mspire_mspire-sequest

mspire_mspire-sequest provides data readers, format conversion, in-silico digestion, isotopic pattern calculation, and peptide false identification rate computation for processing and analysis of mass spectrometry-based proteomics data.

Key Features:

• Efficient Data Handling: Quick and memory-efficient readers for standard XML proteomics formats.
• Format Conversion: Converters for intermediate file types used in spectral-identification workflows, including Bioworks .srf format.
• In-Silico Digestion and Isotopic Pattern Calculation: In-silico peptide digestion and isotopic pattern calculation for interpreting mass spectra.
• Peptide False Identification Rate Calculation: Modules to calculate peptide false identification rates for validation of identifications.

Scientific Applications:

• Mass Spectrometry-Based Proteomics Processing: Processing and parsing of raw and intermediate proteomics data for downstream analysis.
• Protein and Peptide Identification: Support for identifying proteins and peptides from tandem mass spectra.
• Validation and FDR Estimation: Validation of identified peptides through calculation of peptide false identification rates.
• Large-Scale Proteomics Data Handling: Analysis workflows for large and complex proteomics datasets.

Methodology:

Implemented in Ruby with quick, memory-efficient XML proteomics readers, converters for intermediate formats including Bioworks .srf, in-silico digestion, isotopic pattern calculation, and peptide false identification rate computation.