Mass spectrometry-based quantification

Clinical Biochemistry

Volumn 46, Issue 6, 2013, Pages 421-431

  DeSouza, Leroi V ^a   Siu, K W Michael ^a  

^a YORK UNIVERSITY   (Canada)

Author keywords

ICAT; ITRAQ; LC MRM; LC MS MS; Mass tags; Proteolytic cleavage; Relative quantification; SILAC; Stable isotope labeling

Indexed keywords

NITROGEN 15; OXYGEN 18; STABLE ISOTOPE; SYNTHETIC PEPTIDE; DIAGNOSTIC AGENT; PROTEIN;

ANALYTIC METHOD; ARTICLE; CHEMICAL LABELING; CLEAVABLE ISOTOPE CODED AFFINITY TAGS; INTERMETHOD COMPARISON; ISOBARIC TAGS FOR RELATIVE AND ABSOLUTE QUANTITATION; ISOTOPE CODED AFFINITY TAGS; ISOTOPE LABELING; LIMIT OF QUANTITATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN TARGETING; REACTION TIME; SOLID PHASE SYNTHESIS; STABLE ISOTOPE LABELING BY AMINO ACID; TANDEM MASS SPECTROMETRY; TANDEM MASS TAGS; BIOLOGY; DIAGNOSTIC PROCEDURE; GENE EXPRESSION PROFILING; HUMAN; ISOLATION AND PURIFICATION; MEDICAL TECHNOLOGY; METHODOLOGY; PROTEOMICS; REVIEW; STANDARD; DIAGNOSTIC USE; PROCEDURES;

CHROMATOGRAPHY, LIQUID; CLINICAL LABORATORY TECHNIQUES; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; HUMANS; ISOTOPE LABELING; MEDICAL LABORATORY SCIENCE; PROTEINS; PROTEOMICS; REFERENCE STANDARDS; TANDEM MASS SPECTROMETRY;

EID: 84890021402     PISSN: 00099120     EISSN: 18732933     Source Type: Journal    
DOI: 10.1016/j.clinbiochem.2012.10.025     Document Type: Article

References (62)

