A noise model for mass spectrometry based proteomics |
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| Authors: | Du Peicheng Stolovitzky Gustavo Horvatovich Peter Bischoff Rainer Lim Jihyeon Suits Frank |
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| Institution: | 1IBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598, USA, 2University of Groningen, Antonius Deusinglaan 1, Postbus 196, 9700 AD Groningen, The Netherlands and 3Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA |
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| Abstract: | Motivation: Mass spectrometry data are subjected to considerablenoise. Good noise models are required for proper detection andquantification of peptides. We have characterized noise in bothquadrupole time-of-flight (Q-TOF) and ion trap data, and haveconstructed models for the noise. Results: We find that the noise in Q-TOF data from Applied BiosystemsQSTAR fits well to a combination of multinomial and Poissonmodel with detector dead-time correction. In comparison, iontrap noise from Agilent MSD-Trap-SL is larger than the Q-TOFnoise and is proportional to Poisson noise. We then demonstratethat the noise model can be used to improve deisotoping forpeptide detection, by estimating appropriate cutoffs of thegoodness of fit parameter at prescribed error rates. The noisemodels also have implications in noise reduction, retentiontime alignment and significance testing for biomarker discovery. Contact: pdu{at}us.ibm.com Supplementary information: Supplementary data are availableat Bioinfomatics Online.
Associate Editor: Olga Troyanskaya |
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