Comet protocols

Comet specifications

Information


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
Wikipedia https://en.wikipedia.org/wiki/SEQUEST

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Maintainer


  • person_outline Jimmy Eng <>

Additional information


http://proteomicsresource.washington.edu/protocols06/sequest.php

Publications for Comet

Comet IN pipelines

 (58)
2018
PMCID: 5874627
PMID: 29419787
DOI: 10.3390/microorganisms6010013

[…] 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 […]

2018
PMCID: 5885379
PMID: 29618380
DOI: 10.1186/s40425-018-0331-0

[…] ion-routing multipole (normalized collision energy = 65)., mass spectrometry data was processed against the uniprot swiss-prot canonical mouse protein database (v. 2014_05, 16,669 sequences) with sequest ht in proteome discoverer v1.4 (thermo scientific). search settings were: monoisotopic parent ion mass tolerance of 1.25 da, monoisotopic fragment ion tolerance of 1.0 da, tryptic cleavage […]

2017
PMCID: 5397609
PMID: 28065881
DOI: 10.1093/dnares/dsw057

[…] from proteowizard version 3.0.4624 selecting vendor-specific peak picking algorithm.15 all the .mzml files were then independently searched against rat protein sequence file using x!tandem16 and comet17 search. the rat protein sequence contained all the sequence available in uniprot database (february 2015) supplemented with the common laboratory contaminant proteins and decoy sequences […]

2017
PMCID: 5427775
PMID: 28579927
DOI: 10.2174/1570164614666161228124801

[…] total intensities. parent and fragment ions were selected with tolerances of ± 100 ppm and ± 1 da, respectively. all acquired ms/ms data were queried against the ncbi rat protein database using the sequest algorithm (thermo electron, san jose, ca). the resulting sequest output files were loaded for identification of peptides and proteins using peptideprophet and proteinprophet software [15, […]

2017
PMCID: 5427775
PMID: 28579927
DOI: 10.2174/1570164614666161228124801

[…] of ± 100 ppm and ± 1 da, respectively. all acquired ms/ms data were queried against the ncbi rat protein database using the sequest algorithm (thermo electron, san jose, ca). the resulting sequest output files were loaded for identification of peptides and proteins using peptideprophet and proteinprophet software [15, 16], and assembled a complete protein list from the rat urine […]

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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