Journal
NATURE METHODS
Volume 14, Issue 9, Pages 903-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/NMETH.4390
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Funding
- National Institutes of Health [P30 AG013280, R21 CA192983, P41 GM103533, U54 HG008097]
- US Department of Energy, Office of Science, Office of Biological and Environmental Research, and Early Career Research Program
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Data-independent acquisition (DIA) is an emerging mass spectrometry (MS)-based technique for unbiased and reproducible measurement of protein mixtures. DIA tandem mass spectrometry spectra are often highly multiplexed, containing product ions from multiple cofragmenting precursors. Detecting peptides directly from DIA data is therefore challenging; most DIA data analyses require spectral libraries. Here we present PECECAN (http://pecan.maccosslab.org), a library-free, peptide-centric tool that robustly and accurately detects peptides directly from DIA data. PECECAN reports evidence of detection based on product ion scoring, which enables detection of low-abundance analytes with poor precursor ion signal. We demonstrate the chromatographic peak picking accuracy and peptide detection capability of PECECAN, and we further validate its detection with data-dependent acquisition and targeted analyses. Lastly, we used PECECAN to build a plasma proteome library from DIA data and to query known sequence variants.
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