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Comet specifications


Unique identifier OMICS_02399
Name Comet
Alternative name SEQUEST
Software type Package/Module, Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format mzXML,mzML,ms2
Output format out,SQT,pepXML
Operating system Unix/Linux, Windows
Programming languages C, C++
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Jimmy Eng <>

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Publications for Comet

Comet citations


Targeting G protein coupled receptor signaling at the G protein level with a selective nanobody inhibitor

PMCID: 5959942
PMID: 29777099
DOI: 10.1038/s41467-018-04432-0

[…] the amino acid sequence in successive instrument scans. data were analyzed by using all cid spectra collected in the experiment to search whole mouse uniprotkb databases with the search program sequest. search parameters for peptide identification were as follows: minimum precursor mass, 350 da; maximum precursor mass, 5000 da; maximum missed cleavage sites, 2 for trypsin and 6 […]


Rapid labelling and covalent inhibition of intracellular native proteins using ligand directed N acyl N alkyl sulfonamide

PMCID: 5951806
PMID: 29760386
DOI: 10.1038/s41467-018-04343-0

[…] their good fragmentation characteristics. ms/ms spectra were interpreted, and peak lists were generated by proteome discoverer (thermo fisher scientific). searches were performed using the sequest ht (thermo fisher scientific) against the latest uniprot database for whole human proteome (homo sapiens, 9606). the database was searched for tryptic-digested peptides with up to three […]


Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

PMCID: 5946477
PMID: 29747589
DOI: 10.1186/s12864-018-4730-x

[…] database of a. fumigatus af293 (; []) using mascot 2.4 (matrix science, uk), sequest ht and ms amanda including up to two missed tryptic cleavages, a precursor mass tolerance of 10 ppm, and a fragment mass tolerance of 0.02 da. dynamic modifications were oxidation of met […]


Exosome markers associated with immune activation and oxidative stress in HIV patients on antiretroviral therapy

PMCID: 5940833
PMID: 29740045
DOI: 10.1038/s41598-018-25515-4

[…] reverse-phase fractionation was done on a 25 cm c18 column and samples were run on ltq-orbitrap ion-trap mass spectrometer (thermofisher). database search was performed using the software program, sequest (thermofisher). common contaminants (keratin, bovine proteins, mouse/rabbit iggs) were omitted from downstream analysis. remaining proteins identified were compared against existing exosome […]


Phosphorylation of IRE1 at S729 regulates RIDD in B cells and antibody production after immunization

PMCID: 5940306
PMID: 29511123
DOI: 10.1083/jcb.201709137

[…] measured in positive ion mode in the survey scan (ms1), before selection of the top seven ion signals for tandem mass spectrometry. fragment ion mass spectra obtained from lc-ms/ms were submitted to sequest (thermo fisher scientific) and mascot software (matrix science) searches for entries of the appropriate species in the uniprot database. in addition to mass tolerances appropriate […]


Cigarette smoke and chewing tobacco alter expression of different sets of miRNAs in oral keratinocytes

PMCID: 5935709
PMID: 29728663
DOI: 10.1038/s41598-018-25498-2

[…] 25 minutes. the total run time was set to 120 min and acquisition was carried out., proteome discoverer (version software suite (thermo fisher scientific) was used for ms/ms searches using sequest and mascot (version 2.4.1; matrix 617 science) algorithms againt ncbi refseq human protein database (version 75 containing 36,709 protein sequences and known contaminants). the search […]

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Comet institution(s)
University of Washington Department of Genome Sciences, University of Washington, Seattle, WA, USA; Institute for Systems Biology, University of Washington, Seattle, WA, USA
Comet funding source(s)
Supported by NIH awards R01GM096306 (Noble) and P41GM103533 (Noble/MacCoss) and in part by the University of Washington's Proteomics Resource (UWPR95794).

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