SEQUEST pipeline

SEQUEST specifications


Unique identifier OMICS_02399
Alternative name Comet
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
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

A new version of SEQUEST called "Comet" is available on:

Publications for SEQUEST

SEQUEST citations

PMCID: 5955148

[…] ions for 3 seconds following each ms1 scan (15k resolution; agc target=5e4; relative ce ∼32%). proteins were identified by searching the data against mus musculus (swissprot, v2016-04-13) using sequest-ht (proteome discoverer v2.1, thermo scientific). search parameters included ms1 mass tolerance of 10 ppm and fragment tolerance of 0.05 da; two missed cleavages were allowed; […]

PMCID: 5826526

[…] the proteolytic enzyme with two missed cleavages. peptide and fragment mass tolerance were set at ± 1.6 and 0.6 da and precursor mass range of 350–5000 da, and peptide charges were set excluding +1. sequest ht results were filtered with the percolator-based scoring to improve the sensitivity and accuracy of the peptide identification. using a decoy search strategy, target false discovery rates […]

PMCID: 5874627

[…] proteome extraction and analysis. details of the sample digestion, isobaric tag peptide labeling, and 2d-lc-ms/ms analyses are provided in the supplemental methods. ms/ms data were searched using sequest software [42] against a peptide database constructed from a series of dmc isolate genomes and metagenomic datasets and other known rdase sequences, using relatively conservative filters […]

PMCID: 5884642

[…] ms ms1 max inject time, 1e5 agc ms2, 100 ms ms2 max inject time, 20 loop count, 1.8 m/z isolation window, 45 s dynamic exclusion. spectra were searched against the uniprot/swiss-prot database with sequest ht on proteome discoverer software (figures 1 and 2) or maxquant (figure 4). only peptides with medium or greater confidence (5% fdr) were considered for quantitation, and only kinases […]

PMCID: 5735884

[…] dissociation was used to fragment ten most intense multiply charged ions, recorded in the linear ion trap. data were analyzed by proteome discoverer 1.3 (thermo scientific) and searched using sequest (thermo scientific) against the rattus norvegicus protein database. a precursor mass tolerance of 10 ppm and a fragment mass tolerance of 0.8 da were considered in search parameters. data […]

SEQUEST institution(s)
Department of Molecular Biotechnology, University of Washington, Seattle, WA, USA
SEQUEST funding source(s)
Supported by the University of Washington’s Research Royalty Fund and by the National Science Foundation, Science and Technology Center Cooperative agreement 8809710, and Digital Equipment Corporation.

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