A label-free mass spectrometry method for the quantification of protein isotypes

Analytical Biochemistry

Volumn 395, Issue 2, 2009, Pages 217-223

  Winefield, Robert D ^a   Williams, Todd D ^a   Himes, Richard H ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

Label free quantification; Mass spectrometry; Targeted proteomic analysis; Tubulin; Tubulin isotype quantification

Indexed keywords

LANTHANUM COMPOUNDS; MASS SPECTROMETRY;

INTERNAL STANDARDS; ISOTOPICALLY LABELED; LABEL FREE; LABEL-FREE TECHNIQUES; PROTEOMIC ANALYSIS; QUANTITATIVE MASS SPECTROMETRIES; TUBULIN; TUBULIN ISOTYPE QUANTIFICATION;

PEPTIDES;

BETA 1 TUBULIN; BETA 2 TUBULIN; BETA TUBULIN; BETA3 TUBULIN; BETA4B TUBULIN; BETA5 TUBULIN; SYNTHETIC PEPTIDE; TRYPSIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; HELA CELL; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEOMICS; QUANTITATIVE ANALYSIS;

EID: 70349783745     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2009.07.052     Document Type: Article

References (39)

1. Bantscheff M., Schirle M., Sweetman G., Rick J., and Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 389 (2007) 1017-1031
2. Aebersold R., and Mann M. Mass spectrometry-based proteomics. Nature 422 (2003) 198-207
3. Thelen J.J., and Peck S.C. Quantitative proteomics in plants: choices in abundance. Plant Cell 19 (2007) 3339-3346
4. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 (1999) 994-999
5. Oda Y., Huang K., Cross F.R., Cowburn D., and Chait B.T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. USA 96 (1999) 6591-6596
6. Paša-Tolić L., Jensen P.K., Anderson G.A., Lipton M.S., Peden K.K., Martinovic S., Tolic N., Bruce J.E., and Smith R.D. High-throughput proteome-wide precision measurements of protein expression using mass spectrometry. J. Am. Chem. Soc. 121 (1999) 7949-7950
7. Ong S.E., and Mann M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1 (2005) 252-262
8. 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal. Chem. 73 (2001) 2836-2842
9. Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., Khainovski N., Pillai S., Dey S., Daniels S., Purkayastha S., Juhasz P., Martin S., Bartlet-Jones M., He F., Jacobson A., and Pappin D.J. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3 (2004) 1154-1169
10. Schmidt M.W., Houseman A., Ivanov A.R., and Wolf D.A. Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Mol. Syst. Biol. 3 (2007) 79
11. Gerber S.A., Rush J., Stemman O., Kirschner M.W., and Gygi S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 100 (2003) 6940-6945
12. Old W.M., Meyer-Arendt K., Aveline-Wolf L., Pierce K.G., Mendoza A., Sevinsky J.R., Resing K.A., and Ahn N.G. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 4 (2005) 1487-1502
13. America A.H., and Cordewener J.H. Comparative LC-MS: a landscape of peaks and valleys. Proteomics 8 (2008) 731-749
14. Luduena R.F. Multiple forms of tubulin: different gene products and covalent modifications. Intl. Rev. Cytol. 178 (1998) 207-275
15. Khodiyar V.K., Maltais L.J., Sneddon K.M., Smith J.R., Shimoyama M., Cabral F., Dumontet C., Dutcher S.K., Harvey R.J., Lafanechere L., Murray J.M., Nogales E., Piquemal D., Stanchi F., Povey S., and Lovering R.C. A revised nomenclature for the human and rodent α-tubulin gene family. Genomics 90 (2007) 285-289
16. Verdier-Pinard P., Pasquier E., Xiao H., Burd B., Villard C., Lafitte D., Miller L.M., Angeletti R.H., Horwitz S.B., and Braguer D. Tubulin proteomics: towards breaking the code. Anal. Biochem. 384 (2009) 197-206
17. Chelius D., and Bondarenko P.V. Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J. Proteome Res. 1 (2002) 317-323
18. Bondarenko P.V., Chelius D., and Shaler T.A. Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal. Chem. 74 (2002) 4741-4749
19. Nogales E., Wolf S.G., and Downing K.H. Structure of the αβ-tubulin dimer by electron crystallography. Nature 391 (1998) 199-203
