title: InsPecT: identification of posttranslationally modified peptides from tandem mass spectra.
abstract: Reliable identification of posttranslational modifications is key to understanding various cellular regulatory processes. We describe a tool, InsPecT, to identify posttranslational modifications using tandem mass spectrometry data. InsPecT constructs database filters that proved to be very successful in genomics searches. Given an MS/MS spectrum S and a database D, a database filter selects a small fraction of database D that is guaranteed (with high probability) to contain a peptide that produced S. InsPecT uses peptide sequence tags as efficient filters that reduce the size of the database by a few orders of magnitude while retaining the correct peptide with very high probability. In addition to filtering, InsPecT also uses novel algorithms for scoring and validating in the presence of modifications, without explicit enumeration of all variants. InsPecT identifies modified peptides with better or equivalent accuracy than other database search tools while being 2 orders of magnitude faster than SEQUEST, and substantially faster than X!TANDEM on complex mixtures. The tool was used to identify a number of novel modifications in different data sets, including many phosphopeptides in data provided by Alliance for Cellular Signaling that were missed by other tools.
authors: Department of Bioengineering and Computer Science Department, APM 3832, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093-0114, USA. stanner@ucsd.edu
authors: Stephen
authors: S
authors: Tanner
authors: Hongjun
authors: H
authors: Shu
authors: Ari
authors: A
authors: Frank
authors: Ling-Chi
authors: LC
authors: Wang
authors: Ebrahim
authors: E
authors: Zandi
authors: Marc
authors: M
authors: Mumby
authors: Pavel A
authors: PA
authors: Pevzner
authors: Vineet
authors: V
authors: Bafna
mesh_terms: D016208:Databases, Factual; D051550:I-kappa B Kinase / Q000737:chemistry; D007633:Keratins / Q000737:chemistry; D010447:Peptide Hydrolases / Q000737:chemistry; D010455:Peptides / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011499:Protein Processing, Post-Translational / Q000502:physiology*; D012680:Sensitivity and Specificity; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides; D007633:Keratins; D051550:I-kappa B Kinase; D010447:Peptide Hydrolases