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Popular tool citations

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Associated diseases

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Popitam specifications

Information


Unique identifier OMICS_27500
Name Popitam
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A MS/MS peak list.
Operating system Unix/Linux
Programming languages C++, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 4.0.9
Stability Stable
Maintained Yes

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Maintainers


  • person_outline David Goodlett <>
  • person_outline Patricia Hernandez <>

Publications for Popitam

Popitam in publications

 (4)
PMCID: 2932509
PMID: 20824104
DOI: 10.1128/mBio.00158-10

[…] analyzer. tandem mass spectra were deconvoluted and searched with phenyx () to identify and remove the spectra matching non-cross-linked, linear peptides. remaining spectra were searched using popitam () in an “open-search mode” to identify cross-linked peptides., models of the oligomeric forms of prgh, prgk, and invg were produced using the symmetrical assembly protocols () in the rosetta […]

PMCID: 2938055
PMID: 20360032
DOI: 10.1074/mcp.R000001-MCP201

[…] another strategy that, up to now, has only been used with restricted databases is implemented in the tools batch-tag, ms-bridge, and ms-product that are part of the protein prospector package () and popitam (cxms pipeline) (). both are based on the rationale that cross-linked peptides may be considered as a single linear tryptic peptide with a large variable mass modification that corresponds […]

PMCID: 2651596
PMID: 19274088
DOI: 10.1371/journal.pone.0004766

[…] (the net group, inc) and infused into a hybrid-ltq-orbitrap mass spectrometer via electrospray ionization (esi). crosslinked peptides were identified by using the open modification search tool popitam . post-translational modifications that corresponded to peptides were searched to identify intramolecular crosslinks., we thank david virshup for suggesting the investigation of period, […]

PMCID: 2323404
PMID: 18463710
DOI: 10.1371/journal.pcbi.0040012

[…] the distribution. using these curves, probabilities for correct and incorrect identifications can then be generated for any new candidate identifications returned by sequest., a competing package, popitam, was released in 2003 and uses a novel parsing of the ms/ms spectrum for matching against a database, followed by correlation scoring. this package has been specifically designed to address […]


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Popitam institution(s)
Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA; Department of Molecular and Cellular Biology, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA; Swiss Institute of Bioinformatics, Geneva, Switzerland; Department of Computer Science, University of Geneva, Geneva, Switzerland
Popitam funding source(s)
Supported by the National Institute of Allergy and Infectious Diseases (NIAID 1U54 AI57141-01) and the National Cancer Institute (R33CA099139-01).

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