Systematic characterization of high mass accuracy influence on false discovery and probability scoring in peptide mass fingerprinting

Eric D Dodds; Brian H Clowers; Paul J Hagerman; Carlito B Lebrilla

doi:10.1016/j.ab.2007.10.009

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Systematic characterization of high mass accuracy influence on false discovery and probability scoring in peptide mass fingerprinting

Journal article

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Peer reviewed

Systematic characterization of high mass accuracy influence on false discovery and probability scoring in peptide mass fingerprinting

Eric D Dodds, Brian H Clowers, Paul J Hagerman and Carlito B Lebrilla

Analytical biochemistry, Vol.372(2), pp.156-166

2008

DOI: https://doi.org/10.1016/j.ab.2007.10.009

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https://hdl.handle.net/2376/109301

PMCID: PMC2696393

PMID: 17980142

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Abstract

Peptide mass fingerprinting

Mass measurement accuracy

Matrix-assisted laser desorption/ionization

Fourier transform ion cyclotron resonance mass spectrometry

False positive

Whereas the bearing of mass measurement error on protein identification is sometimes underestimated, uncertainty in observed peptide masses unavoidably translates to ambiguity in subsequent protein identifications. Although ongoing instrumental advances continue to make high accuracy mass spectrometry (MS) increasingly accessible, many proteomics experiments are still conducted with rather large mass error tolerances. In addition, the ranking schemes of most protein identification algorithms do not include a meaningful incorporation of mass measurement error. This article provides a critical evaluation of mass error tolerance as it pertains to false positive peptide and protein associations resulting from peptide mass fingerprint (PMF) database searching. High accuracy, high resolution PMFs of several model proteins were obtained using matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI–FTICR–MS). Varying levels of mass accuracy were simulated by systematically modulating the mass error tolerance of the PMF query and monitoring the effect on figures of merit indicating the PMF quality. Importantly, the benefits of decreased mass error tolerance are not manifest in Mowse scores when operating at tolerances in the low parts-per-million range but become apparent with the consideration of additional metrics that are often overlooked. Furthermore, the outcomes of these experiments support the concept that false discovery is closely tied to mass measurement error in PMF analysis. Clear establishment of this relation demonstrates the need for mass error-aware protein identification routines and argues for a more prominent contribution of high accuracy mass measurement to proteomic science.

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Title: Systematic characterization of high mass accuracy influence on false discovery and probability scoring in peptide mass fingerprinting
Creators: Eric D Dodds - Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
Brian H Clowers - Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
Paul J Hagerman - School of Medicine, Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA 95616, USA
Carlito B Lebrilla - Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
Publication Details: Analytical biochemistry, Vol.372(2), pp.156-166
Academic Unit: Chemistry, Department of
Publisher: Elsevier Inc
Identifiers: 99900547238701842
Language: English
Resource Type: Journal article