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PECAN specifications


Unique identifier OMICS_20530
Alternative name PEptide-Centric Analysis
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Centroided DIA data, a list of query (target) peptides, and a background proteome database (typically a species protein sequence database).
Output data Auxiliary scores describing the assigned evidence of detection with an associated retention time for every target peptide and PECAN-generated decoy peptide.
Operating system Unix/Linux
Programming languages Python
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
pymzml, numpy, percolator
Maintained Yes




No version available


  • person_outline Michael J. MacCoss

Publication for PEptide-Centric Analysis

PECAN citations


Statistical control of peptide and protein error rates in large scale targeted DIA analyses

Nat Methods
PMCID: 5581544
PMID: 28825704
DOI: 10.1038/nmeth.4398

[…] o tens of thousands per sample), the presence and quantity of which need to be established and compared over many samples. This presents challenges for peptide and protein-level error rate control in peptide-centric analysis of DIA data, particularly in cases in which comprehensive spectral libraries, i.e. covering a substantial fraction of the proteome–, are being used. Such analyses conduct 10,0 […]


Proteoform Profile Mapping of the Human Serum Complement Component C9 Revealing Unexpected New Features of N , O , and C Glycosylation

Anal Chem
PMCID: 5362742
PMID: 28221766
DOI: 10.1021/acs.analchem.6b04527

[…] 92). Using this method, 15 C9 proteoforms could be validated (Table S2). The unmatched peaks mostly correspond to C9 proteoforms containing two Ca2+ ions and species that were not detected during the peptide centric analysis. For example, the peak at m/z 4479.08 most likely corresponds to the C9 proteoform containing two O-glycans with one and two sialic acids on the core HexNAc1Hex1. Since a pept […]


“Plug and play” investigation of the human phosphoproteome by targeted high resolution mass spectrometry

Nat Methods
PMCID: 5915315
PMID: 27018578
DOI: 10.1038/nmeth.3811
call_split See protocol

[…] um-centric analysis of DIA and PRM mass spectrometry results, we used DIA-Umpire version 1.4 with default parameters to assemble pseudo-MS/MS spectra for the database search pipeline described above. Peptide-centric analysis was performed using Skyline. Signal extraction was performed on +2, +3, +4 precursors and +1, +2 b and y fragment ions. Full MS resolving power was set to 70,000, and MS/MS re […]

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PECAN institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
PECAN funding source(s)
Supported by the National Institutes of Health Grants P30 AG013280, R21 CA192983, P41 GM103533, and U54 HG008097, the US Department of Energy, Office of Science, Office of Biological and Environmental Research, and Early Career Research Program.

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