title: A spectral clustering approach to MS/MS identification of post-translational modifications.
abstract: Unidentified tandem mass spectra typically represent 50-90% of the spectra acquired in proteomics studies. This manuscript describes a novel algorithm, "Bonanza", for clustering spectra without knowledge of peptide or protein identifications. Further analysis leverages existing peptide identifications to infer related, likely valid identifications. Significantly more spectra can be identified with this approach, including spectra with unexpected potential modifications or amino-acid substitutions.
authors.affiliation: Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA. jfalkner@umich.edu
authors.forename: Jayson A
authors.initials: JA
authors.lastname: Falkner
authors.forename: Jarret W
authors.initials: JW
authors.lastname: Falkner
authors.forename: Anastasia K
authors.initials: AK
authors.lastname: Yocum
authors.forename: Philip C
authors.initials: PC
authors.lastname: Andrews
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D016000:Cluster Analysis; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000235:genetics; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D053719:Tandem Mass Spectrometry
chemical_list: D010455:Peptides