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.
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.
Authors: Natasha A Karp; Wolfgang Huber; Pawel G Sadowski; Philip D Charles; Svenja V Hester; Kathryn S Lilley Journal: Mol Cell Proteomics Date: 2010-04-10 Impact factor: 5.911
Authors: Andrew W Dowsey; Jane A English; Frederique Lisacek; Jeffrey S Morris; Guang-Zhong Yang; Michael J Dunn Journal: Proteomics Date: 2010-12 Impact factor: 3.984
Authors: Yi Zhang; Manor Askenazi; Jingrui Jiang; C John Luckey; James D Griffin; Jarrod A Marto Journal: Mol Cell Proteomics Date: 2009-12-17 Impact factor: 5.911
Authors: Thomas M Harris; Peicheng Du; Nicole Kawachi; Thomas J Belbin; Yanhua Wang; Nicolas F Schlecht; Thomas J Ow; Christian E Keller; Geoffrey J Childs; Richard V Smith; Ruth Hogue Angeletti; Michael B Prystowsky; Jihyeon Lim Journal: Arch Pathol Lab Med Date: 2014-10-08 Impact factor: 5.534