Byonic

Byonic, developed by Protein Metrics, is a full tandem mass spectrometry (MS/MS) search engine designed for comprehensive peptide and protein identification. It delivers unequaled sensitivity and high throughput workflows, making it the leading choice for proteomics researchers who require quick, accurate, and flexible mass spectrometry analysis across a wide range of experimental types.

Byonic is built for ease of use and vendor neutrality, seamlessly handling diverse proteomics experiments including data-dependent, data-independent, bottom-up, top-down, glycoprotein, and phosphoprotein analysis. Its broad compatibility with mass spectrometry data formats — including CID, TOF-TOF, QTOF HCD, ETD/ECD, and EThcD — ensures flexibility across different instrument platforms and laboratory environments.

Accurate Scoring and Guided Database Searches

• Sets database search parameters in a semi-automated, guided fashion to improve usability and reduce inadvertent mistakes.
• Delivers greater sensitivity (more true positives) and specificity (fewer false positives) compared to other search engines.
• Enables a wider variety of searches than competing proteomics search engines.
• Customizable search options focus effort on candidate peptides most likely to match mass spectra, finding more true matches more quickly.

Advanced Modification Search Capabilities

• Optimized for complex modification searches of peptides, supporting various combinations of modification types.
• Provides detailed control over the types and numbers of post-translational modifications (PTMs) allowed on candidate peptides.
• Focuses search efforts on peptides most likely to match mass spectra through fine-grained modification control.

Wildcard Search

• Enables study of protein samples with insufficient databases or highly modified proteins.
• Guards against false negatives by identifying sequence variants, unknown modifications, and known but unanticipated modifications.
• Particularly useful for exploratory proteomics research where prior knowledge of modifications may be limited.

Glycopeptide Search

• Identifies glycopeptides without requiring prior knowledge of glycan masses or glycosylation sites.
• Scores and annotates multiple types of glycopeptide fragments to deduce the peptide carrier, glycan, and modification site.
• Provides useful output reports of identified glycopeptides and glycoproteins.

High Throughput Workflows and Reporting

• Optimizes search engine performance for high throughput workflows using focused databases and prebuilt modification lists.
• Includes searchable common contaminants to streamline data analysis.
• Leverages multi-core architecture to accelerate processing speed.
• Generates comprehensive output reports for identified peptides and proteins.

Byonic has been independently evaluated in the community assessment of glycoproteomics informatics solutions published in Nature Methods, and is supported by an extensive knowledge base, video tutorials, and active customer resources. It is available for trial and is suitable for research teams seeking a powerful, flexible, and user-friendly proteomics search platform.