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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

Additional information

Publications for Comet

Comet citations


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

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

[…] btain 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 for chymotryp […]


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

Nat Commun
PMCID: 5951806
PMID: 29760386
DOI: 10.1038/s41467-018-04343-0
call_split See protocol

[…] o 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 miscle […]


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

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

[…] tein 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 and i […]


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

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

[…] n. 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 da […]


Proteome wide analysis of Anopheles culicifacies mosquito midgut: new insights into the mechanism of refractoriness

BMC Genomics
PMCID: 5941458
PMID: 29739330
DOI: 10.1186/s12864-018-4729-3

[…] nalysis. iTRAQ labeling followed by LC/MS/MS has generated raw data from three fractions (250 mM, 350 mM and 450 mM SCX fraction) that were searched using Proteome Discoverer 1.4 and analyzed by both SEQUEST and MASCOT algorithm against UniProt/NCBInr mosquito database.Using iTRAQ ratio criteria, 48 proteins were found to be differentially expressed from the total 130 proteins identified across th […]


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 to the instr […]


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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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