Popitam statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Popitam

Tool usage distribution map

This map represents all the scientific publications referring to Popitam per scientific context
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Associated diseases


Popular tool citations

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Popitam specifications


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




No version available


  • person_outline David Goodlett
  • person_outline Patricia Hernandez

Publications for Popitam

Popitam citations


Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System

PMCID: 2932509
PMID: 20824104
DOI: 10.1128/mBio.00158-10
call_split See protocol

[…] bitrap 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. […]


Probing Native Protein Structures by Chemical Cross linking, Mass Spectrometry, and Bioinformatics*

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 to […]


Interactions between Casein Kinase Iε (CKIε) and Two Substrates from Disparate Signaling Pathways Reveal Mechanisms for Substrate Kinase Specificity

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

[…] olumns (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. […]


Computational Methods for Protein Identification from Mass Spectrometry Data

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

[…] s of 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 th […]


Calibrating E values for MS2 database search methods

Biol Direct
PMCID: 2206012
PMID: 17983478
DOI: 10.1186/1745-6150-2-26

[…] to the E-value reported by another []. Other methods – using correlation, posterior probabilities, score, or Z-score – include, but are not limited to, SEQUEST [], MS-Tag [], Scope [], CIDentify [], Popitam [], ProbID [], and PepSearch []. It is even harder to translate the statistical significance from any of these methods into other methods.Although evaluations of various search engines have be […]

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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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