The Mass Distance Fingerprint: a statistical framework for de novo detection of predominant modifications using high-accuracy mass spectrometry.
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.
Potthast
Frank
F
Functional Genomics Center Zürich, Uni/ETH Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. peptoscope@fgcz.ethz.ch
Gerrits
Bertran
B
Häkkinen
Jari
J
Rutishauser
Dorothea
D
Ahrens
Christian H
CH
Roschitzki
Bernd
B
Baerenfaller
Katja
K
Munton
Richard P
RP
Walther
Pascal
P
Gehrig
Peter
P
Seif
Philipp
P
Seeberger
Peter H
PH
Schlapbach
Ralph
R
D000465:Algorithms; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry
D010455:Peptides