Towards clinical proteomics analysis

Biomedical Chromatography

Volumn 25, Issue 1, 2011, Pages 59-64

  Imai, Kazuhiro ^a   Koshiyama, Akiyo ^a   Nakata, Katsunori ^a  

^a MUSASHINO UNIVERSITY   (Japan)

Author keywords

2D PAGE; Fluorogenic derivatization; LC MS MS; Proteomics analytical methods

Indexed keywords

ELECTROPHORESIS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PROTEINS;

2D-PAGE; ANALYTICAL METHOD; DERIVATIZATIONS; FLUOROGENIC DERIVATIZATION; FLUOROGENICS; LC-MS-MS; LC.MS/MS; PROTEOMIC ANALYSIS; PROTEOMIC ANALYTICAL METHOD; PROTEOMICS;

DIAGNOSIS;

BIOTIN; CORE PROTEIN; ESCHERICHIA COLI PROTEIN; FLUORESCENT DYE; ONCOPROTEIN; PEPTIDE;

ANALYTIC METHOD; CANCER CELL; CATION EXCHANGE; DERIVATIZATION; FLUORESCENCE ANALYSIS; FLUOROGENIC DERIVATIZATION; FUNCTIONAL PROTEOMICS; HEPATITIS C VIRUS; HUMAN; ISOELECTRIC FOCUSING; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; LUNG CANCER; MOLECULAR DYNAMICS; NONHUMAN; PEPTIDE MAPPING; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRECIPITATION; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PURIFICATION; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; REVERSED PHASE LIQUID CHROMATOGRAPHY; REVIEW; SENSITIVITY ANALYSIS; SIGNAL NOISE RATIO; SILVER STAINING; STRUCTURAL PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 78650650948     PISSN: 02693879     EISSN: 10990801     Source Type: Journal    
DOI: 10.1002/bmc.1541     Document Type: Review

References (28)

