Bolt

Bolt performs peptide identification from MS/MS data to enable comprehensive proteome analysis.

Key Features:

• Search space: Searches more than 900,000 protein sequences, including canonical forms, isoforms, mutations, and contaminants.
• PTM support: Accommodates up to 41 post-translational modifications.
• Tryptic specificity: Supports N-terminal and C-terminal partial tryptic searches.
• Input data: Processes MS/MS (tandem mass spectrometry) sequencing data for peptide identification.
• Scalability: Scalable cloud-based architecture for large search spaces and quantitative proteomics analyses.
• Computational performance: Delivers rapid results on standard laptops with reduced computational time compared to traditional high-performance servers.
• Identification confidence: Sixty-one percent of peptides uniquely identified by Bolt are validated by strong fragmentation patterns compared with 13% for SEQUEST and 6% for Mascot.
• Cross-platform verification: Thirty percent of unique Bolt identifications are verified across Bolt, SEQUEST, and Mascot, compared with 20% for SEQUEST and 27% for Mascot.
• Data availability: Data generated using Bolt are available via ProteomeXchange under identifier PXD012700.

Scientific Applications:

• Comprehensive proteome characterization: Enables broader proteome coverage by searching canonical proteins, isoforms, mutations, and contaminants.
• Variant-aware proteomics: Detects peptides corresponding to genetic variants and mutations.
• PTM analysis: Enables identification of peptides carrying up to 41 different post-translational modifications.
• Quantitative proteomics: Supports scalable quantitative proteomic analyses.
• Long-gradient LC-MS/MS analyses: Improves unique peptide identifications in longer gradient experiments relative to SEQUEST and Mascot.

Methodology:

Bolt searches MS/MS spectra against a search space of over 900,000 protein sequences (canonical, isoforms, mutations, contaminants), permits up to 41 PTMs, and performs N-terminal and C-terminal partial tryptic searches.