PECAN (PEptide-Centric Analysis)

PECAN (PEptide-Centric Analysis) performs peptide detection directly from Data-Independent Acquisition (DIA) mass spectrometry data without spectral libraries to enable unbiased, reproducible peptide-centric measurement of complex protein mixtures.

Key Features:

• Library-Free Detection: Operates without spectral libraries, enabling peptide detection directly from DIA data.
• Product Ion Scoring: Reports evidence of peptide detection using product ion scoring to detect peptides including low-abundance analytes with poor precursor ion signals.
• Chromatographic Peak Picking Accuracy: Provides precise chromatographic peak picking to support accurate peptide identification and quantification.

Scientific Applications:

• Protein Mixture Analysis: Enables peptide-centric analysis of complex protein mixtures from DIA mass spectrometry data.
• Variant Detection: Can be used to detect known sequence variants from DIA data.
• Plasma Proteome Library Construction: Supports building plasma proteome libraries directly from DIA data.

Methodology:

PECAN takes a list of peptide sequences and queries each against DIA data in centroid mzML format, reports the best evidence of detection per peptide based on product ion scoring, and produces a PECAN report intended for integration with Percolator to separate correct from incorrect matches while controlling the false discovery rate (FDR).