1. Asamoto H, Ichibangase T, Uchikura K and Imai K. Application of an improved proteomics method, fluorogenic derivatization-liquid chromatography-tandem mass spectrometry, to differential analysis of proteins in small regions of mouse brain. Journal of Chromatography A 2008; 1208(1-2): 147-155.
2. Bland AM, Janech MG, Almeida JS and Arthur JM. Sources of variability among replicate samples separated by two-dimensional gel electrophoresis. Journal of Biomolecular Technology 2010; 21(1): 3-8.
3. Chiangjong W and Thongboonkerd VA. Comparative study of different dyes for the detection of proteomes derived from Escherichia coli and MDCK cells: Sensitivity and selectivity. Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences 2009; 877(14-15): 1433-1439.
4. Gan CS, Chong PK, Pham TK and Wright PC, Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ). Journal of Proteome Research 2007; 6(2): 821-827.
5. Gorg A, Weiss W and Dunn MJ. Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004; 4(12): 3665-3685.
6. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH and Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnology 1999; 17(10): 994-999.
7. Han DK, Eng J, Zhou H and Aebersold R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nature Biotechnology 2001; 19(10): 946-951.
8. Hansen KC, Schmitt-Ulms G, Chalkley RJ, Hirsch J, Baldwin MA and Burlingame AL. Mass spectrometric analysis of protein mixtures at low levels using cleavable C-13-isotope-coded affinity tag and multidimensional chromatography. Molecular and Cellular Proteomics 2003; 2(5): 299-314.
9. Hrebicek T, Dürrschmid K, Auer N, Bayer K and Rizzi A. Effect of CyDye minimum labeling in differential gel electrophoresis on the reliability of protein identification. Electrophoresis 2007; 28(7): 1161-1169.
10. Ichibangase T and Imai K. Application of fluorogenic derivatization-liquid chromatography-tandem mass spectrometric proteome method to skeletal muscle proteins in fast thoroughbred horses. Journal of Proteome Research 2009; 8(4): 2129-2134.
11. Ichibangase T, Moriya K, Koike K and Imai K. A proteomics method revealing disease-related proteins in livers of hepatitis-infected mouse model. Journal of Proteome Research 2007; 6(7): 2841-2849.
12. Ichibangase T, Saimaru H, Takamura N, Kuwahara T, Koyama A, Iwatsubo T and Imai K. Proteomics of Caenorhabditis elegans over-expressing human alpha-synuclein analyzed by fluorogenic derivatization-liquid chromatography/tandem mass spectrometry: identification of actin and several ribosomal proteins as negative markers at early Parkinson's disease stages. Biomedical Chromatography 2008; 22(3): 232-234.
13. Imai K, Ichibangase T, Saitoh R and Hoshikawa Y. A proteomics study on human breast cancer cell lines by fluorogenic derivatization-liquid chromatography/tandem mass spectrometry. Biomedical Chromatography 2008; 22(11): 1304-1314.
14. Keshamouni VG, Michailidis G, Grasso CS, Anthwal S, Strahler JR, Walker A, Arenberg DA, Reddy RC, Akulapalli S, Thannickal VJ, Standiford TJ, Andrews PC and Omenn GS. Differential protein expression profiling by iTRAO-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype. Journal of Proteome Research 2006; 5(5): 1143-1154.
15. Koshiyama A and Imai K. Synthesis and evaluation of a fluorogenic reagent for proteomic studies: 7-fluoro-N-2-(dimethylamino)ethyl-2, 1, 3-benzoxadiazole-4-sulfonamide (DAABD-F). Analyst 2010; 135(8): 2119-2124.
16. Lagadec C, Romon R, Tastet C, Meignan S, Com E, Page A, Bidaux G, Hondermark H and Le Bourhis X. Ku86 is important for TrkA overexpression-induced breast cancer cell invasion. Proteomics Clinical Applications 2010; 4(6-7): 580-590.
17. Li JX, Steen H and Gygi SP. Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents-the yeast salinity stress response. Molecular and Cellular Proteomics 2003; 2(11): 1198-1204.
18. Lopez JL. Two-dimensional electrophoresis in proteome expression analysis. Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences 2007; 849(1-2): 190-202.
19. Mackintosh JA, Choi HY, Bae SH, Veal DA, Bell PJ, Ferrari BC, Van Dyk DD, Verrills NM, Paik YK and Karuso P. A fluorescent natural product for ultra sensitive detection of proteins in one-dimensional and two-dimensional gel electrophoresis. Proteomics 2003; 3(12): 2273-2288.
20. Makridakis M, Roubelakis MG, Bitsika V, Dimuccio V, Samiotaki M, Kossida S, Panayotou G, Coleman J, Candiano G, Anagnou NP and Vlahou A. Analysis of secreted proteins for the study of bladder cancer cell aggressiveness. Journal of Proteome Research 2010; 9(6): 3243-3259.
21. Masuda M, Toriumi C, Santa T and Imai K. Fluorogenic derivatization reagents suitable for isolation and identification of cysteine-containing proteins utilizing high-performance liquid chromatography-tandem mass spectrometry. Analytical Chemistry 2004; 76(3): 728-735.
22. Molloy MP, Donohoe S, Brzezinski EE, Kilby GW, Stevenson TI, Baker JD, Goodlett DR and Gage DA. Large-scale evaluation of quantitative reproducibility and proteome coverage using acid cleavable isotope coded affinity tag mass spectrometry for proteomic profiling. Proteomics 2005; 5(5): 1204-1208.
23. Osorio C, Sullivan PM, He DN, Mace BE, Ervin JF, Strittmatter WJ and Alzate O. Mortalin is regulated by APOE in hippocampus of AD patients and by human APOE in TR mice. Neurobiology of Aging 2007; 28(12): 1853-1862.
24. Ross PL, Huang YN, Marchese JN, 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 DJ. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Molecular Cell Proteomics 2004; 3(12): 1154-1169.
25. Shaw J, Rowlinson R, Nickson J, Stone T, Sweet A, Williams K and Tonge R. Evaluation of saturation labelling two-dimensional difference gel electrophoresis fluorescent dyes. Proteomics 2003; 3(7): 1181-1195.
26. Toriumi C and Imai K. An identification method for altered proteins in tissues utilizing fluorescence derivatization, liquid chromatography, tandem mass spectrometry, and a database-searching algorithm. Analytical Chemistry 2003; 75(15): 3725-3730.
27. Unlu M, Morgan ME and Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 1997; 18(11): 2071-2077.
28. Wu WW, Wang G, Baek SJ and Shen RF. Comparative study of three proteomic quantitative methods, DICE, cICAT, and ITRAQ, using 2D gel- or LC-MALDI TOF/TOF. Journal of Proteome Research 2006; 5(3): 651-658.