Quantitative membrane proteomics applying narrow range peptide isoelectric focusing for studies of small cell lung cancer resistance mechanisms

Proteomics

Volumn 8, Issue 15, 2008, Pages 3008-3018

  Eriksson, Hanna ^a,b   Lengqvist, Johan ^a,b   Hedlund, Joel ^c   Uhlén, Kristina ^d   Orre, Lukas M ^a,b   Bjellqvist, Bengt ^d   Persson, Bengt ^b,c   Lehtiö, Janne ^a,b   Jakobsson, Per Johan ^a,b  

^a KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^b KAROLINSKA INSTITUTE   (Sweden)

^c LINKÖPING UNIVERSITY   (Sweden)

^d GE Healthcare Bio Sciences AB   (Sweden)

Author keywords

Drug resistance; Isoelectric focusing; Lung cancer; Membrane proteins; Quantitative proteomics

Indexed keywords

DOXORUBICIN; MEMBRANE PROTEIN; PROTEOME; SARCOPLASMIC RETICULUM CALCIUM TRANSPORTING ADENOSINE TRIPHOSPHATASE;

ARTICLE; CANCER CELL CULTURE; CANCER RESISTANCE; CELL MEMBRANE; CHEMICAL LABELING; DOWN REGULATION; HUMAN; HUMAN CELL; ISOELECTRIC FOCUSING; ITRAQ LABELING; LIQUID CHROMATOGRAPHY; LUNG SMALL CELL CANCER; MASS SPECTROMETRY; MICROSOME; PH; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONTENT; PROTEIN EXPRESSION; PROTEIN MODIFICATION; PROTEOMICS; QUANTITATIVE ANALYSIS; UPREGULATION; VALIDATION PROCESS; WESTERN BLOTTING;

BLOTTING, WESTERN; CELL LINE, TUMOR; CHROMATOGRAPHY, LIQUID; HUMANS; ISOELECTRIC FOCUSING; LUNG NEOPLASMS; MEMBRANE PROTEINS; MICROSOMES; MODELS, THEORETICAL; NANOTECHNOLOGY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SMALL CELL LUNG CARCINOMA; TANDEM MASS SPECTROMETRY;

EID: 49749131566     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800174     Document Type: Article

References (33)

