Proteomics techniques and reviews

Proteomics definition:

Definition from wikipedia: Proteomics is the large-scale study of protein, particularly their structures and functions. This term was coined to make an analogy with genomics, and while it is often viewed as the "next step", proteomics is much more complicated than genomics. Most importantly, while the genome is a rather constant entity, the proteome differs from cell to cell and is constantly changing through its biochemical interactions with the genome and the environment. One organism has radically different protein expression in different parts of its body, in different stages of its life cycle and in different environmental conditions.

Mesh term of proteomics: The systematic study of the complete complement of proteins (PROTEOME) of organisms.

Commonly used proteomics techniques:

1. Protein separation techniques:
1.1 Protein extraction
1.2 Cell fractionation and protein separation by electrophoresis
1.3 Chromatography protein purification

2. Protein detection techniques:
2.1 Two-dimensional electrophoresis (isoelectric focusing electrophoresis, capillary electrophoresis etc)

3. Image analysis for proteomics experiments

4. Protein and peptide identification by peptide fingerprinting, amino acid sequence analysis, database search

5. Characterization of protein post-translational modification

6. Functional proteomics study

Literatures on proteomics techniques:

1: Schindler J, Nothwang HG.
Aqueous polymer two-phase systems: Effective tools for plasma membrane
proteomics.
Proteomics. 2006 Sep 14; [Epub ahead of print]

2: Andersen JS, Mann M.
Organellar proteomics: turning inventories into insights.
EMBO Rep. 2006 Sep;7(9):874-9.

4: Yende S, Kammerer CM, Angus DC.
Bench-to-bedside review: genetics and proteomics: deciphering gene association
studies in critical illness.
Crit Care. 2006;10(4):227.

5: Schubert P, Hoffman MD, Sniatynski MJ, Kast J.
Advances in the analysis of dynamic protein complexes by proteomics and data
processing.
Anal Bioanal Chem. 2006 Oct;386(3):482-93. Epub 2006 Aug 25.

6: Ro KW, Nayak R, Knapp DR.
Monolithic media in microfluidic devices for proteomics.
Electrophoresis. 2006 Sep;27(18):3547-58.

7: Roe MR, Griffin TJ.
Gel-free mass spectrometry-based high throughput proteomics: tools for studying
biological response of proteins and proteomes.
Proteomics. 2006 Sep;6(17):4678-87.

8: McGregor E, De Souza A.
Proteomics and laser microdissection.
Methods Mol Biol. 2006;333:291-304. Review.

10: Barrios-Llerena ME, Chong PK, Gan CS, Snijders AP, Reardon KF, Wright PC.
Shotgun proteomics of cyanobacteria--applications of experimental and
data-mining techniques.
Brief Funct Genomic Proteomic. 2006 Jun;5(2):121-32. Epub 2006 May 10. Review.

11: Nichols HL, Zhang N, Wen X.
Proteomics and genomics of microgravity.
Physiol Genomics. 2006 Aug 16;26(3):163-71. Epub 2006 May 16.

12: Fu Q, Van Eyk JE.
Proteomics and heart disease: identifying biomarkers of clinical utility.
Expert Rev Proteomics. 2006 Apr;3(2):237-49.

15: Pietrogrande MC, Marchetti N, Dondi F, Righetti PG.
Decoding 2D-PAGE complex maps: relevance to proteomics.
J Chromatogr B Analyt Technol Biomed Life Sci. 2006 Mar 20;833(1):51-62. Epub
2006 Jan 31.

16: Wheelock AM, Goto S.
Effects of post-electrophoretic analysis on variance in gel-based proteomics.
Expert Rev Proteomics. 2006 Feb;3(1):129-42.

19: Guan JQ, Chance MR.
Structural proteomics of macromolecular assemblies using oxidative footprinting
and mass spectrometry.
Trends Biochem Sci. 2005 Oct;30(10):583-92. Review.

20: Vasquez GB, Zullo SJ, Barker PE.
Standards requirements for systems biology approaches to health care:
mitochondrial proteomics.
Mitochondrion. 2004 Mar;3(4):205-15.

21: Ivanov VT, Yatskin ON.
Peptidomics: a logical sequel to proteomics.
Expert Rev Proteomics. 2005 Aug;2(4):463-73.

22: Bronstrup M.
Absolute quantification strategies in proteomics based on mass spectrometry.
Expert Rev Proteomics. 2004 Dec;1(4):503-12. Review.

24: MacCoss MJ.
Computational analysis of shotgun proteomics data.
Curr Opin Chem Biol. 2005 Feb;9(1):88-94. Review.

