title: Fast and accurate database searches with MS-GF+Percolator.
abstract: One can interpret fragmentation spectra stemming from peptides in mass-spectrometry-based proteomics experiments using so-called database search engines. Frequently, one also runs post-processors such as Percolator to assess the confidence, infer unique peptides, and increase the number of identifications. A recent search engine, MS-GF+, has shown promising results, due to a new and efficient scoring algorithm. However, MS-GF+ provides few statistical estimates about the peptide-spectrum matches, hence limiting the biological interpretation. Here, we enabled Percolator processing for MS-GF+ output and observed an increased number of identified peptides for a wide variety of data sets. In addition, Percolator directly reports p values and false discovery rate estimates, such as q values and posterior error probabilities, for peptide-spectrum matches, peptides, and proteins, functions that are useful for the whole proteomics community.
authors.affiliation: Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University , Solna, Sweden.
authors.forename: Viktor
authors.initials: V
authors.lastname: Granholm
authors.forename: Sangtae
authors.initials: S
authors.lastname: Kim
authors.forename: José C F
authors.initials: JC
authors.lastname: Navarro
authors.forename: Erik
authors.initials: E
authors.lastname: Sjölund
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.forename: Lukas
authors.initials: L
authors.lastname: Käll
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D016247:Information Storage and Retrieval; D013058:Mass Spectrometry / Q000379:methods*