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Nat Methods. 2017 Sep;14(9):903-908. doi: 10.1038/nmeth.4390. Epub 2017 Aug 7.

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
2
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
3
Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA.

Abstract

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 PECAN (http://pecan.maccosslab.org), a library-free, peptide-centric tool that robustly and accurately detects peptides directly from DIA data. PECAN 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 PECAN, and we further validate its detection with data-dependent acquisition and targeted analyses. Lastly, we used PECAN to build a plasma proteome library from DIA data and to query known sequence variants.

PMID:
28783153
PMCID:
PMC5578911
DOI:
10.1038/nmeth.4390
[Indexed for MEDLINE]
Free PMC Article

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