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

Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).

Mann, M. Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol. 7, 952–958 (2006).

Wilm, M. & Mann, M. Analytical properties of the nanoelectrospray ion source. Anal. Chem. 68, 1–8 (1996).

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).

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).

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).

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).

Stewart, I.I., Thomson, T. & Figeys, D. 18O labeling: a tool for proteomics. Rapid Commun. Mass Spectrom. 15, 2456–2465 (2001).

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).

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).

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).

Ishihama, Y. et al. Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat. Biotechnol. 23, 617–621 (2005).

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).

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).

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).

Sugiyama,, N., Masuda, T. & Shinoda, K. et al. Mol. Cell. Proteomics online Feb 23 (2007).

Olsen, J.V. et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635–648 (2006).

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).

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).

Ishihama, Y. & Usui, T. USA Patent No. US2006048367 (2006).