A noise model for mass spectrometry based proteomics

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.

[1]  R. A. Leibler,et al.  On Information and Sufficiency , 1951 .

[2]  M. MacCoss,et al.  Evaluation and optimization of ion-current ratio measurements by selected-ion-monitoring mass spectrometry. , 2001, Analytical chemistry.

[3]  Marina Meila,et al.  RAPID COMMUNICATIONS IN MASS SPECTROMETRY Rapid Commun. Mass Spectrom. 2006; 20: 1551–1557 Published online in Wiley InterScience (www.interscience.wiley.com) DOI: 10.1002/rcm.2471 Analysis of the stochastic variation in LTQ single , 2006 .

[4]  Hua Lin,et al.  Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum , 2004, Bioinform..

[5]  Peter B O'Connor,et al.  Quantitative determination of isotope ratios from experimental isotopic distributions. , 2007, Analytical chemistry.

[6]  J. Yergey.  A GENERAL APPROACH TO CALCULATING ISOTOPIC DISTRIBUTIONS FOR MASS SPECTROMETRY. , 1983, Journal of mass spectrometry : JMS.

[7]  Peter B. O’Connor,et al.  Use of Statistical Methods for Estimation of Total Number of Charges in a Mass Spectrometry , 2004 .

[8]  Richard E Higgs,et al.  Comprehensive label-free method for the relative quantification of proteins from biological samples. , 2005, Journal of proteome research.

[9]  Hongyue Dai,et al.  Rosetta error model for gene expression analysis , 2006, Bioinform..

[10]  Peter B O'Connor,et al.  Use of statistical methods for estimation of total number of charges in a mass spectrometry experiment. , 2004, Analytical chemistry.

[11]  Peicheng Du,et al.  Data reduction of isotope-resolved LC-MS spectra , 2007, Bioinform..

[12]  I. Chernushevich,et al.  An introduction to quadrupole-time-of-flight mass spectrometry. , 2001, Journal of mass spectrometry : JMS.

[13]  Jacob D. Jaffe,et al.  MapQuant: Open‐source software for large‐scale protein quantification , 2006, Proteomics.

[14]  Y. Tu,et al.  Quantitative noise analysis for gene expression microarray experiments , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Frank Suits,et al.  Chip‐LC‐MS for label‐free profiling of human serum , 2007, Electrophoresis.

[16]  Pei Wang,et al.  Bioinformatics Original Paper a Suite of Algorithms for the Comprehensive Analysis of Complex Protein Mixtures Using High-resolution Lc-ms , 2022 .

[17]  Eugene A. Kapp,et al.  Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly‐available database , 2005, Proteomics.

[18]  T. Shaler,et al.  Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. , 2003, Analytical chemistry.

[19]  Michael J MacCoss,et al.  Quantitative comparison of proteomic data quality between a 2D and 3D quadrupole ion trap. , 2006, Analytical chemistry.

[20]  Peicheng Du,et al.  Automatic deconvolution of isotope-resolved mass spectra using variable selection and quantized peptide mass distribution. , 2006, Analytical chemistry.

[21]  M. Senko,et al.  Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions , 1995, Journal of the American Society for Mass Spectrometry.

[22]  Ronald C. Beavis.  Chemical mass of carbon in proteins , 1993 .

[23]  F. McLafferty,et al.  Automated reduction and interpretation of , 2000, Journal of the American Society for Mass Spectrometry.