DOI: 10.1002/rcm.2203. Confident protein identification using the average peptide score method coupled with search‐specific, <i>ab initio</i> thresholds

Confident protein identification using the average peptide score method coupled with search‐specific, ab initio thresholds

10.1002/rcm.2203

Crossref journal-article

Wiley

Rapid Communications in Mass Spectrometry (311)

Abstract

AbstractPerhaps the greatest difficulty in interpreting large sets of protein identifications derived from mass spectrometric methods is whether or not to trust the results. For such experiments, the level of confidence in each protein identification made needs to be far greater than the often used 95% significance threshold to avoid the identification of many false‐positives. To provide higher confidence results, we have developed an innovative scoring strategy coupling the recently published Average Peptide Score (APS) method with pre‐filtering of peptide identifications, using a simple peptide quality filter. Iterative generation of these filters in conjunction with reversed database searching is used to determine the correct levels at which the APS and peptide quality thresholds should be set to return virtually zero false‐positive reports. This proceeds without the need to reference a known dataset. Copyright © 2005 John Wiley & Sons, Ltd.

Bibliography

Shadforth, I., Dunkley, T., Lilley, K., Crowther, D., & Bessant, C. (2005). Confident protein identification using the average peptide score method coupled with searchâspecific, ab initio thresholds. Rapid Communications in Mass Spectrometry, 19(22), 3363â3368. Portico.

Authors 5

Ian Shadforth (first)
Tom Dunkley (additional)
Kathryn Lilley (additional)
Daniel Crowther (additional)
Conrad Bessant (additional)

References 13 Referenced 26

10.1007/978-3-642-56895-4_6
10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2
10.1038/10890
10.1002/1615-9861(200210)2:10<1406::AID-PROT1406>3.0.CO;2-9
10.1021/ac001196o
10.1002/pmic.200400869
10.1021/ac0341261
10.1016/1044-0305(94)80016-2
10.1016/j.jchromb.2003.07.019
10.1002/rcm.1741
10.1074/mcp.T400009-MCP200
10.1074/mcp.M400129-MCP200
CottrellJS.BSPR/EBI Meeting Hinxton Hall Cambridge UK 12–13 July 2004.

Dates

Type	When
Created	19 years, 10 months ago (Oct. 18, 2005, 10:46 a.m.)
Deposited	1 year, 10 months ago (Oct. 13, 2023, 2:48 p.m.)
Indexed	3 months, 2 weeks ago (May 21, 2025, 4:46 a.m.)
Issued	19 years, 10 months ago (Oct. 18, 2005)
Published	19 years, 10 months ago (Oct. 18, 2005)
Published Online	19 years, 10 months ago (Oct. 18, 2005)
Published Print	19 years, 9 months ago (Nov. 30, 2005)

Funders 0

None

BibTeX

@article{Shadforth_2005, title={Confident protein identification using the average peptide score method coupled with search‐specific, ab initio thresholds}, volume={19}, ISSN={1097-0231}, url={http://dx.doi.org/10.1002/rcm.2203}, DOI={10.1002/rcm.2203}, number={22}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Shadforth, Ian and Dunkley, Tom and Lilley, Kathryn and Crowther, Daniel and Bessant, Conrad}, year={2005}, month=oct, pages={3363–3368} }

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