title: ISPTM: an iterative search algorithm for systematic identification of post-translational modifications from complex proteome mixtures.
abstract: Identifying protein post-translational modifications (PTMs) from tandem mass spectrometry data of complex proteome mixtures is a highly challenging task. Here we present a new strategy, named iterative search for identifying PTMs (ISPTM), for tackling this challenge. The ISPTM approach consists of a basic search with no variable modification, followed by iterative searches of many PTMs using a small number of them (usually two) in each search. The performance of the ISPTM approach was evaluated on mixtures of 70 synthetic peptides with known modifications, on an 18-protein standard mixture with unknown modifications and on real, complex biological samples of mouse nuclear matrix proteins with unknown modifications. ISPTM revealed that many chemical PTMs were introduced by urea and iodoacetamide during sample preparation and many biological PTMs, including dimethylation of arginine and lysine, were significantly activated by Adriamycin treatment in nuclear matrix associated proteins. ISPTM increased the MS/MS spectral identification rate substantially, displayed significantly better sensitivity for systematic PTM identification compared with that of the conventional all-in-one search approach, and offered PTM identification results that were complementary to InsPecT and MODa, both of which are established PTM identification algorithms. In summary, ISPTM is a new and powerful tool for unbiased identification of many different PTMs with high confidence from complex proteome mixtures.
authors.affiliation: Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States.
authors.forename: Xin
authors.initials: X
authors.lastname: Huang
authors.forename: Lin
authors.initials: L
authors.lastname: Huang
authors.forename: Hong
authors.initials: H
authors.lastname: Peng
authors.forename: Ashu
authors.initials: A
authors.lastname: Guru
authors.forename: Weihua
authors.initials: W
authors.lastname: Xue
authors.forename: Sang Yong
authors.initials: SY
authors.lastname: Hong
authors.forename: Miao
authors.initials: M
authors.lastname: Liu
authors.forename: Seema
authors.initials: S
authors.lastname: Sharma
authors.forename: Kai
authors.initials: K
authors.lastname: Fu
authors.forename: Adam P
authors.initials: AP
authors.lastname: Caprez
authors.forename: David R
authors.initials: DR
authors.lastname: Swanson
authors.forename: Zhixin
authors.initials: Z
authors.lastname: Zhang
authors.forename: Shi-Jian
authors.initials: SJ
authors.lastname: Ding
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D002460:Cell Line; D002852:Chromatography, Ion Exchange; D051379:Mice; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry / Q000302:isolation & purification; D010449:Peptide Mapping / Q000379:methods*; D011499:Protein Processing, Post-Translational; D059748:Proteolysis; D020543:Proteome / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D012372:ROC Curve; D057386:Search Engine; D012984:Software; D053719:Tandem Mass Spectrometry; D014357:Trypsin / Q000737:chemistry
chemical_list: D010446:Peptide Fragments; D020543:Proteome; D014357:Trypsin
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