Mass spectrometry-based quantitative proteomics

Expert Review of Proteomics

Volumn 1, Issue 3, 2004, Pages 317-326

  Heck, Albert J R ^a   Krijgsveld, Jeroen ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Expression proteomics; ICAT; Metabolic labeling; Protein quantification; SILAC

Indexed keywords

ANTIBODY; CELL PROTEIN; PEPTIDE; PROTEOME;

ANTIBODY AFFINITY; BINDING AFFINITY; CYTOLOGY; GENOME; HUMAN; ISOTOPE LABELING; MASS SPECTROMETRY; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; STAINING; TWO DIMENSIONAL GEL ELECTROPHORESIS; ANIMAL; CELL FRACTIONATION; CHEMISTRY; GENE EXPRESSION; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY;

ANIMALS; CELL FRACTIONATION; GENE EXPRESSION; ISOTOPE LABELING; MASS SPECTROMETRY; PROTEOME; PROTEOMICS;

EID: 20444508181     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.1.3.317     Document Type: Review

References (71)

1. Wilkins MR, Sanchez JC, Gooley AA et al. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotech. Genet. Eng. Rev. 13, 19-50 (1995).
2. Gorg A, Obermaier C, Boguth G et al. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21, 1037-1053 (2000).
3. Rabilloud T. Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2, 3-10 (2002).
4. Hamdan M, Righetti PG. Assessment of protein expression by means of 2D gel electrophoresis with and without mass spectrometry. Mass Spectrom. Rev. 22, 272-284 (2003). Overview of gel-based protein quantitation.
5. Molloy MP, Brzezinski EE, Hang J, McDowell MT, VanBogelen RA. Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 3, 1912-1919 (2003).
6. Unlu M, Morgan ME, Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18, 2071-2077 (1997).
7. Patton WF. Detection technologies in proteome analysis. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 771, 3-31 (2002).
8. Alban A, David SO, Bjorkesten L et al. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3, 36-44 (2003).
9. Karp NA, Kreil DP, Lilley KS. Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis. Proteomics 4, 1421-1432 (2004).
10. Chelius D, Bondarenko PV. Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J. Proteome Res. 1, 317-323 (2002).
11. Andersen JS, Wilkinson CJ, Mayor T, Mortensen P, Nigg EA, Mann M. Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426, 570-574 (2003). Demonstration of liquid chromatography-based quantitation of proteins without stable isotope labeling.
12. Jonckheere JA, Thienpont LM, De Leenheer AP, De Backer P, Debackere M, Belpaire FM. Selected ion monitoring assay for bromhexine in biological fluids. Biomed. Mass Spectrom. 7, 582-587 (1980).
13. Sechi S, Oda Y. Quantitative proteomics using mass spectrometry. Curr. Opin. Chem. Biol. 7, 70-77 (2003).
14. Goshe MB, Smith RD. Stable isotope-coded proteomic mass spectrometry. Curr. Opin. Biotechnol. 14, 101-109 (2003).
15. Ong SE, Foster LJ, Mann M. Mass spectrometric-based approaches in quantitative proteomics. Methods 29, 124-130 (2003).
16. Lill J. Proteomic tools for quantitation by mass spectrometry. Mass Spectrom. Rev. 22, 182-194 (2003).
17. Julka S, Regnier F. Quantification in proteomics through stable isotope coding. J. Proteome Res. 350-363 (2004).
18. Geng M, Ji J, Regnier FE. Signature-peptide approach to detecting proteins in complex mixtures. J. Chromatogr. A 870, 295-313 (2000).
19. Ji J, Chakraborty A, Geng M et al. Strategy for qualitative and quantitative analysis in proteomics based on signature peptides. J. Chromatogr. B Biomed. Sci. Appl. 745, 197-210 (2000).
20. Munchbach M, Quadroni M, Miotto G, James P. Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. Anal. Chem. 72, 4047-4057 (2000).
21. Ren D, Penner NA, Slentz BE, Mirzaei H, Regnier F. Evaluating immobilized metal affinity chromatography for the selection of histidine-containing peptides in comparative proteomics. J. Proteome Res. 2, 321-329 (2003).
22. Ren D, Penner NA, Slentz BE, Regnier FE. Histidine-rich peptide selection and quantification in targeted proteomics. J. Proteome Res. 3, 37-45 (2004).