20. Decottignies A., Grant A.M., Nichols J.W., de Wet H., McIntosh D.B., and Goffeau A. ATPase and multidrug transport activities of the overexpressed yeast ABC protein Yor1p. J. Biol. Chem. 273 (1998) 12612-12622
21. Gupta Jr. M.L., Bode C.J., Georg G.I., and Himes R.H. Understanding tubulin-Taxol interactions: mutations that impart Taxol binding to yeast tubulin. Proc. Natl. Acad. Sci. USA 100 (2003) 6394-6397
22. Foland T.B., Dentler W.L., Suprenant K.A., Gupta Jr. M.L., and Himes R.H. Paclitaxel-induced microtubule stabilization causes mitotic block and apoptotic-like cell death in a paclitaxel-sensitive strain of Saccharomyces cerevisiae. Yeast 22 (2005) 971-978
23. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976) 248-254
24. Newton C.N., DeLuca J.G., Himes R.H., Miller H.P., Jordan M.A., and Wilson L. Intrinsically slow dynamic instability of HeLa cell microtubules in vitro. J. Biol. Chem. 277 (2002) 42456-42462
25. Long G.L., and Winefordner J.D. Limits of detection: a closer look at the IUPAC definition. Anal. Chem. 55 (1983) 712A-724A
26. Alterman M.A., Kornilayev B., Duzhak T., and Yakovlev D. Quantitative analysis of cytochrome p450 isozymes by means of unique isozyme-specific tryptic peptides: a proteomic approach. Drug Metab. Dispos. 33 (2005) 1399-1407
27. Risinger A.L., Jackson E.M., Polin L.A., Helms G.L., LeBoeuf D.A., Joe P.A., Hopper-Borge E., Luduena R.F., Kruh G.D., and Mooberry S.L. The taccalonolides: microtubule stabilizers that circumvent clinically relevant taxane resistance mechanisms. Cancer Res. 68 (2008) 8881-8888
28. Hagman C., Ricke D., Ewert S., Bek S., Falchetto R., and Bitsch F. Absolute quantification of monoclonal antibodies in biofluids by liquid chromatography-tandem mass spectrometry. Anal. Chem. 80 (2008) 1290-1296
29. Lehmann U., Wienkoop S., Tschoep H., and Weckwerth W. If the antibody fails: a mass Western approach. Plant J. 55 (2008) 1039-1046
30. Verdier-Pinard P., Wang F., Burd B., Angeletti R.H., Horwitz S.B., and Orr G.A. Direct analysis of tubulin expression in cancer cell lines by electrospray ionization mass spectrometry. Biochemistry 42 (2003) 12019-12027
31. Kamath K., Wilson L., Cabral F., and Jordan M.A. βIII-Tubulin induces paclitaxel resistance in association with reduced effects on microtubule dynamic instability. J. Biol. Chem. 280 (2005) 12902-12907
32. Katsetos C.D., Herman M.M., and Mork S.J. Class III β-tubulin in human development and cancer. Cell Motil. Cytoskel. 55 (2003) 77-96
33. Pasquier E., and Kavallaris M. Microtubules: a dynamic target in cancer therapy. IUBMB Life 60 (2008) 165-170
34. Gan P.P., Pasquier E., and Kavallaris M. Class III β-tubulin mediates sensitivity to chemotherapeutic drugs in non-small cell lung cancer. Cancer Res. 67 (2007) 9356-9363
35. Seve P., Lai R., Ding K., Winton T., Butts C., Mackey J., Dumontet C., Dabbagh L., Aviel-Ronen S., Seymour L., Whitehead M., Tsao M.S., Shepherd F.A., and Reiman T. Class III β-tubulin expression and benefit from adjuvant cisplatin/vinorelbine chemotherapy in operable non-small cell lung cancer: analysis of NCIC JBR.10. Clin. Cancer Res. 13 (2007) 994-999
36. Hayashi Y., Kuriyama H., Umezu H., Tanaka J., Yoshimasu T., Furukawa T., Tanaka H., Kagamu H., Gejyo F., and Yoshizawa H. Class III β-tubulin expression in tumor cells is correlated with resistance to docetaxel in patients with completely resected non-small-cell lung cancer. Intern. Med. 48 (2009) 203-208
37. Seve P., Mackey J., Isaac S., Tredan O., Souquet P.J., Perol M., Lai R., Voloch A., and Dumontet C. Class III β-tubulin expression in tumor cells predicts response and outcome in patients with non-small cell lung cancer receiving paclitaxel. Mol. Cancer Ther. 4 (2005) 2001-2007
38. Burkhart C.A., Kavallaris M., and Band Horwitz S. The role of β-tubulin isotypes in resistance to antimitotic drugs. Biochim. Biophys. Acta 1471 (2001) O1-O9
39. Dumontet C., Jordan M.A., and Lee F.F. Ixabepilone: targeting βIII-tubulin expression in taxane-resistant malignancies. Mol. Cancer Ther. 8 (2009) 17-25