Byonic - OmicsDI

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Department of Radiology Canary Center at Stanford for Cancer Early Detection Stanford School of Medicine Stanford University (7)
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Charles University, Faculty of Pharmacy in Hradec Králové Department of Analytical Chemistry Akademika Heyrovského 1203/8 500 05 Hradec Králové, Czech Republic (5)
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1School of Natural Sciences, Macquarie University, Sydney, NSW, Australia 2Institute for Glyco-core Research (iGCORE), Nagoya University, Aichi, Japan (3)
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Genomics Research Center, Academia Sinica, Taipei, 11529 Taiwan (3)
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Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mount Carmel, Haifa, 3498838, Israel (2)
Head of Scientific Archeology Unit, Weizmann Institute of Science (2)
Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India (2)
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. (2)
Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA (2)
School of Pharmacy, UW-Madison (2)
Department of Biochemistry, University of Utah, Salt Lake City, UT (2)
University of Wisconsin-Madison, Department of Chemistry and School of Pharmacy (2)
Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA. (2)
Institute of Chemistry, Academia Sinica (2)
Department of Chemistry, Washington University in St. Louis (2)
Caltech Proteome Exploration Laboratory (2)
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Modification

1x(15)N labeled L-leucine (1)
2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)

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Quantitative data-independent acquisition glycoproteomics of sparkling wine

We developed an automated workflow that created ion libraries to analyse Sequential Window Acquisition of all THeoretical mass spectra (SWATH) Data Independent Acquisition (DIA) mass spectrometry data based on glycopeptides identified by Byonic. We applied our workflow to three pairs of experimental...

ORGANISM(S): Vitis vinifera (Grape) Saccharomyces cerevisiae (Baker's yeast)

2020-09-18 | PXD019572 | Pride

Evaluation of scoring functions and peptide exposure by fractionation

Evaluation of sensitivity and accuracy of widely used scoring functions Sequest, MaxQuant, Peaks, and Byonic. Spectra from E. coli were matched to human sequences, and human spectra from K052 cells were matched to A. loki sequences to determine specificity of matching and FDR estimation. A subsampli...

ORGANISM(S): Homo sapiens (Human)

2018-10-18 | PXD008463 | Pride

Algorithm benchmark proteogenomics peaks sequest byonic maxquant

PATCH labeling in the BSA through red light

For the liquid chromatography-mass spectrometry (LC-MS) analysis, the 500 μM AP was used to label BSA in the reaction, followed by clicking chemical conjugation with 0.1 mM azide-PEG3-biotin under 0.5 mM CuCl(2), 2 Mm Tris (3-hydroxypropyltriazolylmethyl) amine (THPTA, Sigma-Aldrich) and 5 mM ascorb...

ORGANISM(S): Bos taurus (Bovine)

2025-07-30 | PXD057016 | Pride

Pcn bsa

Automated N-glycopeptide identification in glycoproteomics

Recent advances in software-driven glycopeptide identification in LC-MS/MS-based N-glycoproteomics have facilitated biochemical studies reporting thousands of intact N-glycopeptides, i.e. N-glycan-conjugated peptides, but the automated identification process remains to be scrutinized. Herein, we exp...

ORGANISM(S): Homo sapiens (Human)

2016-08-17 | PXD004243 | Pride

Basigin Byonic Glycoproteomics Glycopeptide N-glycosylation Lc-ms/ms

Mouse Liver Mannose-6-Phosphate Glycoproteome LC-MSMS

This is the raw data and Byonic search results of mouse liver Mannose-6-Phosphate glycoproteome.

ORGANISM(S): Mus musculus (Mouse)

2020-03-11 | PXD012404 | Pride

Mouse liver mannose-6-phosphate glycoproteome

Mouse kidney Mannose-6-Phosphate Glycoproteome LC-MSMS

This is the raw data and Byonic search results of mouse kidney Mannose-6-Phosphate glycoproteome.

ORGANISM(S): Mus musculus (Mouse)

2020-03-11 | PXD012402 | Pride