1. Moore L.J., Machlan L.A. High accuracy determination of calcium in blood serum by isotope dilution mass spectrometry. Anal Chem 1972, 44:2291-2296.
2. Fassett J.D., Paulsen P.J. Isotope dilution mass spectrometry for accurate elemental analysis. Anal Chem 1989, 61:643A-649A.
3. White E., Welch V.M., Sun T., Sniegoski L.T., Schaffer R., Hertz H.S., et al. The accurate determination of serum glucose by isotope dilution mass spectrometry-two methods. Biomed Mass Spectrom 1982, 9:395-405.
4. Cohen A., Hertz H.S., Mandel J., Paule R.C., Schaffer R., Sniegoski L.T., et al. Total serum cholesterol by isotope dilution/ mass spectrometry: a candidate definitive method. Clin Chem 1980, 26:854-860.
5. Barr J.R., Maggio V.L., Patterson D.G., Cooper G.R., Henderson L.O., Turner W.E., et al. Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. Clin Chem 1996, 42:1676-1682.
6. Elliot M.H., Smith D.S., Parker C.E., Borchers C. Current trends in quantitative proteomics. J Mass Spectrom 2009, 44:1637-1660.
7. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17:994-999.
8. Oda Y., Owa T., Sato T., Boucher B., Daniels S., Yamanaka H., et al. Quantitative chemical proteomics for identifying candidate drug targets. Anal Chem 2003, 75:2159-2165.
9. DeSouza L., Diehl G., Yang E.C., Guo J., Rodrigues M.J., Romaschin A.D., et al. Proteomic analysis of the proliferative and secretory phases of the human endometrium: protein identification and differential protein expression. Proteomics 2005, 5:270-281.
10. Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3:1154-1169.
11. DeSouza L.V., Taylor A.M., Li W., Minkoff M.S., Romaschin A.D., Colgan T.J., et al. Multiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantification of endogenous levels of a potential cancer marker in cancerous and normal endometrial tissues. J Proteome Res 2008, 7:3525-3534.
12. Thompson A., Schäfer J., Kuhn K., Kienle S., Schwarz J., Schmidt G., et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003, 75:1895-1904.
13. Schmidt A., Kellermann J., Lottspeich F. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 2005, 5:4-15.
14. Hsu J.-L., Huang S.-Y., Chow N.-H., Chen S.-H. Stable isotope dimethyl labeling for quantitative proteomics. Anal Chem 2003, 75:6843-6852.
15. Melanson J.E., Avery S.L., Pinto D.M. High-coverage quantitative proteomics using amine-specific isotopic labeling. Proteomics 2006, 6:4466-4474.
16. 12C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics 2005, 5:380-387.
17. Smolka M., Zhou H., Aebersold R. Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol Cell Proteomics 2002, 1:19-29.
18. Haqqani A.S., Nesic M., Preston E., Baumann E., Kelly J., Stanimirovic D. Characterization of vascular protein expression patterns in cerebral ischemia/reperfusion using laser capture microdissection and ICAT-nanoLC-MS/MS. FASEB J 2005, 19:1809-1821.
19. Suckau D., Hahner S., Brand S., Jabs W., Schürenberg M., Halder T.M. ICPL: A new quantitative mass spectrometric method for proteomics. Bruker Daltonics Application note # MT-78 Downloaded from. http://www.bdal.com/uploads/media/mt78_icpl.pdf.
20. Leroy B., Rosier C., Erculisse V., Leys N., Mergeay M., Wattiez R. Differential proteomic analysis using isotope-coded protein-labeling strategies: comparison, improvements and application to simulated microgravity effect on Cupriavidus metallidurans CH34. Proteomics 2010, 10:2281-2291.
21. Fleron M., Greffe Y., Musmeci D., Massart A.C., Hennequiere V., Mazzucchelli G., et al. Novel post-digest isotope coded protein labeling method for phospho- and glycoproteome analysis. J Proteomics 2010, 73:1986-2005.
22. Nogueira F.C., Palmisano G., Schwämmle V., Campos F.A., Larsen M.R., Domont G.B., et al. Performance of isobaric and isotopic labeling in quantitative plant proteomics. J Proteome Res 2012, 11:3046-3052.
23. Murphy J.P., Kong F., Pinto D.M., Wang-Pruski G. Relative quantitative proteomic analysis reveals wound response proteins correlated with after-cooking darkening. Proteomics 2010, 10:4258-4269.
24. Oda Y., Huang K., Cross F.R., Cowburn D., Chait B.T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci U S A 1999, 96:6591-6596.
25. Conrads T.P., Alving K., Veenstra T.D., Belov M.E., Anderson G.A., Anderson D.J., et al. Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. Anal Chem 2001, 73:2132-2139.
26. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1:376-386.
27. Hebeler R., Oeljeklaus S., Reidegeld K.A., Eisenacher M., Stephan C., Sitek B., et al. Study of early leaf senescence in Arabidopsis thaliana by quantitative proteomics using reciprocal 14N/15N labeling and difference gel electrophoresis. Mol Cell Proteomics 2008, 7:108-120.
28. Oeljeklaus S., Meyer H.E., Warscheid B. Advancements in plant proteomics using quantitative mass spectrometry. J Proteomics 2009, 72:545-554.
29. Ibarrola N., Kalume D.E., Gronborg M., Iwahori A., Pandey A. A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture. Anal Chem 2003, 75:6043-6049.
