TIMS 2 Rescore

TIMS 2 Rescore optimizes data-driven rescoring of DDA-PASEF data from timsTOF instruments by integrating new prediction models and accepting raw mass spectrometry data with search results from multiple search engines to improve peptide identification accuracy.

Key Features:

• timsTOF MS2 PIP spectrum prediction models: New spectrum prediction models specifically developed for timsTOF MS2 data.
• IM2Deep: A new deep learning-based peptide ion mobility predictor integrated into the rescoring workflow.
• Bruker raw data compatibility: Direct acceptance of Bruker raw mass spectrometry data without format conversion requirements.
• Multi-search engine support: Accepts search results from ProteoScape, MS Amanda, PEAKS, and many other search engines.

Scientific Applications:

• Plasma proteomics: Rescoring of DDA-PASEF data to improve protein identification in complex plasma samples.
• Immunopeptidomics: Enhanced identification of HLA class I and II peptides from immunopeptidomics datasets.
• Metaproteomics: Improved peptide identification in complex microbial community samples analyzed by DDA-PASEF.

Methodology:

Data-driven rescoring workflow optimized for DDA-PASEF data from timsTOF instruments, incorporating timsTOF MS2 PIP spectrum prediction models and IM2Deep for peptide ion mobility prediction.