Encyclopedia of Metagenomics

2015 Edition
| Editors: Karen E. Nelson

Proteomics and Metaproteomics

Reference work entry
DOI: https://doi.org/10.1007/978-1-4899-7478-5_690


Global proteomics; Protein profiling of microbial communities; Proteomics of biological systems


Proteomics pertains to the comprehensive analysis of expressed proteins from a cell, a multicellular system, an extracellular environment, or a large set of recombinant clones. This is achieved using combinations of protein separation, identification, and/or assay techniques, such as liquid chromatography-mass spectrometry (LC-MS), two-dimensional gel electrophoresis-mass spectrometry (2DE-MS), affinity purification-mass spectrometry (AP-MS), and protein- or antibody-based microarrays. The objectives in proteomics research can be diverse; they include protein quantification on a global scale, highly parallel analysis of protein functions and interactions, structural characterization of protein complexes, unraveling trafficking of proteins and their distribution in different cellular compartments, and discovery of protein signatures for a disease state or other...

This is a preview of subscription content, log in to check access.


  1. Chen YT, Chen HW, et al. Multiplexed quantification of 63 proteins in human urine by multiple reaction monitoring-based mass spectrometry for discovery of potential bladder cancer biomarkers. J Proteome. 2012;75(12):3529-45Google Scholar
  2. de Godoy LM, Olsen JV, et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature. 2008;455(7217):1251–4.PubMedGoogle Scholar
  3. Elliott MH, Smith DS, et al. Current trends in quantitative proteomics. J Mass Spectrom. 2009;44(12):1637–60.PubMedGoogle Scholar
  4. Fouts DE, Pieper R, et al. Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury. J Transl Med. 2012;10(1):174.PubMedCentralPubMedGoogle Scholar
  5. Gorg A, Weiss W, et al. Current two-dimensional electrophoresis technology for proteomics. Proteomics. 2004;4(12):3665–85.PubMedGoogle Scholar
  6. Hall-Stoodley L, Costerton JW, et al. Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol. 2004;2(2):95–108.PubMedGoogle Scholar
  7. Ho Y, Gruhler A, et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002;415(6868):180–3.PubMedGoogle Scholar
  8. Kuhner S, van Noort V, et al. Proteome organization in a genome-reduced bacterium. Science. 2009;326(5957):1235–40.PubMedGoogle Scholar
  9. Markert S, Arndt C, et al. Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science. 2007;315(5809):247–50.PubMedGoogle Scholar
  10. Mueller LN, Brusniak MY, et al. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res. 2008;7(1):51–61.PubMedGoogle Scholar
  11. Nagaraj N, Wisniewski JR, et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol. 2011;7:548.PubMedCentralPubMedGoogle Scholar
  12. O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975;250(10):4007–21.PubMedCentralPubMedGoogle Scholar
  13. Olsen JV, Vermeulen M, et al. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal. 2010;3(104):ra3.PubMedGoogle Scholar
  14. Picotti P, Rinner O, et al. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat Methods. 2010;7(1):43–6.PubMedGoogle Scholar
  15. Pieper R, Gatlin CL, et al. The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics. 2003;3(7):1345–64.PubMedGoogle Scholar
  16. Pieper R, Huang ST, et al. Characterizing the dynamic nature of the Yersinia pestis periplasmic proteome in response to nutrient exhaustion and temperature change. Proteomics. 2008;8(7):1442–58.PubMedGoogle Scholar
  17. Prokisch H, Scharfe C, et al. Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol. 2004;2(6):e160.PubMedCentralPubMedGoogle Scholar
  18. Ram RJ, Verberkmoes NC, et al. Community proteomics of a natural microbial biofilm. Science. 2005;308(5730):1915–20.PubMedGoogle Scholar
  19. Rodriguez-Valera F. Environmental genomics, the big picture? FEMS Microbiol Lett. 2004;231(2):153–8.PubMedGoogle Scholar
  20. Speers AE, Cravatt BF. Activity-based protein profiling (ABPP) and click chemistry (CC)-ABPP by MudPIT mass spectrometry. Curr Protoc Chem Biol. 2009;1:29–41.PubMedCentralPubMedGoogle Scholar
  21. van Noort V, Seebacher J, et al. Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol. 2012;8:571.PubMedCentralPubMedGoogle Scholar
  22. Verberkmoes NC, Russell AL, et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2009;3(2):179–89.PubMedGoogle Scholar
  23. Wolf-Yadlin A, Sevecka M, et al. Dissecting protein function and signaling using protein microarrays. Curr Opin Chem Biol. 2009;13(4):398–405.PubMedCentralPubMedGoogle Scholar
  24. Wolters DA, Washburn MP, et al. An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem. 2001;73(23):5683–90.PubMedGoogle Scholar
  25. Yates JR, Ruse CI, et al. Proteomics by mass spectrometry: approaches, advances, and applications. Annu Rev Biomed Eng. 2009;11:49–79.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.J. Craig Venter InstituteRockvilleUSA