Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry.

Journal of Proteome Research
David L TabbCliff Spiegelman

Abstract

The complexity of proteomic instrumentation for LC-MS/MS introduces many possible sources of variability. Data-dependent sampling of peptides constitutes a stochastic element at the heart of discovery proteomics. Although this variation impacts the identification of peptides, proteomic identifications are far from completely random. In this study, we analyzed interlaboratory data sets from the NCI Clinical Proteomic Technology Assessment for Cancer to examine repeatability and reproducibility in peptide and protein identifications. Included data spanned 144 LC-MS/MS experiments on four Thermo LTQ and four Orbitrap instruments. Samples included yeast lysate, the NCI-20 defined dynamic range protein mix, and the Sigma UPS 1 defined equimolar protein mix. Some of our findings reinforced conventional wisdom, such as repeatability and reproducibility being higher for proteins than for peptides. Most lessons from the data, however, were more subtle. Orbitraps proved capable of higher repeatability and reproducibility, but aberrant performance occasionally erased these gains. Even the simplest protein digestions yielded more peptide ions than LC-MS/MS could identify during a single experiment. We observed that peptide lists from pairs...Continue Reading

References

Oct 15, 2003·Rapid Communications in Mass Spectrometry : RCM·Robertson Craig, Ronald C Beavis
Jul 2, 2004·Analytical Chemistry·Katheryn A ResingNatalie G Ahn
Sep 2, 2004·Nature Reviews. Molecular Cell Biology·Hanno Steen, Matthias Mann
Apr 23, 2005·Nature Methods·Theodore BammlerUNKNOWN Members of the Toxicogenomics Research Consortium
Aug 25, 2005·Nature Methods·Daniel Chamrad, Helmut E Meyer
Nov 5, 2005·Molecular & Cellular Proteomics : MCP·Amol PrakashBenno Schwikowski
Feb 3, 2007·Journal of Proteome Research·Paul M van MidwoudHarm A G Niederländer
Aug 7, 2007·Journal of Proteome Research·Bing ZhangDavid L Tabb
Jul 9, 2008·Bioinformatics·Darren KessnerParag Mallick
Mar 5, 2009·Journal of Proteome Research·Michael R HoopmannMichael J MacCoss
May 19, 2009·Nature Methods·Alexander W BellUNKNOWN HUPO Test Sample Working Group
Jun 16, 2009·Journal of Proteome Research·Ze-Qiang MaDavid L Tabb
Oct 20, 2009·Molecular & Cellular Proteomics : MCP·Paul A RudnickStephen E Stein
Oct 28, 2009·Molecular & Cellular Proteomics : MCP·Amanda G PaulovichDaniel C Liebler

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Citations

May 4, 2012·Analytical and Bioanalytical Chemistry·Yao-Yi ChenDavid L Tabb
Jan 18, 2013·Analytical and Bioanalytical Chemistry·Quentin EnjalbertJérôme Lemoine
Aug 21, 2013·International Journal of Hematology·Sophie PaczesnyChristy Mumaw
Apr 8, 2011·Journal of the American Society for Mass Spectrometry·Genna L AndrewsDavid C Muddiman
Aug 1, 2012·Journal of the American Society for Mass Spectrometry·Konstantinos ThalassinosScott J Geromanos
Jul 4, 2013·Journal of the American Society for Mass Spectrometry·Andrew G ChambersChristoph H Borchers
Jun 15, 2010·Journal of the American Society for Mass Spectrometry·Bret CooperWesley M Garrett
Oct 7, 2010·Journal of Proteome Research·Ali R VaezzadehRichard S Lee
Nov 8, 2011·Journal of Proteome Research·Christopher R KinsingerHenry Rodriguez
Dec 4, 2010·Nature Protocols·Nico JehmlichCarsten Vogt
Jun 4, 2010·The Analyst·Carol E ParkerChristoph H Borchers
Jan 21, 2011·Proceedings of the National Academy of Sciences of the United States of America·Qing WangBert Vogelstein
Dec 9, 2010·Molecular & Cellular Proteomics : MCP·Jannie M R DanielsenMichael L Nielsen
Jun 16, 2011·Molecular & Cellular Proteomics : MCP·Niclas OlssonCarl A K Borrebaeck
Feb 4, 2012·Molecular & Cellular Proteomics : MCP·Lisa J ZimmermanDaniel C Liebler
Jul 5, 2012·Molecular & Cellular Proteomics : MCP·Takefumi KikuchiDavid P Carbone
May 1, 2012·Molecular & Cellular Proteomics : MCP·Niclas OlssonChrister Wingren
Nov 5, 2011·Molecular & Cellular Proteomics : MCP·Christopher R KinsingerHenry Rodriguez
Aug 7, 2012·Molecular & Cellular Proteomics : MCP·Amelia C PetersonJoshua J Coon
Aug 4, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yong Fuga LiHaixu Tang
Jul 16, 2010·Bioinformatics·Penghao WangJean Yee Hwa Yang
Jul 26, 2013·Science Translational Medicine·Raymond J LangleyStephen F Kingsmore
Jun 12, 2012·BMC Bioinformatics·Jean-Eudes DazardRob M Ewing
Feb 20, 2013·BMC Bioinformatics·Alexandra ZerckKnut Reinert
Dec 8, 2010·Epigenetics & Chromatin·Barry M ZeeBenjamin A Garcia
Dec 7, 2011·PLoS Computational Biology·Lukas Käll, Olga Vitek
Feb 6, 2014·Journal of the American Society for Mass Spectrometry·Michael S BeremanMichael J MacCoss
Jul 2, 2014·Clinical Proteomics·Christopher R SmithVathany Kulasingam
Apr 1, 2014·Clinical and Translational Medicine·Maria FrantziAgnieszka Latosinska
Sep 28, 2014·Journal of the American Society for Mass Spectrometry·Jesse D CanterburyScott A Shaffer
Jul 18, 2015·Expert Review of Proteomics·Yetrib Hathout
Oct 22, 2013·Expert Review of Molecular Diagnostics·Yansheng LiuRuedi Aebersold

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