Peptide-Centric Approaches Provide an Alternative Perspective To Re-Examine Quantitative Proteomic Data

Analytical Chemistry
Zhibin NingDaniel Figeys

Abstract

Quantitative proteomics can provide rich information on changes in biological functions and processes. However, its accuracy is affected by the inherent information degeneration found in bottom-up proteomics. Therefore, the precise protein inference from identified peptides can be mistaken since an ad hoc rule is used for generating a list of protein groups that depends on both the sample type and the sampling depth. Herein, we propose an alternative approach for examining quantitative proteomic data which is peptide-centric instead of protein-centric. We discuss the feasibility of the peptide-centric approach which was tested on several quantitative proteomic data sets. We show that peptide-centric quantification has several advantages over protein level analysis: (1) it is more sensitive for sample segregation, (2) it avoids the issues associated with protein inference, and (3) it can retrieve significant peptides lost in protein-centric quantification for further downstream analysis.

References

May 23, 2002·Cell·Satchidananda PandaJohn B Hogenesch
Mar 3, 2004·Nucleic Acids Research·Eric W KleeLynda B M Ellis
Jul 13, 2005·Molecular & Cellular Proteomics : MCP·Alexey I Nesvizhskii, Ruedi Aebersold
Nov 4, 2006·Proteomics·Shen HuDavid T Wong
Jan 11, 2007·Nature Biotechnology·John J M Bergeron, Michael Hallett
Apr 30, 2008·Journal of Proteome Research·Xiuxia DuMary S Lipton
Nov 7, 2009·Journal of Proteome Research·Timothy CloughOlga Vitek
Jul 20, 2010·Journal of Proteomics·Manousos Makridakis, Antonia Vlahou
Sep 30, 2010·Journal of Biological Rhythms·Michael E HughesKarl Kornacker
Nov 18, 2010·Proteomics·Manor AskenaziMichal Linial
May 3, 2011·Molecular & Cellular Proteomics : MCP·Chia-Yu YenWilliam M Old
May 20, 2011·Nature·Björn SchwanhäusserMatthias Selbach
May 24, 2011·Journal of Proteome Research·Karen Meyer-ArendtNatalie G Ahn
Nov 1, 2011·BMC Bioinformatics·Seungmook LeeTaesung Park
Mar 24, 2012·Molecular & Cellular Proteomics : MCP·Sally J DeebMatthias Mann
Nov 7, 2012·BMC Bioinformatics·Gorka PrietoRune Matthiesen
Nov 13, 2012·Current Opinion in Biotechnology·Michael R Hoopmann, Robert L Moritz
Nov 17, 2012·Journal of Proteome Research·Bart MesuerePeter Dawyndt
Feb 28, 2013·Nature Methods·Lloyd M SmithUNKNOWN Consortium for Top Down Proteomics
Apr 12, 2013·Expert Review of Proteomics·Julian Whitelegge
May 31, 2013·The Onderstepoort Journal of Veterinary Research·Inge-Marie PetzerTheodorus J van der Schans
May 30, 2014·Nature·Min-Sik KimAkhilesh Pandey
May 30, 2014·Nature·Mathias WilhelmBernhard Kuster
Nov 30, 2014·Molecular & Cellular Proteomics : MCP·Bobbie-Jo M Webb-RobertsonKatrina M Waters
Jul 29, 2015·Molecular & Cellular Proteomics : MCP·Ying S TingMichael J MacCoss
Sep 19, 2015·Journal of Proteome Research·Tomi SuomiLaura L Elo

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Citations

Mar 18, 2017·Molecular & Cellular Proteomics : MCP·Bo ZhangLukas Käll
Jul 20, 2019·Proteomics·Danielle L PetersDaniel Figeys
Mar 9, 2017·Expert Review of Proteomics·Sebastian FunkeFranz H Grus
Oct 6, 2020·Expert Review of Proteomics·Rui VitorinoFrancisco Amado

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