23. 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry. Electrophoresis 17, 945-953 (1996).
24. Mirgorodskaya OA, Kozmin YP, Titov MI, Korner R, Sonksen CP, Roepstorff P. Quantitation of peptides and proteins by matrix-assisted laser desorption/ionization mass spectrometry using (IS)O-labeled internal standards. Rapid Commun. Mass Spectrum. 14, 1226-1232 (2000).
25. 18O labeling mass spectrometry for the rapid identification of marker/target proteins. Anal. Chem. 73, 3742-3750 (2001).
26. 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem. 73, 2836-2842 (2001).
27. 18O labeling. Anal. Chem. 74, 4417-4422 (2002).
28. 18O labeling: a tool for proteomics. Rapid Commun. Mass Spectrom. 15, 2456-2465 (2001).
29. 18O labeling. J. Proteome Res. 3, 455-462 (2004).
30. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol. 17, 994-999 (1999).
31. 13C-ICAT and multi-dimensional chromatography. Mol. Cell Proteomics 2(5), 299-314 (2003).
32. Li J, Steen H, Gygi SP. Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response. Mol. Cell Proteomics 2, 1198-1204 (2003).
33. Zhou H, Ranish JA, Watts JD, Aebersold R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometiy. Nature Biotechnol. 20, 512-515 (2002).
34. Zhou H, Boyle R, Aebersold R. Quantitative protein analysis by solid phase isotope tagging and mass spectrometry. Methods Mol. Biol. 261, 511-518 (2004).
35. Han DK, Eng J, Zhou H, Aebersold R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nature Biotechnol. 19, 946-951 (2001).
36. Meehan KL, Sadar MD. Quantitative profiling of LNCaP prostate cancer cells using isotope-coded affinity tags and mass spectrometry. Proteomics 4, 1116-1134 (2004).
37. Li C, Hong Y, Tan YX et al. Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromarography mass spectrometry. Mol. Cell Proteomics 3, 399-409 (2004).
38. Martin DB, Gifford DR, Wright ME et al. Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium. Cancer Res. 64, 347-355 (2004).
39. Goshe MB, Conrads TP, Panisko EA, Angell NH, Veenstra TD, Smith RD. Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. Anal. Chem. 73, 2578-2586 (2001).
40. Goshe MB, Veenstra TD, Panisko EA, Conrads TP, Angell NH, Smith RD. Phosphoprotein isotope-coded affinity tags: application to the enrichment and identification of low-abundance phosphoproteins. Anal. Chem. 74, 607-616 (2002).
41. Oda Y, Nagasu T, Chait BT. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nature BiotechnoL 19, 379-382 (2001).
42. Zhou H, Watts JD, Aebersold R. A systematic approach to the analysis of protein phosphorylation. Nature Biotechnol. 19, 375-378 (2001).
43. Qian WJ, Goshe MB, Camp DG II, Yu LR, Tang K, Smith RD. Phosphoprotein isotope-coded solid-phase tag approach for enrichment and quantitative analysis of phosphopeptides from complex mixtures. Anal. Chem. 75, 5441-5450 (2003).
44. Lahm HW, Langen H. Mass spectrometry: a tool for the identification of proteins separated by gels. Electrophoresis 21, 2105-2114 (2000).
45. Oda Y, Huang K, Cross FR, Cowburn D, Chait BT. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl Acad. Sci. USA 96, 6591-6596 (1999).
46. Conrads TP, Alving K, Veenstra TD et al. Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. Anal. Chem. 73, 2132-2139 (2001).
47. Washburn MP, Ulaszek R, Deciu C, Schieltz DM, Yates JR III. Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal. Chem. 74, 1650-1657 (2002).
48. MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR III. A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal Chem. 75, 6912-6921 (2003).
49. Blagoev B, Ong SE, Kratchmarova I, Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nature Biotechnol. 9, 1139-1145 (2004).
50. Krijgsveld J, Ketting RF, Mahmoudi T et al. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nature Biotechnol. 21, 927-931 (2003). Demonstration of the application of in vivo stable isotope labeling in multicellular organisms.
