In mass spectrometry–based proteomics, data-independent acquisition (DIA) strategies can acquire a single data set useful for both identification and quantification of detectable peptides in a complex mixture. However, DIA data are noisy owing to a typical five- to tenfold reduction in precursor selectivity compared to data obtained with data-dependent acquisition or selected reaction monitoring. We demonstrate a multiplexing strategy, MSX, for DIA analysis that increases precursor selectivity fivefold.
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Stahl, D.C., Swiderek, K.M., Davis, M.T. & Lee, T.D. J. Am. Soc. Mass Spectrom. 7, 532–540 (1996).
Liu, H., Sadygov, R.G. & Yates, J.R. Anal. Chem. 76, 4193–4201 (2004).
Michalski, A., Cox, J. & Mann, M. J. Proteome Res. 10, 1785–1793 (2011).
Wenner, B.R. & Lynn, B.C. J. Am. Soc. Mass Spectrom. 15, 150–157 (2004).
Hoopmann, M.R., Finney, G.L. & MacCoss, M.J. Anal. Chem. 79, 5620–5632 (2007).
Purvine, S., Eppel, J.T., Yi, E.C. & Goodlett, D.R. Proteomics 3, 847–850 (2003).
Myung, S. et al. Anal. Chem. 75, 5137–5145 (2003).
Venable, J.D., Dong, M.Q., Wohlschlegel, J., Dillin, A. & Yates, J.R. Nat. Methods 1, 39–45 (2004).
Panchaud, A. et al. Anal. Chem. 81, 6481–6488 (2009).
Weisbrod, C.R., Eng, J.K., Hoopmann, M.R., Baker, T. & Bruce, J.E. J. Proteome Res. 11, 1621–1632 (2012).
Gillet, L.C. et al. Mol. Cell Proteomics 11, O111.016717 (2012).
Williams, E.R., Loh, S.Y., McLafferty, F.W. & Cody, R.B. Anal. Chem. 62, 698–703 (1990).
MacLean, B. et al. Bioinformatics 26, 966–968 (2010).
US National Institute of Standards and Technology. NIST Peptide Tandem Mass Spectral Libraries (eds. Stein, S.E. & Rudnick, P.A.) 〈http://peptide.nist.gov/〉 (2009; 24 May 2011 builds).
Yost, R.A. & Enke, C.G. Anal. Chem. 51, 1251–1264 (1979).
Frahm, J.L., Howard, B.E., Heber, S. & Muddiman, D.C. J. Mass Spectrom. 41, 281–288 (2006).
Gay, S., Binz, P.A., Hochstrasser, D.F. & Appel, R.D. Electrophoresis 20, 3527–3534 (1999).
Frewen, B.E., Merrihew, G.E., Wu, C.C., Noble, W.S. & MacCoss, M.J. Anal. Chem. 78, 5678–5684 (2006).
Lawson, C.L. & Hanson, R.J. Solving Least Squares Problems (Society for Industrial and Applied Mathematics, Philadelphia, 1995).
Chambers, M.C. et al. Nat. Biotechnol. 30, 918–920 (2012).
The authors acknowledge financial support from US National Institutes of Health grants R01 GM103551, P41 GM103533 and F31 AG037265.
All authors received financial support from Thermo Fisher Scientific. A.K., J.D.C., M.K. and V.Z. are employees of Thermo Fisher Scientific, the company that markets and sells the mass spectrometry instrumentation used in this manuscript. Thermo Fisher will make the methods described herein available to their customers in version 2.2 SP1 of the Q-Exactive software.
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Egertson, J., Kuehn, A., Merrihew, G. et al. Multiplexed MS/MS for improved data-independent acquisition. Nat Methods 10, 744–746 (2013). https://doi.org/10.1038/nmeth.2528
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