This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Aebersold, R. & Mann, M. Nature 422, 198–207 (2003).
Domon, B. & Aebersold, R. Nat. Biotechnol. 28, 710–721 (2010).
Purvine, S., Eppel, J.-T.T., Yi, E.C. & Goodlett, D.R. Proteomics 3, 847–850 (2003).
Venable, J.D., Dong, M.-Q., Wohlschlegel, J., Dillin, A. & Yates, J.R. Nat. Methods 1, 39–45 (2004).
Plumb, R.S. et al. Rapid Commun. Mass Spectrom. 20, 1989–1994 (2006).
Panchaud, A. et al. Anal. Chem. 81, 6481–6488 (2009).
Panchaud, A., Jung, S., Shaffer, S.A., Aitchison, J.D. & Goodlett, D.R. Anal. Chem. 83, 2250–2257 (2011).
Bern, M. et al. Anal. Chem. 82, 833–841 (2010).
Wong, J., Schwahn, A. & Downard, K. BMC Bioinformatics 10, 244 (2009).
Carvalho, P.C. et al. Bioinformatics 26, 847–848 (2010).
Geromanos, S.J. et al. Proteomics 9, 1683–1695 (2009).
Li, G.-Z. et al. Proteomics 9, 1696–1719 (2009).
Blackburn, K., Mbeunkui, F., Mitra, S.K., Mentzel, T. & Goshe, M.B. J. Proteome Res. 9, 3621–3637 (2010).
Huang, X. et al. Anal. Chem. 83, 6971–6979 (2011).
Geiger, T., Cox, J. & Mann, M. Mol. Cell. Proteomics 9, 2252–2261 (2010).
Gillet, L.C. et al. Mol. Cell. Proteomics 11, O111.016717 (2012).
Lange, V., Picotti, P., Domon, B. & Aebersold, R. Mol. Syst. Biol. 4, 222 (2008).
Domon, B. & Aebersold, R. Science 312, 212–217 (2006).
Sherman, J., McKay, M.J., Ashman, K. & Molloy, M.P. Mol. Cell. Proteomics 8, 2051–2062 (2009).
Röst, H., Malmström, L. & Aebersold, R. Mol. Cell. Proteomics 11, 540–549 (2012).
Michalski, A., Cox, J. & Mann, M. J. Proteome Res. 10, 1785–1793 (2011).
Picotti, P., Bodenmiller, B., Mueller, L.N., Domon, B. & Aebersold, R. Cell 138, 795–806 (2009).
MacLean, B. et al. Bioinformatics 26, 966–968 (2010).
Ince, D.C., Hatton, L. & Graham-Cumming, J. Nature 482, 485–488 (2012).
Martens, L. et al. Mol. Cell. Proteomics 10, R110.000133 (2010).
Deutsch, E.W. Mol. Cell. Proteomics 11, 1612–1621 (2012).
Escher, C. et al. Proteomics 12, 1111–1121 (2012).
Reiter, L. et al. Nat. Methods 8, 430–435 (2011).
Malmström, L., Malmström, J., Selevsek, N., Rosenberger, G. & Aebersold, R. J. Proteome Res. 11, 1644–1653 (2012).
Wenschuh, H. et al. Biopolymers 55, 188–206 (2000).
Hilpert, K., Winkler, D.F. & Hancock, R.E. Nat. Protoc. 2, 1333–1349 (2007).
Elias, J.E. & Gygi, S.P. Nat. Methods 4, 207–214 (2007).
Malmström, J. et al. J. Biol. Chem. 287, 1415–1425 (2012).
Deutsch, E.W., Lam, H. & Aebersold, R. EMBO Rep. 9, 429–434 (2008).
Shea, P.R. et al. Proc. Natl. Acad. Sci. USA 108, 5039–5044 (2011).
Malke, H., Steiner, K., McShan, W.M. & Ferretti, J.J. Int. J. Med. Microbiol. 296, 259–275 (2006).
Sturm, M. et al. BMC Bioinformatics 9, 163 (2008).
Acknowledgements
H.L.R. was funded by ETH (ETH-30 11-2), G.R. and S.M.M. were funded by the Swiss Federal Commission for Technology and Innovation CTI (13539.1 PFFLI-LS), P.N., L.G. and R.A. were funded by the advanced European Research Council grant Proteomics v3.0 (233226), L.G. and R.A. were funded by PhosphonetX project of SystemsX.ch, J.M. was funded by the Swedish Research Council (project 2008-3356), the Crafoord Foundation (20100892) and the Swedish Foundation for Strategic Research (FFL4). Further funding was provided to R.A. by the Swiss National Science Foundation. We would like to thank the SyBIT project of SystemsX.ch for support and maintenance of the lab-internal computing infrastructure, the ITS HPC team (Brutus) and the OpenMS developers for including OpenSWATH in the OpenMS framework and fixing MS Windows compatibility bugs.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
J.M. is co-founder and board member of Biognosys AG. J.M. and R.A. hold shares of Biognosys AG, which operates in the field covered by the article. The research group of R.A. is supported by AB SCIEX by providing access to prototype instrumentation.
Supplementary information
Supplementary Text and Figures
Supplementary Notes (PDF 11676 kb)
Source data
Rights and permissions
About this article
Cite this article
Röst, H., Rosenberger, G., Navarro, P. et al. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol 32, 219–223 (2014). https://doi.org/10.1038/nbt.2841
Published:
Issue Date:
DOI: https://doi.org/10.1038/nbt.2841