source software suite that provides uniform analysis of LC-MS/MS data from raw data to quantified sample proteins. In a straightforward manner, users can extract MS/MS information from raw data of many instrument formats, submit them to search engines for peptide identification, validate the results to remove false hits, combine together results of multiple search engines, infer sample proteins that gave rise to the identified peptides, and perform quantitation at the peptide and protein levels.
authors.affiliation: Rosetta Biosoftware, Seattle, WA, USA. adk7000@gmail.com
authors.forename: Andrew
authors.initials: A
authors.lastname: Keller
authors.forename: David
authors.initials: D
authors.lastname: Shteynberg
mesh_terms: D020407:Internet; D007553:Isotope Labeling; D013058:Mass Spectrometry / Q000379:methods*; D008970:Molecular Weight; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis / Q000737:chemistry; D020539:Sequence Analysis, Protein; D012984:Software; D013223:Statistics as Topic; D014584:User-Computer Interface
chemical_list: D010455:Peptides; D029701:Saccharomyces cerevisiae Proteins