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MaxQuant.Live enables global targeting of more than 25,000 peptides

View ORCID ProfileChristoph Wichmann, View ORCID ProfileFlorian Meier, View ORCID ProfileSebastian Virreira Winter, Andreas-David Brunner, Jürgen Cox, Matthias Mann
doi: https://doi.org/10.1101/443838
Christoph Wichmann
Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany
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Florian Meier
Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, GermanyNovo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Sebastian Virreira Winter
Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
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Andreas-David Brunner
Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
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Jürgen Cox
Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany
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Matthias Mann
Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, GermanyNovo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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ABSTRACT

Mass spectrometry (MS)-based proteomics is often performed in a shotgun format, in which as many peptide precursors as possible are selected from full or MS1 scans so that their fragment spectra can be recorded in MS2 scans. While achieving great proteome depths, shotgun proteomics cannot guarantee that each precursor will be fragmented in each run. In contrast, targeted proteomics aims to reproducibly and sensitively record a restricted number of precursor/fragment combinations in each run, based on pre-scheduled mass-to-charge and retention time windows. Here we set out to merge these two concepts by a global targeting approach in which an arbitrary number of precursors of interest are detected in real-time, followed by standard fragmentation or advanced peptide-specific analyses. We made use of a fast application programming interface to a quadrupole Orbitrap instrument and real-time recalibration in mass, retention time and intensity dimensions to predict precursor identity. MaxQuant.Live is freely available (www.maxquant.live) and has a graphical user interface to specify many pre-defined data acquisition strategies. Acquisition speed is as fast as with the vendor software and the power of our approach is demonstrated with the acquisition of breakdown curves for hundreds of precursors of interest. We also uncover precursors that are not even visible in MS1 scans, using elution time prediction based on the auto-adjusted retention time alone. Finally, we successfully recognized and targeted more than 25,000 peptides in single LC-MS runs. Global targeting combines the advantages of two classical approaches in MS-based proteomics, while greatly expanding the analytical toolbox.

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Posted October 15, 2018.
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MaxQuant.Live enables global targeting of more than 25,000 peptides
Christoph Wichmann, Florian Meier, Sebastian Virreira Winter, Andreas-David Brunner, Jürgen Cox, Matthias Mann
bioRxiv 443838; doi: https://doi.org/10.1101/443838
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MaxQuant.Live enables global targeting of more than 25,000 peptides
Christoph Wichmann, Florian Meier, Sebastian Virreira Winter, Andreas-David Brunner, Jürgen Cox, Matthias Mann
bioRxiv 443838; doi: https://doi.org/10.1101/443838

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