{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T22:22:46Z","timestamp":1767824566810,"version":"3.49.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3120,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: \u00a0pdu@us.ibm.com<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinfomatics Online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn078","type":"journal-article","created":{"date-parts":[[2008,3,20]],"date-time":"2008-03-20T00:25:10Z","timestamp":1205972710000},"page":"1070-1077","source":"Crossref","is-referenced-by-count":57,"title":["A noise model for mass spectrometry based proteomics"],"prefix":"10.1093","volume":"24","author":[{"given":"Peicheng","family":"Du","sequence":"first","affiliation":[{"name":"1 IBM 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"}]},{"given":"Gustavo","family":"Stolovitzky","sequence":"additional","affiliation":[{"name":"1 IBM 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"}]},{"given":"Peter","family":"Horvatovich","sequence":"additional","affiliation":[{"name":"1 IBM 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"}]},{"given":"Rainer","family":"Bischoff","sequence":"additional","affiliation":[{"name":"1 IBM 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"}]},{"given":"Jihyeon","family":"Lim","sequence":"additional","affiliation":[{"name":"1 IBM 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"}]},{"given":"Frank","family":"Suits","sequence":"additional","affiliation":[{"name":"1 IBM 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"}]}],"member":"286","published-online":{"date-parts":[[2008,3,18]]},"reference":[{"key":"2023020210014167200_B1","doi-asserted-by":"crossref","first-page":"3575","DOI":"10.1093\/bioinformatics\/bth446","article-title":"Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum","volume":"20","author":"Anderle","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020210014167200_B2","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1021\/ac00052a030","article-title":"Chemical mass of carbon in proteins","volume":"65","author":"Beavis","year":"1993","journal-title":"Anal. 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