Intact protein profiling in breast cancer biomarker discovery: Protein identification issue and the solutions based on 3D protein separation, bottom-up and top-down mass spectrometry

Proteomics

Volumn 13, Issue 7, 2013, Pages 1053-1058

  Bouchal, Pavel ^a,b   Dvorakova, Monika ^a,b   Scherl, Alexander ^c   Garbis, Spiros D ^d   Nenutil, Rudolf ^b   Vojtesek, Borivoj ^b  

^a MASARYK UNIVERSITY   (Czech Republic)

^b MASARYK MEMORIAL CANCER INSTITUTE   (Czech Republic)

^c UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^d UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

Breast cancer; FT MS; MALDI TOF MS; SELDI TOF MS; Technology

Indexed keywords

BIOLOGICAL MARKER;

ARTICLE; BREAST CANCER; CONTROLLED STUDY; HUMAN; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

AMINO ACID SEQUENCE; BREAST NEOPLASMS; FEMALE; HUMANS; MOLECULAR SEQUENCE DATA; NEOPLASM PROTEINS; PEPTIDES; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TUMOR MARKERS, BIOLOGICAL;

EID: 84875888096     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200121     Document Type: Article

References (27)

1. Karpova, M. A., Moshkovskii, S. A., Toropygin, I. Y., Archakov, A. I., Cancer-specific MALDI-TOF profiles of blood serum and plasma: biological meaning and perspectives. J. Proteomics 2010, 73, 537-551.
2. Gemoll, T., Roblick, U. J., Auer, G., Jornvall, H. et al., SELDI-TOF serum proteomics and colorectal cancer: a current overview. Arch. Physiol. Biochem. 2010, 116, 188-196.
3. Caffrey, R. E., A review of experimental design best practices for proteomics based biomarker discovery: focus on SELDI-TOF. Methods Mol. Biol. 2010, 641, 167-183.
4. Jourdain, S., Bulman, A., Dalmasso, E., The lucid proteomics system for top-down biomarker research. Arch. Physiol. Biochem. 2010, 116, 158-162.
5. Maeland Nilsen, M., Uleberg, K. E., Janssen, E. A., Baak, J. P. et al., From SELDI-TOF MS to protein identification by on-chip elution. J. Proteomics 2011, 74, 2995-2998.
6. Lehr, S., Biomarker discovery using SELDI-TOF protein chip technology. Arch. Physiol. Biochem. 2010, 116, 157.
7. Bulman, A. L., Dalmasso, E. A., Purification and identification of candidate biomarkers discovered using SELDI-TOF MS. Methods Mol. Biol. 2012, 818, 49-66.
8. Peng, J., Stanley, A. J., Cairns, D., Selby, P. J. et al., Using the protein chip interface with quadrupole time-of-flight mass spectrometry to directly identify peaks in SELDI profiles-initial evaluation using low molecular weight serum peaks. Proteomics 2009, 9, 492-498.
9. Hogdall, E., Fung, E. T., Christensen, I. J., Yip, C. et al., Proteomic biomarkers for overall and progression-free survival in ovarian cancer patients. Proteomics Clin. Appl. 2010, 4, 940-952.
10. Sussulini, A., Dihazi, H., Banzato, C. E., Arruda, M. A. et al., Apolipoprotein A-I as a candidate serum marker for the response to lithium treatment in bipolar disorder. Proteomics 2011, 11, 261-269.
11. Buhimschi, I. A., Using SELDI-TOF mass spectrometry on amniotic fluid and for clinical proteomics and theranostics in disorders of pregnancy. Methods Mol. Biol. 2012, 818, 171-197.
12. Bornemann, S., Rietschel, B., Baltruschat, S., Karas, M. et al., A novel polyacrylamide gel system for proteomic use offering controllable pore expansion by crosslinker cleavage. Electrophoresis 2010, 31, 585-592.
13. Schagger, H., Tricine-SDS-PAGE. Nat. Protoc. 2006, 1, 16-22.
14. Thomas, J. M., Hodes, M. E., A new discontinuous buffer system for the electrophoresis of cationic proteins at near-neutral pH. Anal. Biochem. 1981, 118, 194-196.
15. Kyte, J., Rodriguez, H., A discontinuous electrophoretic system for separating peptides on polyacrylamide gels. Anal. Biochem. 1983, 133, 515-522.
16. Wiltfang, J., Arold, N., Neuhoff, V., A new multiphasic buffer system for sodium dodecyl sulfate-polyacrylamide gel electrophoresis of proteins and peptides with molecular masses 100, 000-1000, and their detection with picomolar sensitivity. Electrophoresis 1991, 12, 352-366.
17. Brozkova, K., Budinska, E., Bouchal, P., Hernychova, L. et al., Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression. Breast Cancer Res. 2008, 10, R48.
18. Bouchal, P., Roumeliotis, T., Hrstka, R., Nenutil, R. et al., Biomarker discovery in low-grade breast cancer using isobaric stable isotope tags and two-dimensional liquid chromatography-tandem mass spectrometry (iTRAQ-2DLC-MS/MS) based quantitative proteomic analysis. J. Proteome Res. 2009, 8, 362-373.
19. Holcakova, J., Hernychova, L., Bouchal, P., Brozkova, K. et al., Identification of alpha B-crystallin, a biomarker of renal cell carcinoma by SELDI-TOF MS. Int. J. Biol. Markers 2008, 23, 48-53.
20. Bouchal, P., Jarkovsky, J., Hrazdilova, K., Dvorakova, M. et al., The new platinum-based anticancer agent LA-12 induces retinol binding protein 4 in vivo. Proteome Sci. 2011, 9, 68.
21. Zamdborg, L., LeDuc, R. D., Glowacz, K. J., Kim, Y. B. et al., ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry. Nucleic Acids Res. 2007, 35, W701-706.
22. Liu, X., Sirotkin, Y., Shen, Y., Anderson, G. et al., Protein identification using top-down. Mol. Cell Proteomics 2012, 11, M111 008524.
23. Zhou, J., Allred, D. C., Avis, I., Martinez, A. et al., Differential expression of the early lung cancer detection marker, heterogeneous nuclear ribonucleoprotein-A2/B1 (hnRNP-A2/B1) in normal breast and neoplastic breast cancer. Breast Cancer Res. Treat. 2001, 66, 217-224.
24. Tauler, J., Zudaire, E., Liu, H., Shih, J. et al., hnRNP A2/B1 modulates epithelial-mesenchymal transition in lung cancer cell lines. Cancer Res. 2010, 70, 7137-7147.
25. Kellie, J. F., Tran, J. C., Lee, J. E., Ahlf, D. R. et al., The emerging process of top down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput. Mol. Biosyst. 2010, 6, 1532-1539.
26. Coelho Graca, D., Lescuyer, P., Clerici, L., Tsybin, Y. O. et al., Electron transfer dissociation mass spectrometry of hemoglobin on clinical samples. J. Am. Soc. Mass Spectrom. 2012, 23, 1750-1756.
27. Wu, S., Lourette, N. M., Tolic, N., Zhao, R. et al., An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications. J. Proteome Res. 2009, 8, 1347-1357.