theospec

theospec predicts theoretical MS/MS spectra from peptide sequences to enable verification of peptide sequence matches and ion assignments in proteomics mass spectrometry analyses.

Key Features:

• Theoretical Spectrum Calculation: Calculates theoretical MS/MS spectra from amino acid sequences of peptides, including expected fragment ion series.
• Peptide Match Verification: Provides theoretical spectra for validating ion matching and peptide identifications produced by database search algorithms applied to DNA or protein databases.
• Integration Capability: Operates independently of specific operating systems to allow incorporation into computational workflows and pre-existing analysis environments.
• Output Formats: Exports theoretical spectra in graphical and tabular formats for comparison with experimental MS/MS data.

Scientific Applications:

• Proteomics peptide identification verification: Comparison of theoretical and experimental MS/MS spectra to assess the accuracy of peptide identifications.
• Validation of ion matching in database search workflows: Assessment of ion assignments produced by algorithms that search peptide sequences within DNA or protein databases.

Methodology:

Input peptide sequences are used to generate theoretical MS/MS spectra by computing expected ion fragmentation patterns based on mass spectrometry principles, and the resulting spectra are compared against experimental data to assess peptide identification accuracy.