@inbook{b3688d05f9044d0d9ac7e2b6a6dfa1a9,
title = "Informatics of protein and posttranslational modification detection via shotgun proteomics",
abstract = "Frequently, proteomic LC-MS/MS data may contain sets of modi fi cations that evade identi fi cation during standard database search. For many laboratories, the standard technique to seek posttranslational modi fi cations (PTMs) adds a short list of speci fi ed mass shifts to database search con fi guration. This technique provides information for only the speci fi ed PTMs, takes substantial time to run, and drives false discoveries upward through an exponential expansion of search space. This protocol describes a more structured approach to blind PTM discovery through reducing protein lists, targeting attention to a datadriven list of mass shifts, and seeking the resulting short list of modi fi cations through targeted search.",
keywords = "Database search, Posttranslational modi fi cation, Protein identi fi cation, Proteome informatics, Sequence tagging, Shotgun proteomics, Software",
author = "Holman, {Jerry D.} and Surendra Dasari and Tabb, {David L.}",
year = "2013",
doi = "10.1007/978-1-62703-360-2_14",
language = "English (US)",
isbn = "9781627033596",
series = "Methods in Molecular Biology",
pages = "167--179",
editor = "Ming Zhou and Timothy Veenstra",
booktitle = "Proteomics for Biomarker Discovery",
}