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Comprehensive peptide quantification for data independent acquisition mass spectrometry using chromatogram libraries

View ORCID ProfileBrian C. Searle, Lindsay K. Pino, Jarrett D. Egertson, Ying S. Ting, Robert T. Lawrence, View ORCID ProfileJudit Villén, View ORCID ProfileMichael J. MacCoss
doi: https://doi.org/10.1101/277822
Brian C. Searle
1Department of Genome Sciences, University of Washington, Seattle, WA, USA
2Proteome Software, Portland, OR, USA
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Lindsay K. Pino
1Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Jarrett D. Egertson
1Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Ying S. Ting
1Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Robert T. Lawrence
1Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Judit Villén
1Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Michael J. MacCoss
1Department of Genome Sciences, University of Washington, Seattle, WA, USA
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  • For correspondence: maccoss@uw.edu
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ABSTRACT

Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. We introduce a new experimental workflow that uses this technique to construct chromatogram libraries that capture fragment ion chromatographic peak shape and retention time for every detectable peptide in an experiment. These coordinates calibrate information in spectrum libraries or protein databases to a specific mass spectrometer and chromatography setup, and enable sensitive peptide detection in quantitative experiments. We also present EncyclopeDIA, a software tool for generating and searching chromatogram libraries, and demonstrate the performance of our workflow by quantifying proteins in human and yeast cells. We find that by exploiting calibrated retention time and fragmentation specificity in chromatogram libraries, EncyclopeDIA can detect and quantify >50% more peptides from DIA experiments than with DDA-based spectrum libraries alone.

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Posted March 07, 2018.
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Comprehensive peptide quantification for data independent acquisition mass spectrometry using chromatogram libraries
Brian C. Searle, Lindsay K. Pino, Jarrett D. Egertson, Ying S. Ting, Robert T. Lawrence, Judit Villén, Michael J. MacCoss
bioRxiv 277822; doi: https://doi.org/10.1101/277822
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Comprehensive peptide quantification for data independent acquisition mass spectrometry using chromatogram libraries
Brian C. Searle, Lindsay K. Pino, Jarrett D. Egertson, Ying S. Ting, Robert T. Lawrence, Judit Villén, Michael J. MacCoss
bioRxiv 277822; doi: https://doi.org/10.1101/277822

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