Comparative proteomic profiling of membrane proteins in rat cerebellum, spinal cord, and sciatic nerve

Journal of Proteome Research

Volumn 8, Issue 5, 2009, Pages 2418-2425

  Lu, Aiping ^a   Wiśniewski, Jacek R ^a   Mann, Matthias ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

Cerebellum; Ion channels; Neurotransmitter receptor; Proteomics; Sciatic nerve; Spinal cord

Indexed keywords

ABC TRANSPORTER; ION CHANNEL; MEMBRANE PROTEIN; NEUROTRANSMITTER RECEPTOR;

ANIMAL TISSUE; ARTICLE; CEREBELLUM; GEL PERMEATION CHROMATOGRAPHY; GENE IDENTIFICATION; LIQUID CHROMATOGRAPHY; MEMORY; NEUROTRANSMISSION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEOMICS; RAT; SCIATIC NERVE; SPINAL CORD;

ANIMALS; CEREBELLUM; CHROMATOGRAPHY, LIQUID; ION CHANNELS; MEMBRANE PROTEINS; PROTEOMICS; RATS; RECEPTORS, NEUROTRANSMITTER; SCIATIC NERVE; SPINAL CORD; TANDEM MASS SPECTROMETRY;

MURINAE; RATTUS;

EID: 66749090994     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr8010364     Document Type: Article

References (34)

