Industrialization of Proteomics: Scaling UpProteomics Processes

Abstract

The industrial scale approach to biofluid analysis contrasts withthe high throughput approach (using human plasma as an example).

Keywords: industrial‐scale; plasma; serum; mass spectrometry; high throughput; bioinformatics

Figure 1.

Plasma protein concentrations. Graph showing a proposed log–log relationship between plasma protein concentration and number of proteins at the various concentrations. Some well‐known proteins are indicated at their normal plasma concentrations showing a known dynamic range spanning 12 orders of magnitude (albumin to tumor necrosis factor). The advantage of large sample size is indicated by the difference between the dotted line (1 nM, sensitivity 100 fM, sample size 0.1 ml) and the dashed line (0.1 pM, sensitivity 100 fM, sample size 1 l). (Original slide courtesy of D. Hochstrasser, modified.) mM: millimolar; μM: micromolar; nM: nanomolar; pM: picomolar; fM: femtomolar; aM: attomolar; zM: zeptomolar; yM: yactomolar.

Figure 2.

In‐depth industrial‐scale proteomics. A portion of each of a set of carefully selected samples from patients with a disease is pooled, while separate portions are retained unpooled. Small squares represent an example of a protein common to all diseased samples, and the small triangle represents a protein present in one particular sample (phenotypic variation), prior to and after extensive separation. Identified/characterized proteins populate a database. Similar analysis of a control set permits comparisons to be made. The unpooled portions of the individual samples are used for screening for proteins of interest using arrays or other appropriate high‐throughput assays.

Figure 3.

Donor sample‐based high‐throughput proteomics. A large set of small samples (here 10000) from patients with a disease is analyzed. Similar analysis of a control set permits comparisons to be made.

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References

Cahill DJ (2001) Protein and antibody arrays and their medical applications. Journal of Immunological Methods 250: 81–91.

Ezzel C (2002) Move over, human genome. Scientific American April: 42–47.

Graves PR and Haystead TAJ (2002) Molecular biologists's guide to proteomics. Microbiology and Molecular Biology Reviews 66: 39–63.

Lander ES, Linton LM, Birren B, et al. (2001) International human genome sequencing consortium: initial sequencing and analysis of the human genome. Nature 409: 860–921.

Mann M, Hendrickson RC and Pandey A (2001) Analysis of proteins and proteomes by mass spectrometry. Annual Review of Biochemistry 70: 437–473.

Venter JC, Adams MD, Myers EW, et al. (2001) The sequence of the human genome. Science 291: 1304–1351.

Zuo X and Speicher DW (2002) Comprehensive analysis of complex proteomes using microscale solution isoelectric focusing prior to narrow pH range two‐dimensional electrophoresis. Proteomics 2: 58–68.

Further Reading

Arrel DK and Van Eyk JE (2001) Cardiovascular proteomics, evolution and potential. Circulation Research 88: 763–773.

Ho Y, Gruhler A, Heilbut A et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180–183.

Kersten B, Bürkle L, Kuhn EJ, et al. (2002) Large‐scale plant proteomics. Plant Molecular Biology 48: 133–141.

Subramanian G, Adams MD, Venter JC and Broder S (2001) Implications of the human genome for understanding human biology and medicine. Journal of the American Medical Association 286: 2296–2307.

Weinstein JN (2001) Searching for pharmacogenomic markers: the synergy between omic and hypothesis‐driven research. Disease Markers 17: 77–88.

Web Links

Expert Protein Analysis System (ExPASy) http://www.expasy.ch

Human Proteome Organization (HUPO) http://www.hupo.org

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How to Cite close
Rose, Keith(Jan 2006) Industrialization of Proteomics: Scaling UpProteomics Processes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0006199]