MyriMatch protocols

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MyriMatch specifications

Information


Unique identifier OMICS_05383
Name MyriMatch
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for MyriMatch

MyriMatch in pipelines

 (12)
2018
PMCID: 5768655
PMID: 29375523
DOI: 10.3389/fmicb.2017.02658

[…] converted into the mzml file format using msconvert (). the saprolegnia protein database (20,088 entries) was then searched using several search engines in parallel, i.e., ms-gf+ () v1.0 (v8299), myrimatch () (version 2.1.120), comet () (version 2013.01 rev.0) and x!tandem () (version 2011.12.01.1; labkey, insilicos, isb, seattle, wa, united states). the following settings were used […]

2018
PMCID: 5850319
PMID: 29535201
DOI: 10.1128/mBio.02061-17

[…] against a constructed fasta database containing all proteins predicted from the sequenced genome of desulfobulbus oralis, concatenated with common contaminants and reversed-decoy sequences using myrimatch version 2.2 (). peptides were identified and proteins inferred using idpicker version 3.1 () with an experimental false-discovery rate (fdr) of <1% at the peptide level. peptide […]

2017
PMCID: 5327387
PMID: 28240279
DOI: 10.1038/srep43583

[…] spectra were searched against the c. thermocellum atcc 27405 proteome database – concatenated with common contaminants and reversed protein entries to assess false-discovery rates (fdr) – using myrimatch v. 2.1. peptide spectrum matches were filtered by idpicker v.3 (fdr < 1%), assigned matched-ion intensities, and peptide abundance distributions normalized and assembled to proteins […]

2016
PMCID: 4788478
PMID: 26989779
DOI: 10.1126/sciadv.1501254

[…] fragmentation spectra (ms/ms) were searched against the c. thermocellum 1313 proteome database concatenated with common contaminants and reversed sequences to control false discovery rates using myrimatch v.2.1 (). peptide spectrum matches (psms) were filtered by idpicker v.3 () and assigned matched-ion intensities (mits) based on observed peptide fragment peaks. psm mits were summed […]

2016
PMCID: 4890492
PMID: 27257435
DOI: 10.1186/s13068-016-0528-8

[…] fragmentation spectra (ms/ms) were searched against the c. thermocellum 1313 proteome database concatenated with common contaminants and reversed sequences to control false-discovery rates using myrimatch v.2.1 []. peptide spectrum matches (psm) were filtered by idpicker v.3 [] using a peptide-level fdr of <1 % per sample run and assigned matched-ion intensities (mit) based on observed […]


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MyriMatch in publications

 (75)
PMCID: 5893878
PMID: 29636439
DOI: 10.1128/mBio.00441-18

[…] sequences (ncbi refseq_2011), common contaminants, and reverse protein sequences, which were used to control the false-discovery rate (fdr). collected ms/ms spectra were matched to peptides using myrimatch v2.1 (), filtered, and assembled into proteins using idpicker v3.0 (). all searches included the following peptide modifications: a static cysteine modification (+57.02 da), an n-terminal […]

PMCID: 5865380
PMID: 29588665
DOI: 10.1186/s13068-018-1076-1

[…] mass spectrometer., acquired ms/ms spectra were matched with theoretical tryptic peptides generated from a concatenated c. bescii proteome fasta database with contaminants and decoy sequences using myrimatch v. 2.1 []. peptide spectral matches (psm) were filtered to achieve peptide false-discovery rates (fdr) < 1% and assembled to their respective proteins using idpicker v. 3.0 []. protein […]

PMCID: 5850319
PMID: 29535201
DOI: 10.1128/mBio.02061-17

[…] against a constructed fasta database containing all proteins predicted from the sequenced genome of desulfobulbus oralis, concatenated with common contaminants and reversed-decoy sequences using myrimatch version 2.2 (). peptides were identified and proteins inferred using idpicker version 3.1 () with an experimental false-discovery rate (fdr) of <1% at the peptide level. peptide […]

PMCID: 5813909
PMID: 29447168
DOI: 10.1371/journal.pone.0190019

[…] target database, was appended in order to discern the false-discovery rate (fdr) at the spectral level. for standard database searching, the peptide fragmentation spectra (ms/ms) were searched with myrimatch algorithm v2.2 []. myrimatch was configured to derive fully-tryptic peptides with the following parameters: unlimited missed cleavages, parent mass tolerance of 10 ppm, a fragment mass […]

PMCID: 5820608
PMID: 29527292
DOI: 10.5256/f1000research.14081.r27680

[…] to mgf format using peak view v1.2.0.3 (rrid: scr_015786)(sciex) and searched using mascot server v2.5.1 (rrid:scr_014322)(matrix science, london, uk), omssa v2.1.9 , x!tandem 2013.02.01.1 , and myrimatch v2.2.140 against a composite target/decoy database built from the oncorhynchus mykiss sequences at uniprot/swissprot knowledgebase (available here, last update: 2017/01/26, 50.125 […]


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MyriMatch institution(s)
Mass Spectrometry Research Center / Departments of Biomedical Informatics and Biochemistry, Vanderbilt University Medical Center, Nashville, TN, USA

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