Modification site localization scoring: strategies and performance.

Molecular & Cellular Proteomics : MCP
Robert J Chalkley, Karl R Clauser

Abstract

Using enrichment strategies many research groups are routinely producing large data sets of post-translationally modified peptides for proteomic analysis using tandem mass spectrometry. Although search engines are relatively effective at identifying these peptides with a defined measure of reliability, their localization of site/s of modification is often arbitrary and unreliable. The field continues to be in need of a widely accepted metric for false localization rate that accurately describes the certainty of site localization in published data sets and allows for consistent measurement of differences in performance of emerging scoring algorithms. In this article are discussed the main strategies currently used by software for modification site localization and ways of assessing the performance of these different tools. Methods for representing ambiguity are reviewed and a discussion of how the approaches transfer to different data types and modifications is presented.

References

Jan 19, 2000·Nature·B D Strahl, C D Allis
Jun 14, 2005·Trends in Biochemical Sciences·Tony Pawson, John D Scott
Aug 2, 2005·Nature Cell Biology·Donald S KirkpatrickSteven P Gygi
May 4, 2006·Molecular & Cellular Proteomics : MCP·Ralph A BradshawRuedi Aebersold
Apr 15, 2008·Molecular & Cellular Proteomics : MCP·Claudio P AlbuquerqueHuilin Zhou
Jun 12, 2008·Journal of Proteome Research·Brian E RuttenbergJason D Hoffert
Jan 16, 2009·Proceedings of the National Academy of Sciences of the United States of America·Danielle L SwaneyJoshua J Coon
Mar 12, 2009·Journal of Proteome Research·Christopher M BaileyHelen J Cooper
May 22, 2009·Proceedings of the National Academy of Sciences of the United States of America·Robert J ChalkleyA L Burlingame
Jun 9, 2009·Journal of Mass Spectrometry : JMS·Paul J BoersemaAlbert J R Heck
Jan 6, 2010·ACS Chemical Biology·Paul A GrimsrudJoshua J Coon
Feb 20, 2010·Science·Shimin ZhaoKun-Liang Guan
Nov 9, 2010·Molecular & Cellular Proteomics : MCP·Mikhail M SavitskiBernhard Kuster
Nov 11, 2010·Nucleic Acids Research·Holger DinkelFrancesca Diella
Nov 11, 2010·Methods in Molecular Biology·Eric W Deutsch
Nov 18, 2010·Nucleic Acids Research·Florian GnadMatthias Mann
Dec 25, 2010·Cell·Edward L HuttlinSteven P Gygi
Jan 25, 2011·Journal of Proteome Research·Jürgen CoxMatthias Mann
Apr 15, 2011·Molecular & Cellular Proteomics : MCP·Peter R BakerRobert J Chalkley
Oct 11, 2011·Nature Methods·Douglas H PhanstielJoshua J Coon
Nov 15, 2011·Journal of Proteome Research·Thomas TausKarl Mechtler

❮ Previous
Next ❯

Citations

May 19, 2012·Molecular & Cellular Proteomics : MCP·Adrian Guthals, Nuno Bandeira
Nov 20, 2013·Proceedings of the National Academy of Sciences of the United States of America·Justin W WalleySteven P Briggs
Dec 1, 2012·Expert Review of Proteomics·Marc VaudelLennart Martens
Jun 19, 2014·Proceedings of the National Academy of Sciences of the United States of America·Alexander LeitnerRuedi Aebersold
Oct 10, 2015·Proteomics·Marc VaudelHarald Barsnes
Jan 19, 2016·Biochimica Et Biophysica Acta·Silke OeljeklausBettina Warscheid
Jan 6, 2016·Mass Spectrometry Reviews·Han HuJoseph Zaia
Dec 6, 2014·Proteomics·Dave C H LeeSimon J Hubbard
Jan 12, 2013·Proteomics·Marc VaudelRené P Zahedi
May 12, 2012·The Biochemical Journal·Jay J Thelen, Ján A Miernyk
Feb 18, 2015·Chemical Reviews·He HuangYingming Zhao
Mar 9, 2013·Journal of Proteomics·Florian P Breitwieser, Jacques Colinge
Oct 29, 2014·Computational and Structural Biotechnology Journal·Yu Liu, Mark R Chance
Feb 28, 2015·Journal of Proteome Research·Ritu ChaudharyIsgouhi Kaloshian
Apr 7, 2016·Annual Review of Analytical Chemistry·Ludovic C GilletRuedi Aebersold
Aug 20, 2016·Science·Justin W WalleySteven P Briggs
Oct 11, 2016·Analytical and Bioanalytical Chemistry·Robert J Chalkley, Peter R Baker
Nov 4, 2016·Journal of Proteome Research·Fengchao YuWeichuan Yu
Jun 13, 2017·Nature Biotechnology·George RosenbergerRuedi Aebersold
Mar 5, 2014·Molecular & Cellular Proteomics : MCP·Peter R Baker, Robert J Chalkley
Nov 5, 2013·Molecular & Cellular Proteomics : MCP·Robert J ChalkleyRui-Xiang Sun
Jan 16, 2014·Molecular & Cellular Proteomics : MCP·Jesse G MeyerElizabeth A Komives
Jul 1, 2017·Journal of Proteome Research·Matthieu DavidDominique Tessier
May 19, 2017·Molecular & Cellular Proteomics : MCP·Juan Antonio VizcaínoAndrew R Jones
Dec 7, 2017·Frontiers in Chemistry·Livia Rosa-FernandesGiuseppe Palmisano
Jun 13, 2018·Expert Review of Proteomics·Ruzanna MnatsakanyanRené P Zahedi
Dec 24, 2018·International Journal of Molecular Sciences·Dana PascoviciMehdi Mirzaei
Jan 1, 2014·Scientific Data·George RosenbergerRuedi Aebersold
Oct 27, 2011·Molecular & Cellular Proteomics : MCP·Jordane BiarcRalph A Bradshaw
Oct 24, 2017·Laboratory Investigation; a Journal of Technical Methods and Pathology·Kevin Adam, Tony Hunter
May 31, 2012·Molecular & Cellular Proteomics : MCP·Jonathan C TrinidadAlma L Burlingame
Jun 10, 2020·Nature Structural & Molecular Biology·Jong Woo BaeJong-Seo Kim
Sep 18, 2020·Molecular & Cellular Proteomics : MCP·Jason C Maynard, Robert J Chalkley

❮ Previous
Next ❯

Related Concepts

Related Feeds

ASBMB Publications

The American Society for Biochemistry and Molecular Biology (ASBMB) includes the Journal of Biological Chemistry, Molecular & Cellular Proteomics, and the Journal of Lipid Research. Discover the latest research from ASBMB here.