Comet protocols

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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



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  • person_outline Jimmy Eng <>

Additional information

Publications for Comet

Comet in pipelines

PMCID: 5765118
PMID: 29323256
DOI: 10.1038/s41598-017-18985-5

[…] 2.5 s. dynamic exclusion was used with 60 s duration. precursors with unassigned charge state or charge state 1 were excluded. an underfill ratio of 1% was used., the ms raw files were searched using sequest and the output was further refined by percolator on the software platform proteome discoverer 1.4 (thermo) against the human uniprot database (90440 entries, including 23204 isoforms) and filt […]

PMCID: 5774092
PMID: 29347954
DOI: 10.1186/s13071-018-2618-x

[…] file ). the sequences were split when the program detected stop codons (*), undefined amino acids (x) or gaps (-). the search of ms/ms raw files against these databases was conducted using the sequest algorithm (proteome discoverer 1.3; thermo scientific) with the constraints previously described []. for peptide validation, the proteome discoverer 1.3 software was used by filtering based […]

PMCID: 5775567
PMID: 29351798
DOI: 10.1186/s12967-018-1388-8

[…] usa). for database searching, ms/ms spectra were analyzed using the mascot algorithm (version 2.3.0, matrix science, boston, ma, usa) against the uniprot human sequence database searched with sequest engine against using the following parameters: full trypsin digest with maximum 1 missed cleavages, fixed modification carbamidomethylation of cysteine (+ 57.021 da), variable modification […]

PMCID: 5826277
PMID: 29515544
DOI: 10.3389/fmicb.2018.00262

[…] during 30 s after selection for ms/ms was enabled to allow for detection of as many precursors as possible., raw data from the ms analysis was searched against ncbi s. aureus mssa476 using the sequest algorithm in proteome discoverer version 2.1 (). data were filtered to a 1% peptide and protein level false positive rate using a reverse database approach (). the area under the curve […]

PMCID: 5826526
PMID: 29481576
DOI: 10.1371/journal.pone.0193104

[…] database (75568 sequences, and 32232886 residues). the reviewed protein sequences of mouse were downloaded from uniprot protein database ( january 15, 2016. the considerations in sequest searches for normal peptides were used carbamidomethylation of cysteine as static modification and oxidation of methionine as a dynamic modification. trypsin was indicated as the proteolytic […]

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Comet in publications

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 […]

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 […]

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 […]

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 […]

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 […]

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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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