On the Proper Use of Mass Accuracy in Proteomics*

Mass measurement is the main outcome of mass spectrometry-based proteomics yet the potential of recent advances in accurate mass measurements remains largely unexploited. There is not even a clear definition of mass accuracy in the proteomics literature, and we identify at least three uses of this term: anecdotal mass accuracy, statistical mass accuracy, and the maximum mass deviation (MMD) allowed in a database search. We suggest using the second of these terms as the generic one. To make the best use of the mass precision offered by modern instruments we propose a series of simple steps involving recalibration of the data on “internal standards” contained in every proteomics data set. Each data set should be accompanied by a plot of mass errors from which the appropriate MMD can be chosen. More advanced uses of high mass accuracy include an MMD that depends on the signal abundance of each peptide. Adapting search engines to high mass accuracy in the MS/MS data is also a high priority. Proper use of high mass accuracy data can make MS-based proteomics one of the most “digital” and accurate post-genomics disciplines.

[1]  Alexander Makarov,et al.  Dynamic range of mass accuracy in LTQ orbitrap hybrid mass spectrometer , 2006, Journal of the American Society for Mass Spectrometry.

[2]  Brendan K Faherty,et al.  Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics*S , 2006, Molecular & Cellular Proteomics.

[3]  Mikhail M Savitski,et al.  ModifiComb, a New Proteomic Tool for Mapping Substoichiometric Post-translational Modifications, Finding Novel Types of Modifications, and Fingerprinting Complex Protein Mixtures* , 2006, Molecular & Cellular Proteomics.

[4]  Xiaohui S. Xie,et al.  A Mammalian Organelle Map by Protein Correlation Profiling , 2006, Cell.

[5]  M. Mann,et al.  Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap*S , 2005, Molecular & Cellular Proteomics.

[6]  Dekel Tsur,et al.  Identification of post-translational modifications by blind search of mass spectra , 2005, Nature Biotechnology.

[7]  M. Mann,et al.  Trypsin Cleaves Exclusively C-terminal to Arginine and Lysine Residues*S , 2004, Molecular & Cellular Proteomics.

[8]  Bernhard Spengler,et al.  De novo sequencing, peptide composition analysis, and composition-based sequencing: A new strategy employing accurate mass determination by fourier transform ion cyclotron resonance mass spectrometry , 2004, Journal of the American Society for Mass Spectrometry.

[9]  Waltraud X. Schulze,et al.  A Novel Proteomic Screen for Peptide-Protein Interactions* , 2004, Journal of Biological Chemistry.

[10]  M. Mann,et al.  Proteomic characterization of the human centrosome by protein correlation profiling , 2003, Nature.

[11]  Neil Hall,et al.  Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry , 2002, Nature.

[12]  Alexey I Nesvizhskii,et al.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.

[13]  Timothy D. Veenstra,et al.  AN ACCURATE MASS TAG STRATEGY FOR QUANTITATIVE AND HIGH THROUGHPUT PROTEOME MEASUREMENTS , 2002 .

[14]  Roman A. Zubarev,et al.  Accuracy Requirements for Peptide Characterization by Monoisotopic Molecular Mass Measurements , 1996 .