title: A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry.
abstract: A novel algorithm, PILOT_PTM, has been developed for the untargeted identification of post-translational modifications (PTMs) on a template sequence. The algorithm consists of an analysis of an MS/MS spectrum via an integer linear optimization model to output a rank-ordered list of PTMs that best match the experimental data. Each MS/MS spectrum is analyzed by a preprocessing algorithm to reduce spectral noise and label potential complimentary, offset, isotope, and multiply charged peaks. Postprocessing of the rank-ordered list from the integer linear optimization model will resolve fragment mass errors and will reorder the list of PTMs based on the cross-correlation between the experimental and theoretical MS/MS spectrum. PILOT_PTM is instrument-independent, capable of handling multiple fragmentation technologies, and can address the universe of PTMs for every amino acid on the template sequence. The various features of PILOT_PTM are presented, and it is tested on several modified and unmodified data sets including chemically synthesized phosphopeptides, histone H3-(1-50) polypeptides, histone H3-(1-50) tryptic fragments, and peptides generated from proteins extracted from chromatin-enriched fractions. The data sets consist of spectra derived from fragmentation via collision-induced dissociation, electron transfer dissociation, and electron capture dissociation. The capability of PILOT_PTM is then benchmarked using five state-of-the-art methods, InsPecT, Virtual Expert Mass Spectrometrist (VEMS), Mod(i), Mascot, and X!Tandem. PILOT_PTM demonstrates superior accuracy on both the small and large scale proteome experiments. A protocol is finally developed for the analysis of a complete LC-MS/MS scan using template sequences generated from SEQUEST and is demonstrated on over 270,000 MS/MS spectra collected from a total chromatin digest.
authors.affiliation: Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, USA.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Baliban
authors.forename: Peter A
authors.initials: PA
authors.lastname: DiMaggio
authors.forename: Mariana D
authors.initials: MD
authors.lastname: Plazas-Mayorca
authors.forename: Nicolas L
authors.initials: NL
authors.lastname: Young
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Garcia
authors.forename: Christodoulos A
authors.initials: CA
authors.lastname: Floudas
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D002853:Chromatography, Liquid; D030562:Databases, Protein; D006367:HeLa Cells; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D010748:Phosphopeptides / Q000138:chemical synthesis / Q000737:chemistry; D011499:Protein Processing, Post-Translational; D015203:Reproducibility of Results; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D006657:Histones; D010748:Phosphopeptides