Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips (original) (raw)

References

  1. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).
    Article CAS Google Scholar
  2. Mann, M. Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol. 7, 952–958 (2006).
    Article CAS Google Scholar
  3. Wilm, M. & Mann, M. Analytical properties of the nanoelectrospray ion source. Anal. Chem. 68, 1–8 (1996).
    Article CAS Google Scholar
  4. Kussmann, M., Lassing, U., Sturmer, C.A., Przybylski, M. & Roepstorff, P. Matrix-assisted laser desorption/ionization mass spectrometric peptide mapping of the neural cell adhesion protein neurolin purified by sodium dodecyl sulfate polyacrylamide gel electrophoresis or acidic precipitation. J. Mass Spectrom. 32, 483–493 (1997).
    Article CAS Google Scholar
  5. Erdjument-Bromage, H. et al. Examination of micro-tip reversed-phase liquid chromatographic extraction of peptide pools for mass spectrometric analysis. J. Chromatogr. A 826, 167–181 (1998).
    Article CAS Google Scholar
  6. Gobom, J., Nordhoff, E., Mirgorodskaya, E., Ekman, R. & Roepstorff, P. Sample purification and preparation technique based on nano-scale reversed-phase columns for the sensitive analysis of complex peptide mixtures by matrix-assisted laser desorption/ionization mass spectrometry. J. Mass Spectrom. 34, 105–116 (1999).
    Article CAS Google Scholar
  7. 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. 75, 663–670 (2003).
    Article CAS Google Scholar
  8. Stewart, I.I., Thomson, T. & Figeys, D. 18O labeling: a tool for proteomics. Rapid Commun. Mass Spectrom. 15, 2456–2465 (2001).
    Article CAS Google Scholar
  9. Larsen, M.R., Cordwell, S.J. & Roepstorff, P. Graphite powder as an alternative or supplement to reversed-phase material for desalting and concentration of peptide mixtures prior to matrix-assisted laser desorption/ionization-mass spectrometry. Proteomics 2, 1277–1287 (2002).
    Article CAS Google Scholar
  10. Callesen, A.K. et al. Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 19, 1578–1586 (2005).
    Article CAS Google Scholar
  11. Ishihama, Y., Rappsilber, J. & Mann, M. Modular stop and go extraction tips with stacked disks for parallel and multidimensional peptide fractionation in proteomics. J. Proteome Res. 5, 988–994 (2006).
    Article CAS Google Scholar
  12. Ishihama, Y. et al. Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat. Biotechnol. 23, 617–621 (2005).
    Article CAS Google Scholar
  13. Saito, H., Oda, Y., Sato, T., Kuromitsu, J. & Ishihama, Y. Multiplexed two-dimensional liquid chromatography for MALDI and nanoelectrospray ionization mass spectrometry in proteomics. J. Proteome Res. 5, 1803–1807 (2006).
    Article CAS Google Scholar
  14. Kokubu, M., Ishihama, Y., Sato, T., Nagasu, T. & Oda, Y. Specificity of immobilized metal affinity-based IMAC/C18 tip enrichment of phosphopeptides for protein phosphorylation analysis. Anal. Chem. 77, 5144–5154 (2005).
    Article CAS Google Scholar
  15. Larsen, M.R., Thingholm, T.E., Jensen, O.N., Roepstorff, P. & Jorgensen, T.J. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell. Proteomics 4, 873–886 (2005).
    Article CAS Google Scholar
  16. Sugiyama,, N., Masuda, T. & Shinoda, K. et al. Mol. Cell. Proteomics online Feb 23 (2007).
  17. Olsen, J.V. et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635–648 (2006).
    Article CAS Google Scholar
  18. Villen, J., Beausoleil, S.A., Gerber, S.A. & Gygi, S.P. Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. USA 104, 1488–1493 (2007).
    Article CAS Google Scholar
  19. Bodenmiller, B., Mueller, L.N., Mueller, M., Domon, B. & Aebersold, R. Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat. Methods 4, 231–237 (2007).
    Article CAS Google Scholar
  20. Ishihama, Y. & Usui, T. USA Patent No. US2006048367 (2006).

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