Home LiteratureArticle Details
PMID: 20622845 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Options and considerations when selecting a quantitative proteomics strategy.

Nature biotechnology ·Vol. 28 ·No. 7 ·2010-07-00 ·Pages 710-21

Domon B, Aebersold R

Abstract

The vast majority of proteomic studies to date have relied on mass spectrometric techniques to identify, and in some cases quantify, peptides that have been generated by proteolysis. Current approaches differ in the types of instrument used, their performance profiles, the manner in which they interface with biological research strategies, and their reliance on and use of prior information. Here, we consider the three main mass spectrometry (MS)-based proteomic approaches used today: shotgun (or discovery), directed and targeted strategies. We discuss the principles of each technique, their strengths and weaknesses and the dependence of their performance profiles on the composition of the biological sample. Our goal is to provide a rational framework for selecting strategies optimally suited to address the specific research issue under consideration.

MeSH Terms
Chromatography, Liquid Limit of Detection Mass Spectrometry/methods Proteomics
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Domon Bruno
Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. [email protected]
Aebersold Ruedi
References (34)
34 references, click to expand
  1. Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.
    Mol Cell Proteomics. 2010 Feb;9(2):242-54 PMID: 19858499
  2. Single and multiple ion recording techniques for the analysis of diphenylhydantoin and its major metabolite in plasma.
    Biomed Mass Spectrom. 1977 Feb;4(1):36-41 PMID: 836941
  3. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast.
    Nature. 2008 Oct 30;455(7217):1251-4 PMID: 18820680
  4. Mass spectrometry-based proteomics.
    Nature. 2003 Mar 13;422(6928):198-207 PMID: 12634793
  5. Directed mass spectrometry: towards hypothesis-driven proteomics.
    Curr Opin Chem Biol. 2009 Dec;13(5-6):510-7 PMID: 19775930
  6. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.
    Nat Biotechnol. 2009 Jul;27(7):633-41 PMID: 19561596
  7. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry.
    J Proteome Res. 2010 Feb 5;9(2):761-76 PMID: 19921851
  8. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry.
    Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9528-33 PMID: 15210983
  9. Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry.
    Mol Cell Proteomics. 2005 Apr;4(4):419-34 PMID: 15741312
  10. Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans.
    Nature. 2009 Aug 6;460(7256):762-5 PMID: 19606093
  11. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.
    Nat Methods. 2009 Jun;6(6):423-30 PMID: 19448641
  12. A database of mass spectrometric assays for the yeast proteome.
    Nat Methods. 2008 Nov;5(11):913-4 PMID: 18974732
  13. Proteomics: a pragmatic perspective.
    Nat Biotechnol. 2010 Jul;28(7):695-709 PMID: 20622844
  14. Collisions or electrons? Protein sequence analysis in the 21st century.
    Anal Chem. 2009 May 1;81(9):3208-15 PMID: 19364119
  15. An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures.
    Mol Cell Proteomics. 2008 Nov;7(11):2138-50 PMID: 18511481
  16. Scoring proteomes with proteotypic peptide probes.
    Nat Rev Mol Cell Biol. 2005 Jul;6(7):577-83 PMID: 15957003
  17. The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer.
    Anal Chem. 2000 Feb 1;72(3):552-8 PMID: 10695141
  18. Large-scale analysis of the yeast proteome by multidimensional protein identification technology.
    Nat Biotechnol. 2001 Mar;19(3):242-7 PMID: 11231557
  19. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks.
    Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5860-5 PMID: 17389395
  20. Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes.
    PLoS Biol. 2009 Mar 3;7(3):e48 PMID: 19260763
  21. Mass spectrometry and protein analysis.
    Science. 2006 Apr 14;312(5771):212-7 PMID: 16614208
  22. Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.
    Mol Cell Proteomics. 2009 Dec;8(12):2796-808 PMID: 19651622
  23. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS.
    Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6940-5 PMID: 12771378
  24. Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT.
    Mol Cell Proteomics. 2007 Aug;6(8):1416-27 PMID: 17510050
  25. Implications of new proteomics strategies for biology and medicine.
    J Proteome Res. 2004 Mar-Apr;3(2):253-60 PMID: 15113101
  26. MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research.
    Anal Chem. 2000 May 1;72(9):2132-41 PMID: 10815976
  27. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents.
    Mol Cell Proteomics. 2004 Dec;3(12):1154-69 PMID: 15385600
  28. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites.
    Mol Cell Proteomics. 2007 Oct;6(10):1809-17 PMID: 17644760
  29. A probability-based approach for high-throughput protein phosphorylation analysis and site localization.
    Nat Biotechnol. 2006 Oct;24(10):1285-92 PMID: 16964243
  30. The pros and cons of peptide-centric proteomics.
    Nat Biotechnol. 2010 Jul;28(7):659-64 PMID: 20622832
  31. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes.
    Nat Methods. 2010 Jan;7(1):43-6 PMID: 19966807
  32. The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions.
    J Proteome Res. 2008 May;7(5):1994-2006 PMID: 18361515
  33. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification.
    Mol Cell Proteomics. 2008 Oct;7(10):1952-62 PMID: 18534968
  34. Quantitative mass spectrometry in proteomics: a critical review.
    Anal Bioanal Chem. 2007 Oct;389(4):1017-31 PMID: 17668192
Article Info
Journal
Nature biotechnology
Abbr.
Nat Biotechnol
ISSN
1546-1696
DOI
10.1038/nbt.1661
Email
[email protected]
Published
2010-07-00
Epub
2010-00-09
Pages
710-21
Language
English
Region
United States
NLM ID
9604648
Subset
IM
External Links
PubMed source DOI: 10.1038/nbt.1661 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2