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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Related Experiment Video

Updated: May 15, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Byonic: advanced peptide and protein identification software.

Marshall Bern1,2, Yong J Kil1, Christopher Becker1

  • 1Protein Metrics Inc, San Carlos, California.

Current Protocols in Bioinformatics
|December 21, 2012
PubMed
Summary
This summary is machine-generated.

Byonic software enhances peptide and protein identification using tandem mass spectrometry. It supports numerous variable modifications and unknown modifications, improving proteomic analysis.

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Last Updated: May 15, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Peptide-based Identification of Functional Motifs and their Binding Partners
14:28

Peptide-based Identification of Functional Motifs and their Binding Partners

Published on: June 30, 2013

Split-BioID — Proteomic Analysis of Context-specific Protein Complexes in Their Native Cellular Environment
09:02

Split-BioID — Proteomic Analysis of Context-specific Protein Complexes in Their Native Cellular Environment

Published on: April 20, 2018

Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Tandem mass spectrometry is crucial for peptide and protein identification.
  • Existing software like SEQUEST and Mascot have limitations in handling complex modifications.
  • The need for advanced software to manage a high number of variable modifications is critical.

Purpose of the Study:

  • To introduce Byonic, a novel software package for peptide and protein identification.
  • To highlight Byonic's advanced capabilities in handling variable modifications and glycopeptides.
  • To demonstrate Byonic's advantages over existing proteomic search software.

Main Methods:

  • Utilizing Byonic software for peptide and protein identification via tandem mass spectrometry.
  • Defining and applying an extensive range of variable modification types with specific occurrence limits.
  • Employing Byonic's Wildcard Search for unanticipated modifications.
  • Using Byonic's Glycopeptide Search for identifying glycopeptides without prior mass or site information.

Main Results:

  • Byonic enables the simultaneous search of hundreds of modification types without combinatorial explosion.
  • The software allows for flexible control over modification occurrences, distinguishing between chance and clustered modifications.
  • Byonic facilitates the identification of unknown or unanticipated modifications.
  • Glycopeptide identification is achievable even without prior knowledge of glycan structures or sites.

Conclusions:

  • Byonic represents a significant advancement in peptide and protein identification software.
  • Its flexible modification handling and specialized search functions overcome limitations of previous tools.
  • Byonic expands the scope of proteomic analysis, particularly for complex samples and post-translational modifications.