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PeptidePicker specifications


Unique identifier OMICS_13604
Name PeptidePicker
Interface Application programming interface
Restrictions to use None
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus


  • person_outline Christoph Borchers

Publication for PeptidePicker

PeptidePicker citations


A Multiplexed Cytokeratin Analysis Using Targeted Mass Spectrometry Reveals Specific Profiles in Cancer Related Pleural Effusions12

PMCID: 4954941
PMID: 27435923
DOI: 10.1016/j.neo.2016.06.002
call_split See protocol

[…] Peptide selection for MRM analysis was performed according to the criteria described previously by manual selection and the aid of the PeptidePicker software . In brief, chosen proteotypic peptides met the following conditions: sequence uniqueness in the human proteome; numerous observations in spectral libraries; length not exceedin […]


Exploring the potential of public proteomics data

PMCID: 4738454
PMID: 26449181
DOI: 10.1002/pmic.201500295

[…] pecific proteins in a given instrumental setup can be found. Note that it is also possible to develop tools to look for novel transitions in publicly available shotgun datasets. For example, MRMaid , PeptidePicker , , and ProteomicsDB do this by reusing identification data coming from PRIDE and other sources.One particular type of data reuse, already popular in other disciplines, is to analyze da […]


An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64

PMCID: 4655102
PMID: 26618079
DOI: 10.7717/peerj.1401

[…] was found, which are highly indicative for the protein B6T173. Since the protein is related to post-harvest insect resistance, those peptide MS transitions could serve for the screening of seeds. The PeptidePicker workflow delivers theoretical peptides for targeted proteomics (). However, if experimental data are available, the Association Analysis includes all possible variables which affect the […]


PeptideManager: a peptide selection tool for targeted proteomic studies involving mixed samples from different species

Front Genet
PMCID: 4151198
PMID: 25228907
DOI: 10.3389/fgene.2014.00305

[…] ll as the number of allowed miscleavages (0–2) can be selected. Once created, the database is indexed in PeptideManager and is immediately available for search requests.Contrary to similar tools like PeptidePicker (Mohammed et al., ), CONSeQuence (Eyers et al., ) or even Skyline (Maclean et al., ), PeptideManager is solely intended to build a peptide database, to allow search queries within these […]


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PeptidePicker institution(s)
University of Victoria — Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, Canada; Center for Proteomics and Metabolomics, Leiden University Medical Center, Netherlands; Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC, Canada
PeptidePicker funding source(s)
This work was supported by the Genome Canada and Genome British Columbia, the UVic-Genome British Columbia Proteomics Centre and the Dutch Organization for Scientific Research (Nederlandse Organisatie voor Wetenschappelijk Onderzoek, NWO) grants Q16 NRG-2010.06 and VI-917.11.398.

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