26: Righetti PG, Castagna A, Antonucci F, Piubelli C, Cecconi D, Campostrini N,
Antonioli P, Astner H, Hamdan M.
Critical survey of quantitative proteomics in two-dimensional electrophoretic
approaches.
J Chromatogr A. 2004 Oct 8;1051(1-2):3-17. Review.

27: Visintin M, Meli GA, Cannistraci I, Cattaneo A.
Intracellular antibodies for proteomics.
J Immunol Methods. 2004 Jul;290(1-2):135-53. Review.

28: Taback B, Hoon DS.
Circulating nucleic acids and proteomics of plasma/serum: clinical utility.
Ann N Y Acad Sci. 2004 Jun;1022:1-8. Review.

29: Righetti PG, Campostrini N, Pascali J, Hamdan M, Astner H.
Quantitative proteomics: a review of different methodologies.
Eur J Mass Spectrom (Chichester, Eng). 2004;10(3):335-48. Review.
PMID: 15187293 [PubMed - indexed for MEDLINE]

30: Asenjo JA, Andrews BA.
Is there a rational method to purify proteins? From expert systems to
proteomics.
J Mol Recognit. 2004 May-Jun;17(3):236-47. Review.

31: Ornstein DK, Petricoin EF 3rd.
Proteomics to diagnose human tumors and provide prognostic information.
Oncology (Williston Park). 2004 Apr;18(4):521-9; discussion 529-32. Review.

32: Van den Bergh G, Arckens L.
Fluorescent two-dimensional difference gel electrophoresis unveils the
potential of gel-based proteomics.
Curr Opin Biotechnol. 2004 Feb;15(1):38-43. Review.

36: Wilson KE, Ryan MM, Prime JE, Pashby DP, Orange PR, O'Beirne G, Whateley
JG, Bahn S, Morris CM.
Functional genomics and proteomics: application in neurosciences.
J Neurol Neurosurg Psychiatry. 2004 Apr;75(4):529-38. Review.

37: Doytchinova IA, Taylor P, Flower DR.
Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the
Immunone.
J Biomed Biotechnol. 2003;2003(5):267-290.

38: Butterfield DA, Castegna A.
Proteomics for the identification of specifically oxidized proteins in brain:
technology and application to the study of neurodegenerative disorders.
Amino Acids. 2003 Dec;25(3-4):419-25. Epub 2003 Aug 21. Review.

39: Lee WC, Lee KH.
Applications of affinity chromatography in proteomics.
Anal Biochem. 2004 Jan 1;324(1):1-10. Review.

41: Aparicio OM.
Tackling an essential problem in functional proteomics of Saccharomyces
cerevisiae.
Genome Biol. 2003;4(10):230. Epub 2003 Sep 24. Review.

42: van Eijk HM, Deutz NE.
Plasma protein synthesis measurements using a proteomics strategy.
J Nutr. 2003 Jun;133(6 Suppl 1):2084S-2089S. Review.

43: Lubec G, Krapfenbauer K, Fountoulakis M.
Proteomics in brain research: potentials and limitations.
Prog Neurobiol. 2003 Feb;69(3):193-211. Review.

44: Kozarich JW.
Activity-based proteomics: enzyme chemistry redux.
Curr Opin Chem Biol. 2003 Feb;7(1):78-83. Review.

46: Kennedy S.
The role of proteomics in toxicology: identification of biomarkers of toxicity
by protein expression analysis.
Biomarkers. 2002 Jul-Aug;7(4):269-90. Review.

47: Brive L, Abagyan R.
Computational structural proteomics.
Ernst Schering Res Found Workshop. 2002;(38):149-66. Review. No abstract
available.

48: Ong SE, Pandey A.
An evaluation of the use of two-dimensional gel electrophoresis in proteomics.
Biomol Eng. 2001 Nov;18(5):195-205. Review.

49: Mirzabekov A, Kolchinsky A.
Emerging array-based technologies in proteomics.
Curr Opin Chem Biol. 2002 Feb;6(1):70-5. Review.

51: Herbert BR, Harry JL, Packer NH, Gooley AA, Pedersen SK, Williams KL.
What place for polyacrylamide in proteomics?
Trends Biotechnol. 2001 Oct;19(10 Suppl):S3-9. Review.

52: Moseley MA.
Current trends in differential expression proteomics: isotopically coded tags.
Trends Biotechnol. 2001 Oct;19(10 Suppl):S10-6. Review.

53: Jain KK.
Applications of proteomics in oncology.
Pharmacogenomics. 2000 Nov;1(4):385-93. Review.

55: VanBogelen RA, Schiller EE, Thomas JD, Neidhardt FC.
Diagnosis of cellular states of microbial organisms using proteomics.
Electrophoresis. 1999 Aug;20(11):2149-59. Review.

Last update 07-Apr-2005, Rating n/a of 0 votes.