Vonode

Vonode performs de novo sequencing of peptides from high-resolution tandem mass spectra to enable precise peptide identification, including post-translational modifications and amino acid polymorphisms, in high-throughput shotgun proteomics data.

Key Features:

• High-resolution tandem MS support: Operates on spectra acquired by hybrid instruments such as LTQ-Orbitrap and LTQ-FT to leverage superior mass accuracy.
• Mass-accuracy-based scoring: Implements a unique scoring system that evaluates sequence tags primarily using the mass accuracy information of fragment ions.
• Consensus sequence tag inference: Infers consensus sequence tags from fragment ion evidence to improve reliability of peptide sequence calls.
• Demonstrated performance: On 40,297 spectra from a 24-hour proteomics measurement of Rhodopseudomonas palustris, inferred consensus tags for 11,422 spectra with an average peptide length of 5.5 residues and 84% accuracy.
• Comparative performance: Outperformed PepNovo v2.0 in both the number of de novo sequenced spectra and overall sequencing accuracy.
• Application to shotgun proteomics: Designed to work within high-throughput shotgun proteomics workflows for analysis of complex peptide mixtures.

Scientific Applications:

• Peptide de novo sequencing: Determination of peptide sequences directly from high-resolution tandem mass spectra without database search.
• Post-translational modification identification: Facilitates detection and localization of post-translational modifications using high-accuracy fragment ion masses.
• Amino acid polymorphism detection: Enables identification of amino acid polymorphisms from fragment ion mass patterns in high-resolution spectra.
• High-throughput proteomics analysis: Applied to large-scale shotgun proteomics datasets generated on LTQ-Orbitrap and LTQ-FT instruments.

Methodology:

Evaluates sequence tags primarily using fragment ion mass accuracy information and infers consensus sequence tags from high-resolution tandem mass spectra.