51. Hunter TC, Yang L, Zhu H, Majidi V, Bradbury EM, Chen X. Peptide mass mapping constrained with stable isotope-tagged peptides for identification of protein mixtures. Anal. Chem. 73, 4891-4902 (2001).
52. Zhu H, Pan S, Gu S, Bradbury EM, Chen X. Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom, 16, 2115-2123 (2002). One of the first studies showing the labeling of cells in culture with isotope-coded amino acids for mass spectrometry-based quantitation of proteins.
53. Veenstra TD, Martinovic S, Anderson GA, Pasa-Tolic L, Smith RD. Proteome analysis using selective incorporation of isotopically labeled amino acids. J. Am. Soc. Mass Spectrom. 11, 78-82 (2000).
54. Martinovic S, Veenstra TD, Anderson GA, Pasa-Tolic L, Smith RD. Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level. J. Mass Spectrom. 37, 99-107 (2002).
55. Ong SE, Blagoev B, Kratchmarova I et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics 1, 376-386 (2002).
56. Zhang R, Sioma CS, Thompson RA, Xiong L, Regnier FE. Controlling deuterium isotope effects in comparative proteomics. Anal. Chem. 74, 3662-3669 (2002). Critical evaluation of isotope effects during liquid chromatography of mass-tagged peptides.
57. Ibarrola N, Kalume DE, Gronborg M, Iwahori A, Pandey A. A proteomic approach for quatification of phosphorylation using stable isotope labeling in cell culture. Anal. Chem. 75, 6043-6049 (2003).
58. Stemmann O, Zou H, Gerber SA, Gygi SP, Kirschner MW. Dual inhibition of sister chromatid separation at metaphase. Cell 107, 715-726 (2001).
59. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl Acad. Sci. USA 100, 6940-6945 (2003). Demonstration of absolute quantitation of proteins and their modifications
60. Barnidge DR, Dratz EA, Martin T, Bonilla LE, Moran LB, Lindall A. Absolute quantification of the G protein-coupled receptor rhodopsin by LC/MS/MS using proteolysis product peptides and synthetic peptide standards. Anal. Chem. 75, 445-451 (2003).
61. Barr JR, Maggio VL, Patterson DG Jr et al. Isotope dilution - mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. Clin. Chem. 42, 1676-1682 (1996).
62. Jeppsson JO, Kobold U, Barr J et al. Approved IFCC reference method for the measurement of HbA1c in human blood. Clin. Chem. Lab. Med. 40, 78-89 (2002).
63. Hoelzel W, Weykamp C, Jeppsson JO et al. IFCC reference system for measurement of hemoglobin A1c in human blood and the national standardization schemes in the United States, Japan, and Sweden: a method-comparison study. Clin. Chem. 50, 166-174 (2004).
64. Gavin AC, Bosche M, Krause R et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).
65. de Boer E, Rodriguez P, Bonte E et al. Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc. Natl Acad. Sci. USA 100, 7480-7485 (2003).
66. Bouwmeester T, Bauch A, Ruffner H et al. A physical and functional map of the human TNF-α/NF-κB signal transduction pathway. Nature Cell Biol. 6, 97-105 (2004).
67. Ranish JA, Yi EC, Leslie DM et al. The study of macromolecular complexes by quantitative proteomics. Nature Genet. 33, 349-355 (2003). Demonstration of various concepts attainable with stable isotope labeling to elucidate protein interaction networks, shown here for isotope-coded affinity tag.
68. Brand M, Ranish JA, Kummer NT et al. Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nature Struct. Mol. Biol. 11, 73-80 (2004).
69. Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ, Mann M. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nature Biotechnol. 21, 315-318 (2003). Delineation of epidermal growth factor (EGF) receptor-interacting partners in EGF-stimulated cells using stable isotope labeling by amino acids in cell cultures.
70. Foster LJ, De Hoog CL, Mann M. Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc. Natl Acad. Sci. USA 30, 30 (2003).
71. Schulze WX, Mann M. A novel proteomic screen for peptide-protein interactions. J. Biol Chem. 279, 1056-1064 (2004).