inSPIRE

inSPIRE improves peptide-spectrum match (PSM) identification by rescoring database search results using Prosit MS spectral predictions to increase accuracy and sensitivity of mass spectrometry-based proteomic analyses.

Key Features:

• Spectral Prediction Integration: Uses Prosit MS spectral predictions to inform rescoring by comparing predicted spectra with experimental spectra for each PSM.
• Compatibility with Database Search Engines: Accepts results from common database search engines for downstream rescoring.
• Large-Scale Rescoring Capability: Supports rescoring of mass spectrometry data from multiple search files simultaneously.
• Enhanced Sensitivity to Amino Acid Variations: Detects minor differences in amino acid residue positions to differentiate peptides, including those from nonspecific cleavage events.
• Versatility Across Sample Types: Applicable to tryptic proteome digests and immunopeptidomes.

Scientific Applications:

• Immunopeptidomics: Boosts PSM identification rates to improve characterization of peptide repertoires presented by major histocompatibility complex (MHC) molecules.
• Noncanonical Peptide Identification: Enhances detection of noncanonical peptides that do not follow typical proteolytic cleavage patterns.
• Tryptic Proteome Analysis: Improves peptide identification in tryptic proteome digests for general proteomic studies.

Methodology:

inSPIRE uses Prosit MS spectral predictions to rescore database search results, integrates additional scoring metrics, supports rescoring of multiple search files simultaneously, and has been benchmarked on ground truth datasets.