A noise model for mass spectrometry based proteomics.
BACKGROUND
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.
Du
Peicheng
P
IBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598, USA. pdu@us.ibm.com
Stolovitzky
Gustavo
G
Horvatovich
Peter
P
Bischoff
Rainer
R
Lim
Jihyeon
J
Suits
Frank
F
D016477:Artifacts; D003198:Computer Simulation; D008956:Models, Chemical; D015233:Models, Statistical; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D020539:Sequence Analysis, Protein / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
D011506:Proteins