Byonic: Advanced Peptide and Protein Identification Software
Open accessAbstract
Byonic is the name of a software package for peptide and protein identification by tandem mass spectrometry. This software, which has only recently become commercially available, facilitates a much wider range of search possibilities than previous search software such as SEQUEST and Mascot. Byonic allows the user to define an essentially unlimited number of variable modification types. Byonic also allows the user to set a separate limit on the number of occurrences of each modification type, so that a search may consider only one or two chance modifications such as oxidations and deamidations per peptide, yet allow three or four biological modifications such as phosphorylations, which tend to cluster together. Hence, Byonic can search for tens or even hundreds of modification types simultaneously without a prohibitively large combinatorial explosion. Byonic's Wildcard Search allows the user to search for unanticipated or even unknown modifications alongside known modifications. Finally, Byonic's Glycopeptide Search allows the user to identify glycopeptides without prior knowledge of glycan masses or glycosylation sites. Curr. Protoc. Bioinform. 40:13.20.1‐13.20.14. © 2012 by John Wiley & Sons, Inc.
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Only proteins with five unique detected peptides each with a peptide spectral match score cutoff greater than 300 were considered.
“only proteins, with five unique detected peptides each with a peptide spectral match score cutoff greater than 300, were considered.33”
From ApoE is Secreted as a Lipid Nanoparticle by Mammalian Cells: Implications for Alzheimer’s Disease Pathogenesis (2025) · cites this paper as [33]
The PSM List section describes 300 as a good Byonic score, and the Advanced Tab section says a reasonable score threshold for most searches falls between 200 and 400. The Protein List section defines the unique-peptide count, but the paper does not prescribe five unique peptides per protein or a universal cutoff above 300; those appear to be the citing study’s selection criteria (page numbers unavailable). (LLM, conf=0.86)
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Research works printed but not linked: 10
- Bern M Cai Y Goldberg D 2007 Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectreometry Anal Chem 79 1393 1400 17243770
- Bern M Finney G Hoopmann MR Merrihew G Toth MJ MacCoss MJ 2009 Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry Anal Chem 82 833 841 20039681 PMC2813958
- Bern M Saladino J Sharp JS 2010 Conversion of methionine into homocysteic acid in heavily oxidized proteomics samples Rapid Commun Mass Spectrom 24 768 772 20169556 PMC2935272
- Bhatia S Kil YJ Ueberheide B Chait BT Tayo L Cruz L Lu B Yates JR Bern M 2012 Constrained de novo sequencing of cone snail toxins J Proteome Res to appear PMC3412931 22709442
- Charvatova O Foley BL Bern MW Sharp JS Orlando R Woods RJ 2008 Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1 J Am Soc Mass Spectrom 19 1692 1705 18707901 PMC2607067
- Craig R Beavis RC 2004 TANDEM: matching proteins with tandem mass spectra Bioinformatics 20 1466 1467 14976030
- Eng J McCormack AL Yates JR 1994 An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database J Am Soc Mass Spectrom 5 976 989 24226387
- Kil YJ Becker C Sandoval W Goldberg D Bern M 2011 Preview: a program for surveying shotgun proteomics tandem mass spectrometry data Anal Chem 83 5259 5267 21619057 PMC3134881
- Perkins DN Pappin DJ Creasy DM Cottrell JS 1999 Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 20 3551 3567 10612281
- Zhu Y Guo T Park JE Li X Meng W Datta A Bern M Lim SK Sze SK 2009 Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting Mol Cell Proteomics 8 1999 2010 19473960 PMC2722762
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- Authors
- Bern, M., Kil, Y. J., & Becker, C.
- Affiliations
- Palo Alto Research Center (US)
- Protein Metrics (United States) (US)
- Venue
- Current Protocols in Bioinformatics
- Publisher
- Wiley
- Published
- 2012-12
- Volume
- 40
- Issue
- 1
- Pages
- 13.20.1-13.20.14
- ISSN
- 1934-3396 (ISSN-L)
- 1934-340X
- PMC
- PMC3545648
- OpenAlex
- W2110438218
- Cited by
- 659
- References
- 0
- Citations by year
- 2026: 36 · 2025: 52 · 2024: 66 · 2023: 66 · 2022: 83 · 2021: 92 · 2020: 64 · 2019: 48 · 2018: 45 · 2017: 47 · 2016: 33 · 2015: 16 · 2014: 7 · 2013: 2
- FWCI
- 3.53
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Current Protocols in Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (R21GM085718)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- peptide identification, protein identification, tandem mass spectrometry, phosphorylation, glycopeptide identification, glycosylation sites, wildcard search
- MeSH terms
- Glycosylation, Peptides, Proteins, Software, Mass Spectrometry, Databases, Protein, Proteomics
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