Skip to main content

Proteomics and Metaproteomics

  • Living reference work entry
  • First Online:
Encyclopedia of Metagenomics

Synonyms

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

Definition

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 via an institution to check access.

Access this chapter

Institutional subscriptions

References

  • 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):3529-45

    Article  CAS  Google Scholar 

  • de Godoy LM, Olsen JV, et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature. 2008;455(7217):1251–4.

    Article  PubMed  Google Scholar 

  • Elliott MH, Smith DS, et al. Current trends in quantitative proteomics. J Mass Spectrom. 2009;44(12):1637–60.

    CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gorg A, Weiss W, et al. Current two-dimensional electrophoresis technology for proteomics. Proteomics. 2004;4(12):3665–85.

    Article  PubMed  Google Scholar 

  • Hall-Stoodley L, Costerton JW, et al. Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol. 2004;2(2):95–108.

    Article  CAS  PubMed  Google Scholar 

  • Ho Y, Gruhler A, et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002;415(6868):180–3.

    Article  CAS  PubMed  Google Scholar 

  • Kuhner S, van Noort V, et al. Proteome organization in a genome-reduced bacterium. Science. 2009;326(5957):1235–40.

    Article  PubMed  Google Scholar 

  • Markert S, Arndt C, et al. Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science. 2007;315(5809):247–50.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • Nagaraj N, Wisniewski JR, et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol. 2011;7:548.

    Article  PubMed Central  PubMed  Google Scholar 

  • O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975;250(10):4007–21.

    PubMed Central  PubMed  Google Scholar 

  • Olsen JV, Vermeulen M, et al. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal. 2010;3(104):ra3.

    PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • Prokisch H, Scharfe C, et al. Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol. 2004;2(6):e160.

    Article  PubMed Central  PubMed  Google Scholar 

  • Ram RJ, Verberkmoes NC, et al. Community proteomics of a natural microbial biofilm. Science. 2005;308(5730):1915–20.

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez-Valera F. Environmental genomics, the big picture? FEMS Microbiol Lett. 2004;231(2):153–8.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    PubMed Central  PubMed  Google Scholar 

  • 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.

    PubMed Central  PubMed  Google Scholar 

  • Verberkmoes NC, Russell AL, et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2009;3(2):179–89.

    Article  CAS  PubMed  Google Scholar 

  • Wolf-Yadlin A, Sevecka M, et al. Dissecting protein function and signaling using protein microarrays. Curr Opin Chem Biol. 2009;13(4):398–405.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wolters DA, Washburn MP, et al. An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem. 2001;73(23):5683–90.

    Article  CAS  PubMed  Google Scholar 

  • Yates JR, Ruse CI, et al. Proteomics by mass spectrometry: approaches, advances, and applications. Annu Rev Biomed Eng. 2009;11:49–79.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Rembert Pieper .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this entry

Cite this entry

Pieper, R., Huang, ST., Suh, MJ. (2013). Proteomics and Metaproteomics. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_690-9

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_690-9

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4614-6418-1

  • eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences

Publish with us

Policies and ethics