1. Vercauteren, F. G.; Bergeron, J. J.; Vandesande, F.; Arckens, L.; Quirion, R. Proteomic approaches in brain research and neurop- harmacology. Eur. J. Pharmacol . 2004, 500 (1-3), 385-98.
2. Grant, K. J.; Wu, C. C. Advances in neuromembrane proteomics: efforts towards a comprehensive analysis of membrane proteins in the brain. Briefings Funct. Genomics Proteomics 2007, 6 (1), 59-69.
3. Wu, C. C.; MacCoss, M. J.; Howell, K. E.; Yates, J. R., III. A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol . 2003, 21 (5), 532-8.
4. Nagaraj, N.; Lu, A.; Mann, M.; Wisniewski, J. R. Detergent-based but gel-free method allows identification of several hundred membrane proteins in single MS runs. J. Proteome Res . 2008.
5. Nielsen, P. A.; Olsen, J. V.; Podtelejnikov, A. V.; Andersen, J. R.; Mann, M.; Wissniewski, J. R. Proteomic mapping of brain plasma membrane proteins. Mol. Cell. Proteomics 2005, 4 (4), 402-8.
6. Schindler, J.; Lewandrowski, U.; Sickmann, A.; Friauf, E.; Nothwang, H. G. Proteomic analysis of brain plasma membranes isolated by affinity two-phase partitioning. Mol. Cell. Proteomics 2006, 5 (2), 390-400.
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 (10), 994-9.
8. Olsen, J. V.; Andersen, J. R.; Nielsen, P. A.; Nielsen, M. L.; Figeys, D.; Mann, M.; Wisniewski, J. R. HysTag-a novel proteomic quantification tool applied to differential display analysis of membrane proteins from distinct areas ofmouse brain. Mol. Cell. Proteomics 2004, 3 (1), 82-92.
9. Han, D. K.; Eng, J.; Zhou, H.; Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope- coded affinity tags and mass spectrometry. Nat. Biotechnol . 2001, 19 (10), 946-51.
10. Olsen, J. V.; Nielsen, P. A.; Andersen, J. R.; Mann, M.; Wissniewski, J. R. Quantitative proteomic profiling of membrane proteins from the mouse brain cortex, hippocampus, and cerebellum using the HysTag reagent: mapping of neurotransmitter receptors and ion channels. Brain Res . 2007, 1134 (1), 95-106.
11. Stewart, 1.1.; Zhao, L.; Le Bihan, T.; Larsen, B.; Scozzaro, S.; Figeys, D.; Mao, G. D.; Ornatsky, O.; Dharsee, M.; Orsi, C.; Ewing, R.; Goh, T. The reproducible acquisition of comparative liquid chroma- tography/tandem mass spectrometry data from complex biological samples. Rapid Commun. Mass Spectrom . 2004, 18 (15), 1697-710.
12. Bukhman, Y. V.; Dharsee, M.; Ewing, R.; Chu, P.; Topaloglou, T.; Le Bihan, T.; Goh, T.; Duewel, H.; Stewart, I. I.; Wisniewski, J. R.; Ng, N. F. Design and analysis of quantitative differential proteomics investigations using lc-ms technology. J. Bioinf. Comput. Biol . 2008, 6 (1), 107-23.
13. Kristensen, D. B.; Brond, J. C.; Nielsen, P. A.; Andersen, J. R.; Sorensen, O. T.; Jorgensen, V.; Budin, K.; Matthiesen, J.; Veno, P.; Jespersen, H. M.; Ahrens, C. H.; Schandorff, S.; Ruhoff, P. T.; Wisniewski, J. R.; Bennett, K. L.; Podtelejnikov, A. V. Experimental Peptide Identification Repository (EPIR): an integrated peptide- centric platform for validation and mining of tandem mass spectrometry data. Mol. Cell. Proteomics 2004, 3 (10), 1023-38.
14. Le Bihan, T.; Goh, T.; Stewart, I. I.; Salter, A. M.; Bukhman, Y. V.; Dharsee, M.; Ewing, R.; Wissniewski, J. R. Differential analysis of membrane proteins in mouse fore- and hindbrain using a label- free approach. J. Proteome Res . 2006, 5 (10), 2701-10.
15. Butt, R. H.; Pfeifer, T. A.; Delaney, A.; Grigliatti, T. A.; Tetzlaff, W. G.; Coorssen, J. R. Enabling coupled quantitative genomics and proteomics analyses from rat spinal cord samples. Mol. Cell. Proteomics 2007, 6 (9), 1574-88.
16. Dreger, M.; Mika, J.; Bieller, A.; Jahnel, R.; Gillen, C.; Schaefer, M. K.; Weihe, E.; Hucho, F. Analysis of the dorsal spinal cord synaptic architecture by combined proteome analysis and in situ hybridization. J. Proteome Res . 2005, 4 (2), 238-239.
17. Ekegren, T.; Hanrieder, J.; Aquilonius, S. M.; Bergquist, J. Focused proteomics in post-mortem human spinal cord. J. Proteome Res . 2006, 5 (9), 2364-71.
18. Kunz, S.; Tegeder, I.; Coste, O.; Marian, C.; Pfenninger, A.; Corvey, C.; Karas, M.; Geisslinger, G.; Niederberger, E. Comparative proteomic analysis of the rat spinal cord in inflammatory and neuropathic pain models. Neurosci. Lett . 2005, 381 (3), 289-93.
19. Yu, L. R.; Conrads, T. P.; Uo, T.; Kinoshita, Y.; Morrison, R. S.; Lucas, D. A.; Chan, K. C.; Blonder, J.; Issaq, H. J.; Veenstra, T. D. Global analysis of the cortical neuron proteome. Mol. Cell. Proteomics 2004, 3 (9), 896-907.
20. Wang, H.; Qian, W. J.; Chin, M. H.; Petyuk, V. A.; Barry, R. C.; Liu, T.; Gritsenko, M. A.; Mottaz, H. M.; Moore, R. J.; Camp, D. G., II.; Khan, A. H.; Smith, D. J.; Smith, R. D. Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment. J. Proteome Res . 2006, 5 (2), 361-9.
21. Jimenez, C. R.; Stam, F. J.; Li, K. W.; Gouwenberg, Y.; Hornshaw, M. P.; De Winter, F.; Verhaagen, J.; Smit, A. B. Proteomics of the injured rat sciatic nerve reveals protein expression dynamics during regeneration. Mol. Cell. Proteomics 2005, 4 (2), 120-32.
22. Rappsilber, J.; Ishihama, Y.; Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem . 2003, 75 (3), 663-70.
23. Olsen, J. V.; Mann, M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc. Natl. Acad. Sci. U.S.A . 2004, 101 (37), 13417-22.
24. Olsen, J. V.; de Godoy, L. M.; Li, G.; Macek, B.; Mortensen, P.; Pesch, R.; Makarov, A.; Lange, O.; Horning, S.; Mann, M. Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 2005, 4 (12), 2010-21.
25. Cox, J.; Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome- wide protein quantification. Nat. Biotechnol . 2008, 26 (12), 136772.
26. Zubarev, R.; Mann, M. On the proper use of mass accuracy in proteomics. Mol. Cell. Proteomics 2007, 6 (3), 377-81.
27. Dean, M.; Rzhetsky, A.; Allikmets, R. The human ATP-binding cassette (ABC) transporter superfamily. Genome Res . 2001, 11 (7), 1156-66.
28. Juliano, R. L.; Ling, V. A surface glycoprotein modulating drug permeability in Chinese hamster ovary cell mutants. Biochim. Biophys. Acta 1976, 455 (1), 152-62.
29. Deeley, R. G.; Westlake, C.; Cole, S. P. Transmembrane transport of endo- and xenobiotics by mammalian ATP-binding cassette multidrug resistance proteins. Physiol. Rev . 2006, 86 (3), 849-99.
30. Hediger, M. A.; Romero, M. F.; Peng, J. B.; Rolfs, A.; Takanaga, H.; Bruford, E. A. The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteinslntroduction. Pfleugers Arch . 2004, 447 (5), 465-8.
31. Drews, J. Drug discovery: a historical perspective. Science 2000, 287 (5460), 1960-4.
32. Wisniewski, J. R. Protocol to enrich and analyze plasma membrane proteins from frozen tissues. Methods Mol. Biol . 2008, 432, 175-83.
33. Cox, J.; Mann, M. Is proteomics the new genomics. Cell 2007, 130 (3), 395-8.
34. Kruger, M.; Moser, M.; Ussar, S.; Thievessen, I.; Luber, C. A.; Forner, F.; Schmidt, S.; Zanivan, S.; Fassler, R.; Mann, M. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 2008, 134 (2), 353-64.