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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 citations

 (47)
library_books

Structure of a cleavage independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer

2018
Nat Commun
PMCID: 5955915
PMID: 29769533
DOI: 10.1038/s41467-018-04272-y

[…] enrichment, 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 […]

library_books

Oligomannose Rich Membranes of Dying Intestinal Epithelial Cells Promote Host Colonization by Adherent Invasive E. coli

2018
Front Microbiol
PMCID: 5915571
PMID: 29720971
DOI: 10.3389/fmicb.2018.00742

[…] The acquired raw files were analyzed with Byonic™ v2.7.7 (Protein Metrics Inc., San Carlos, CA, USA) to identify N-linked glycopeptides. The following parameters were used: CEACAM proteins of the Uniprot database (entry P40199 for human CEACA […]

call_split

Alterations of the Human Skin N and O Glycome in Basal Cell Carcinoma and Squamous Cell Carcinoma

2018
PMCID: 5871710
PMID: 29619343
DOI: 10.3389/fonc.2018.00070
call_split See protocol

[…] peptide 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. […]

library_books

Elucidation of cross species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment

2018
BMC Evol Biol
PMCID: 5819086
PMID: 29463217
DOI: 10.1186/s12862-018-1141-1

[…] s 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 from hig […]

call_split

Development of an LC MS/MS peptide mapping protocol for the NISTmAb

2018
Anal Bioanal Chem
PMCID: 5830484
PMID: 29411091
DOI: 10.1007/s00216-018-0848-6
call_split See protocol

[…] nalyses 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), t […]

library_books

Identification of protein W, the elusive sixth subunit of the Rhodopseudomonas palustris reaction center light harvesting 1 core complex

2018
Biochim Biophys Acta
PMCID: 5764122
PMID: 29126780
DOI: 10.1016/j.bbabio.2017.11.001

[…] or protein identification, Amazon MS data-files were first converted to Mascot Generic File (MGF) format using a script provided by Bruker. Amazon MGF and Q Exactive RAW data-files were uploaded into Byonic v. 2.9.38 (Protein Metrics) for searching against the Uniprot reference proteome database for Rps. palustris (ID: UP000001426, 4811 entries, 9 July 2016). […]

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

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