Byonic protocols

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Byonic specifications

Information


Unique identifier OMICS_02471
Name Byonic
Software type Package/Module
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Byonic

Byonic in pipeline

2014
PMCID: 4165458
PMID: 25162384
DOI: 10.1021/ac502790j

[…] peptide retaining the innermost glcnac. they illustrated the diagnostic value of this fragment in n-linked glycopeptide identification by comparing data interpretation delivered by sweet heart and byonic, a commercially available search engine that is marketed for glycosylation analysis (proteinmetrics/thermo). the data analyzed derived from a tryptic digest of recombinant human soluble […]


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Byonic in publications

 (46)
PMCID: 5955915
PMID: 29769533
DOI: 10.1038/s41467-018-04272-y

[…] glycopeptides were analyzed by lc-esi ms employing a q-exactive orbitrap mass spectrometer (thermo fisher) and higher energy collisional dissociation (hcd) fragmentation of glycopeptides. byonic (version 2.7) and byologic software (version 2.3; protein metrics inc.) were used for data analysis and glycopeptide identification. the relative abundance of individual glycoforms on specific […]

PMCID: 5915571
PMID: 29720971
DOI: 10.3389/fmicb.2018.00742

[…] in figures . from the obtained higher-energy collisional dissociation (hcd) fragmentation data, the proteome targeted against the ceacam6 protein and the n-glycome were performed directly using byonic™ v2.7.7 software. ceacam6 had the highest score among all samples (table ). all byonic™-annotated ceacam6 glycopeptide-containing hcd spectra were inspected manually to verify the annotation., […]

PMCID: 5871710
PMID: 29619343
DOI: 10.3389/fonc.2018.00070

[…] tolerance: 10 ppm, fragment tolerance: 0.02 da; missed cleavages: 1; database: swissprot 2015_12 (550,116 sequence); taxonomy: human (20,268 sequence). the subsequent glycopeptide analysis by byonic (version 2.7.4) used the following settings: maximum number of missed cleavages: 2; fragmentation type: qtof/hcd; precursor tolerance: 10 ppm; fragment tolerance: 20 ppm., statistical analysis […]

PMCID: 5819086
PMID: 29463217
DOI: 10.1186/s12862-018-1141-1

[…] spectrometry data in proteomics commonly either relies on the matching of ms/ms spectra to a protein sequence database of the target species by the use of a dedicated algorithm (for example mascot, byonic or maxquant; [–]), or through de novo only protein sequencing without a provided protein sequence database (for example peaks de novo, novor or pepnovo; [–]). de novo algorithms suffer […]

PMCID: 5830484
PMID: 29411091
DOI: 10.1007/s00216-018-0848-6

[…] were performed on optimized tryptic digest samples to map peptide identifications to tic and uv peaks in the peptide map. in-silico peptide identification was performed on lc-ms/ms data using byonic v 2.7.2 (protein metrics inc., san carlos, ca) []. mass spectra were searched against the nistmab amino acid sequence, the human proteome (for identification of potential human contaminants), […]


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Byonic institution(s)
Palo Alto Research Center, Palo Alto, CA, USA

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