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Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries
Institution:1. Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA;2. Proteome Software, Inc. Portland, Oregon, USA;3. Department of Genome Sciences, University of Washington, Seattle, Washington, USA;4. Institute for Systems Biology, Seattle, Washington, USA
Abstract:
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  • Highlights
    • •Rapid DIA-only library building with gas-phase fractionation.
    • •Recommended DIA acquisition strategies with staggered windows and forbidden zones.
    • •Optimized DIA instrument settings for several Thermo Orbitrap instruments.
    • •Data analysis tutorial using open source DIA software.
    Keywords:Data evaluation  label-free quantification  mass spectrometry  protein identification  quantification  data independent acquisition  DIA
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