1. Wallin, E., von Heijne, G., Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 1998, 7, 1029-1038.
2. Yildirim, M. A., Goh, K. I., Cusick, M. E., Barabasi, A. L., Vidal, M., Drug-target network. Nat. Biotechnol. 2007, 25, 1119-1126.
3. Macfarlane, D. E., Two dimensional benzyldimethyl-n-hexadecylammonium chloride - sodium dodecyl sulfate preparative polyacrylamide gel electrophoresis: A high capacity high resolution technique for the purification of proteins from complex mixtures. Anal. Biochem. 1989, 176, 457-463.
4. Hartinger, J., Stenius, K., Hogemann, D., Jahn, R., 16-BAC/SDS-PAGE: A two-dimensional gel electrophoresis system suitable for the separation of integral membrane proteins. Anal. Biochem. 1996, 240, 126-133.
5. Schagger, H., von Jagow, G., Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal. Biochem. 1991, 199, 223-231.
6. Rais, I., Karas, M., Schagger, H., Two-dimensional electrophoresis for the isolation of integral membrane proteins and mass spectrometry identification. Proteomics 2004, 4, 2567-2571.
7. Washburn, M. P., Wolters, D., Yates, J. R., III, Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19, 242-247.
8. Wu, C. C., Yates, J. R., III, The application of mass spectrometry to membrane proteomics. Nat. Biotechnol. 2003, 21, 262-267.
9. Cargile, B. J., Sevinsky, J. R., Essader, A. S.,Stephenson, J. L., Jr., Bundy, J. L., Immobilized pH gradient isoelectric focusing as a first-dimension separation in shotgun proteomics. J. Biomol. Tech. 2005, 16, 181-189.
10. Chick, J. M., Haynes, P. A., Molloy, M. P., Bjellqvist, B. et al., Characterization of the rat liver membrane proteome using peptide immobilized pH gradient isoelectric focusing. J. Proteome Res. 2008, 7, 1036-1045.
11. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154-1169.
12. Lengqvist, J., Uhlen, K., Lehtio, J., iTRAQ compatibility of peptide immobilized pH gradient isoelectric focusing. Proteomics 2007, 7, 1746-1752.
13. Cole, S. P., Bhardwaj, G., Gerlach, J. H., Mackie, J. E. et al., Overexpression of a transporter gene in a multidrug-resistant human lung cancer cell line. Science 1992, 258, 1650-1654.
14. Nielsen, D., Maare, C., Skovsgaard, T., Cellular resistance to anthracyclines. Gen. Pharmacol. 1996, 27, 251-255.
15. Wessel, D., Flügge, U. I., A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 1984, 138, 141-143.
16. Shilov, I. V., Seymour, S. L., Patel, A. A., Loboda, A. et al., The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol. Cell. Proteomics 2007, 6, 1638-1655.
17. Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. L., Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 2001, 305, 567-580.
18. Persson, B., Argos, P., Topology prediction of membrane proteins. Protein Sci. 1996, 5, 363-371.
19. Stephenson, J. L., Jr., Bunger, M. K., Cargile, B. J., Sevinsky, J. R., 7th Siena Meeting from Genome to Proteome: Back to the Future, Siena, Italy 2006.
20. Gan, C. S., Chong, P. K., Pham, T. K., Wright, P. C., Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ). J. Proteome Res. 2007, 6, 821-827.
21. Ahram, M., Litou, Z. I., Fang, R., Al-Tawallbeh, G., Estimation of membrane proteins in the human proteome. In Silico Biol. 2006, 6, 379-386.
22. Moller, S., Croning, M. D., Apweiler, R., Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 2001, 17, 646-653.
23. Persson, B., Argos, P., Prediction of membrane protein topology utilizing multiple sequence alignments. J. Protein Chem. 1997, 16, 453-457.
24. Milpetz, F., Argos, P., Persson, B., TMAP: A new email and WWW service for membrane-protein structural predictions. Trends Biochem. Sci. 1995, 20, 204-205.
25. Nilsson, J., Persson, B., Von Heijne, G., Prediction of partial membrane protein topologies using a consensus approach. Protein Sci. 2002, 11, 2974-2980.
26. Scherl, A., Francois, P., Charbonnier, Y., Deshusses, J. M. et al., Exploring glycopeptide-resistance in Staphylococcus aureus: A combined proteomics and transcriptomics approach for the identification of resistance-related markers. BMC Genomics 2006, 7, 296.
27. Mirza, S. P., Halligan, B. D., Greene, A. S., Olivier, M., Improved method for the analysis of membrane proteins by mass spectrometry. Physiol. Genomics 2007, 30, 89-94.
28. Nielsen, M. L., Savitski, M. M., Zubarev, R. A., Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics. Mol. Cell. Proteomics 2006, 5, 2384-2391.
29. Picotti, P., Aebersold, R., Domon, B., The implications of proteolytic background for shotgun proteomics. Mol. Cell. Proteomics 2007, 6, 1589-1598.
30. Desiere, F., Deutsch, E. W., King, N. L., Nesvizhskii, A. I. et al., The PeptideAtlas project. Nucleic Acids Res. 2006, 34, D655-658.
31. Essader, A. S., Cargile, B. J., Bundy, J. L., Stephenson, J. L. Jr., A comparison of immobilized pH gradient isoelectric focusing and strong-cation-exchange chromatography as a first dimension in shotgun proteomics. Proteomics 2005, 5, 24-34.
32. Demaurex, N., Distelhorst, C., Cell biology. Apoptosis - the calcium connection. Science 2003, 300, 65-67.
33. 2+ concentration of the endoplasmic reticulum is a key determinant of ceramide-induced apoptosis: Significance for the molecular mechanism of Bcl-2 action. EMBO J. 2001, 20, 2690-2701.