30. 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res 2003, 2:173-181.
31. Ong S.E., Mann M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc 2006, 1:2650-2660.
32. Ong S.E., Mittler G., Mann M. Identifying and quantifying in vivo methylation sites by heavy methyl SILAC. Nat Methods 2004, 1:119-126.
33. Ibarrola N., Molina H., Iwahori A., Pandey A. A novel proteomic approach for specific identification of tyrosine kinase substrates using [13C]tyrosine. J Biol Chem 2004, 279:15805-15813.
34. Krijgsveld J., Ketting R.F., Mahmoudi T., Johansen J., Artal-Sanz M., Verrijzer C.P., et al. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol 2003, 21:927-931.
35. Krüger M., Moser M., Ussar S., Thievessen I., Luber C.A., Forner F., et al. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 2008, 134:353-364.
36. Ren F., Wu H., Lei Y., Zhang H., Liu R., Zhao Y., et al. Quantitative proteomics identification of phosphoglycerate mutase 1 as a novel therapeutic target in hepatocellular carcinoma. Mol Cancer 2010, 9:81.
37. Matic I., Jaffray E.G., Oxenham S.K., Groves M.J., Barratt C.L., Tauro S., et al. Absolute SILAC-compatible expression strain allows Sumo-2 copy number determination in clinical samples. J Proteome Res 2011, 10:4869-4875.
38. Geiger T., Cox J., Ostasiewicz P., Wisniewski J.R., Mann M. Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods 2010, 7:383-385.
39. Bendall S.C., Hughes C., Stewart M.H., Doble B., Bhatia M., Lajoie G.A. Prevention of amino acid conversion in SILAC experiments with embryonic stem cells. Mol Cell Proteomics 2008, 7:1587-1597.
40. Gerber S.A., Rush J., Stemman O., Kirschner M.W., Gygi S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A 2003, 100:6940-6945.
41. Pratt J.M., Simpson D.M., Doherty M.K., Rivers J., Gaskell S.J., Beynon R.J. Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat Protoc 2006, 1:1029-1043.
42. Rivers J., Simpson D.M., Robertson D.H., Gaskell S.J., Beynon R.J. Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT. Mol Cell Proteomics 2007, 6:1416-1427.
43. 18O labeled amino acides for use as internal standards with mass spectrometry. Biomed Mass Spectrom 1979, 6:309-314.
44. 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 2001, 73:2836-2842.
45. Julka S., Regnier F.E. Quantification in proteomics through stable isotope coding: a review. J Proteome Res 2004, 3:350-363.
46. 18O-labeling strategies for quantitative proteomics. Mass Spectrom Rev 2007, 26:121-136.
47. Gevaert K., Impens F., Ghesquiere B., Van Damme P., Lambrechts A., Vandekerckhove J. Stable isotopic labeling in proteomics. Proteomics 2008, 8:4873-4885.
48. 18O exchange of truncated peptide substrates. J Proteome Res 2003, 2:147-152.
49. Brown K.J., Fenselau C. Investigation of doxorubicin resistance in MCF-7 breast cancer cells using shot-gun comparative proteomics with proteolytic 18O labeling. J Proteome Res 2004, 3:455-462.
50. Blonder J., Hale M.L., Chan K.C., Yu L.R., Lucas D.A., Conrads T.P., et al. Quantitative profiling of the detergent-resistant membrane proteome of iota-b toxin induced vero cells. J Proteome Res 2005, 4:523-531.
51. 18O labeling. Mol Cell Proteomics 2006, 5:1382-1395.
52. Staes A., Demol H., Van Damme J., Martens L., Vandekerckhove J., Gevaert K. Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18. J Proteome Res 2004, 3:786-791.
53. Rappsilber J., Ryder U., Lamond A.I., Mann M. Large-scale proteomic analysis of the human spliceosome. Genome Res 2002, 12:1231-1245.
54. Ishihama Y., Oda Y., Tabata T., Sato T., Nagasu T., Rappsilber J., et al. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 2005, 4:1265-1272.
55. Chen C.-H. Review of a current role of mass spectrometry for proteome research. Anal Chim Acta 2008, 624:16-36.
56. Simpson K.L., Whetton A.D., Dive C. Quantitative mass spectrometry-based techniques for clinical use: biomarker identification and quantification. J Chromatogr B Analyt Technol Biomed Life Sci 2009, 877:1240-1249.
57. Zhu W., Smith J.W., Huang C.M. Mass spectrometry-based label-free quantitative proteomics. J Biomed Biotechnol 2010, 2010:840518.
58. Asara J.M., Christofk H.R., Freimark L.M., Cantley L.C. A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics 2008, 8:994-999.
59. Lu P., Vogel C., Wang R., Yao X., Marcotte E.M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 2007, 25:117-124.
60. Braisted J.C., Kuntumalla S., Vogel C., Marcotte E.M., Rodrigues A.R., Wang R., et al. The APEX quantitative proteomics tool: generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics 2008, 9:529.
61. Arike L., Valgepea K., Peil L., Nahku R., Adamberg K., Vilu R. Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli. J Proteomics 2012, 75:5437-5448.
62. Schwanhäusser B., Busse D., Li N., Dittmar G., Schuchhardt J., Wolf J., et al. Global quantification of mammalian gene expression control. Nature 2011, 473:337-342.