title: The Mass Distance Fingerprint: a statistical framework for de novo detection of predominant modifications using high-accuracy mass spectrometry.
abstract: We describe a statistical measure, Mass Distance Fingerprint, for automatic de novo detection of predominant peptide mass distances, i.e., putative protein modifications. The method's focus is to globally detect mass differences, not to assign peptide sequences or modifications to individual spectra. The Mass Distance Fingerprint is calculated from high accuracy measured peptide masses. For the data sets used in this study, known mass differences are detected at electron mass accuracy or better. The proposed method is novel because it works independently of protein sequence databases and without any prior knowledge about modifications. Both modified and unmodified peptides have to be present in the sample to be detected. The method can be used for automated detection of chemical/post-translational modifications, quality control of experiments and labeling approaches, and to control the modification settings of protein identification tools. The algorithm is implemented as a web application and is distributed as open source software.
authors.affiliation: Functional Genomics Center Zürich, Uni/ETH Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. peptoscope@fgcz.ethz.ch
authors.forename: Frank
authors.initials: F
authors.lastname: Potthast
authors.forename: Bertran
authors.initials: B
authors.lastname: Gerrits
authors.forename: Jari
authors.initials: J
authors.lastname: Häkkinen
authors.forename: Dorothea
authors.initials: D
authors.lastname: Rutishauser
authors.forename: Christian H
authors.initials: CH
authors.lastname: Ahrens
authors.forename: Bernd
authors.initials: B
authors.lastname: Roschitzki
authors.forename: Katja
authors.initials: K
authors.lastname: Baerenfaller
authors.forename: Richard P
authors.initials: RP
authors.lastname: Munton
authors.forename: Pascal
authors.initials: P
authors.lastname: Walther
authors.forename: Peter
authors.initials: P
authors.lastname: Gehrig
authors.forename: Philipp
authors.initials: P
authors.lastname: Seif
authors.forename: Peter H
authors.initials: PH
authors.lastname: Seeberger
authors.forename: Ralph
authors.initials: R
authors.lastname: Schlapbach
mesh_terms: D000465:Algorithms; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry
chemical_list: D010455:Peptides