Refining comparative proteomics by spectral counting to account for shared peptides and multiple search engines.

Analytical and Bioanalytical Chemistry
Yao-Yi ChenDavid L Tabb

Abstract

Spectral counting has become a widely used approach for measuring and comparing protein abundance in label-free shotgun proteomics. However, when analyzing complex samples, the ambiguity of matching between peptides and proteins greatly affects the assessment of peptide and protein inventories, differentiation, and quantification. Meanwhile, the configuration of database searching algorithms that assign peptides to MS/MS spectra may produce different results in comparative proteomic analysis. Here, we present three strategies to improve comparative proteomics through spectral counting. We show that comparing spectral counts for peptide groups rather than for protein groups forestalls problems introduced by shared peptides. We demonstrate the advantage and flexibility of this new method in two datasets. We present four models to combine four popular search engines that lead to significant gains in spectral counting differentiation. Among these models, we demonstrate a powerful vote counting model that scales well for multiple search engines. We also show that semi-tryptic searching outperforms tryptic searching for comparative proteomics. Overall, these techniques considerably improve protein differentiation on the basis of spec...Continue Reading

References

Oct 30, 2001·Behavioural Brain Research·Y BenjaminiI Golani
Nov 25, 2003·Analytical Chemistry·Alexey I NesvizhskiiRuedi Aebersold
Feb 21, 2004·Bioinformatics·Robertson Craig, Ronald C Beavis
Jun 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Daniel R RhodesArul M Chinnaiyan
Oct 12, 2004·Journal of Proteome Research·Xiaoyu YangJeffrey A Kowalak
Oct 23, 2004·Proceedings of the National Academy of Sciences of the United States of America·Dafang WanJianren Gu
May 30, 2007·Molecular & Cellular Proteomics : MCP·Paola PicottiBruno Domon
Aug 7, 2007·Journal of Proteome Research·Bing ZhangDavid L Tabb
Nov 16, 2007·Journal of Proteome Research·Shuangshuang JinJohn H Miller
Dec 11, 2007·Journal of Proteome Research·Lukas KällWilliam Stafford Noble
Jan 5, 2008·Journal of Proteome Research·Brian C SearleAlexey I Nesvizhskii
Jan 18, 2008·Journal of Proteome Research·Xiaoyun FuJay W Heinecke
Jul 9, 2008·Bioinformatics·Darren KessnerParag Mallick
Jun 16, 2009·Journal of Proteome Research·Ze-Qiang MaDavid L Tabb
Feb 6, 2010·Journal of Proteome Research·Surendra DasariDavid L Tabb
Jul 1, 2010·Journal of Proteome Research·Ming LiRobbert J C Slebos
Oct 4, 2011·Bioinformatics·Ze-Qiang MaDaniel C Liebler
Nov 23, 2011·Journal of Proteome Research·Patrick J HalveyRobbert J C Slebos
Nov 1, 1994·Journal of the American Society for Mass Spectrometry·J K EngJ R Yates

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Citations

Jun 26, 2015·Scientific Data·Robbert J C SlebosDaniel C Liebler
Jan 21, 2021·Journal of Proteome Research·Gurjeet KaurPerminder Sachdev

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