Kojak protocols

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Kojak specifications

Information


Unique identifier OMICS_08032
Name Kojak
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
License Apache License version 2.0
Computer skills Advanced
Version 1.4.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Robert L. Moritz <>

Publication for Kojak

Kojak in pipeline

2017
PMCID: 5354518
PMID: 28191870
DOI: 10.7554/eLife.21069.038

[…] into mzml using msconvert from proteowizard (). standard linear peptide searches were performed using comet to identify all proteins in the sample (). cross-linked peptides were identified using the kojak version 1.4.2 cross-link identification software () following the author’s instructions (http://www.kojak-ms.org). kojak results were exported to percolator version 2.08 () to produce […]


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Kojak in publications

 (7)
PMCID: 5501500
PMID: 28695211
DOI: 10.1126/sciadv.1700479

[…] for ms/ms, the collision energy was set to 35%. data were analyzed using the dxmsms match program from our icc-class (isotopically coded cleavable cross-linking analysis software suite), or with kojak (). for scoring and assignment of the ms/ms spectra, b and y ions were primarily used, with additional confirmation from collision-induced dissociation cleavage of the cross-linker, whenever […]

PMCID: 5354518
PMID: 28191870
DOI: 10.7554/eLife.21069.038

[…] into mzml using msconvert from proteowizard (). standard linear peptide searches were performed using comet to identify all proteins in the sample (). cross-linked peptides were identified using the kojak version 1.4.2 cross-link identification software () following the author’s instructions (http://www.kojak-ms.org). kojak results were exported to percolator version 2.08 () to produce […]

PMCID: 5047652
PMID: 27454319
DOI: 10.1021/acs.analchem.6b02082

[…] spectra have to be matched with peptide sequences by database search. for this purpose, a number of tools have been developed,, for example, plink, protein prospector,, stavrox, xquest, kojak, xi,, or even search engines based on linear peptide identification search paradigms such as mascot. one of the challenges in identifying cross-linked peptides is the unequal fragmentation […]

PMCID: 5127641
PMID: 27805565
DOI: 10.7554/eLife.20352.031

[…] with shaking. digested samples were acidified with 5m hcl prior to being stored at −80°c until analysis. ms analysis was performed on a q-exactive (thermo fisher scientific) and analyzed using the kojak (version 1.4.2) cross-link identification software as previously described (; )., retroviral expression constructs in the pmig vector (murine stem cell virus-ires-gfp) expressing […]

PMCID: 4660060
PMID: 26560693
DOI: 10.1038/ncomms9673

[…] other methods (). our method also has key advantages: it performs well without isotopic labelling, post cross-linking fractionation or enrichment of cross-linked peptides. data analysis using our kojak cross-link identification algorithm is simple, fully automated and faster than existing methods., our cross-linking analysis of free dam1 complex in the absence of mts identified 678 udrs at 1% […]


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Kojak institution(s)
Institute for Systems Biology, Seattle, WA, USA
Kojak funding source(s)
This work was partially supported with federal funds from the National Science Foundation MRI grant no. 0923536 and from the National Institutes of Health National Institute of General Medical Sciences under grant nos. 2P50 GM076547/Center for Systems Biology, GM087221, S10RR027584, and P41 GM103533.

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