A noise model for mass spectrometry based proteomics

Peicheng Du, Gustavo Stolovitzky, Peter Horvatovich, Rainer Bischoff, Jihyeon Lim, Frank Suits

Research output: Contribution to journalArticle

41 Citations (Scopus)

Abstract

Motivation: Mass spectrometry data are subjected to considerable noise. Good noise models are required for proper detection and quantification of peptides. We have characterized noise in both quadrupole time-of-flight (Q-TOF) and ion trap data, and have constructed models for the noise. Results: We find that the noise in Q-TOF data from Applied Biosystems QSTAR fits well to a combination of multinomial and Poisson model with detector dead-time correction. In comparison, ion trap noise from Agilent MSD-Trap-SL is larger than the Q-TOF noise and is proportional to Poisson noise. We then demonstrate that the noise model can be used to improve deisotoping for peptide detection, by estimating appropriate cutoffs of the goodness of fit parameter at prescribed error rates. The noise models also have implications in noise reduction, retention time alignment and significance testing for biomarker discovery.

Original languageEnglish (US)
Pages (from-to)1070-1077
Number of pages8
JournalBioinformatics
Volume24
Issue number8
DOIs
StatePublished - Apr 2008

Fingerprint

Proteomics
Mass Spectrometry
Mass spectrometry
Noise
Time-of-flight
Trap
Peptides
Multinomial Model
Ions
Poisson Model
Noise Reduction
Biomarkers
Goodness of fit
Model
Quantification
Error Rate
Siméon Denis Poisson
Alignment
Noise abatement
Acoustic noise

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Du, P., Stolovitzky, G., Horvatovich, P., Bischoff, R., Lim, J., & Suits, F. (2008). A noise model for mass spectrometry based proteomics. Bioinformatics, 24(8), 1070-1077. https://doi.org/10.1093/bioinformatics/btn078

A noise model for mass spectrometry based proteomics. / Du, Peicheng; Stolovitzky, Gustavo; Horvatovich, Peter; Bischoff, Rainer; Lim, Jihyeon; Suits, Frank.

In: Bioinformatics, Vol. 24, No. 8, 04.2008, p. 1070-1077.

Research output: Contribution to journalArticle

Du, P, Stolovitzky, G, Horvatovich, P, Bischoff, R, Lim, J & Suits, F 2008, 'A noise model for mass spectrometry based proteomics', Bioinformatics, vol. 24, no. 8, pp. 1070-1077. https://doi.org/10.1093/bioinformatics/btn078
Du P, Stolovitzky G, Horvatovich P, Bischoff R, Lim J, Suits F. A noise model for mass spectrometry based proteomics. Bioinformatics. 2008 Apr;24(8):1070-1077. https://doi.org/10.1093/bioinformatics/btn078
Du, Peicheng ; Stolovitzky, Gustavo ; Horvatovich, Peter ; Bischoff, Rainer ; Lim, Jihyeon ; Suits, Frank. / A noise model for mass spectrometry based proteomics. In: Bioinformatics. 2008 ; Vol. 24, No. 8. pp. 1070-1077.
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