OpenTIMS

OpenTIMS provides programmatic access to raw Bruker timsTOF Pro LC-TIMS-MS data by reading Bruker TDF files with a C++ library, exposing Python (TimsPy) and R (TimsR) interfaces, and converting TDF to HDF5 for analysis of trapped ion mobility spectrometry (TIMS) coupled to time-of-flight (TOF) mass spectrometry in proteomics, lipidomics, and metabolomics.

Key Features:

• C++ TDF reader: A C++ library that reads Bruker TDF files and extracts raw LC-TIMS-MS data.
• TimsPy: A Python interface built on OpenTIMS to access timsTOF raw data programmatically.
• TimsR: An R interface that leverages OpenTIMS to provide programmatic access to timsTOF raw data.
• TDF to HDF5 conversion: Translation of Bruker's proprietary TDF format into HDF5 for downstream analysis.
• Compatibility with large-data tools: Output suitable for Python tools such as vaex to handle large datasets.

Scientific Applications:

• Proteomics: Analysis of timsTOF Pro datasets for protein identification and quantification.
• Lipidomics: Access and processing of timsTOF-derived lipidomics data.
• Metabolomics: Handling and analysis of metabolomics datasets generated by LC-TIMS-MS.
• Large LC-TIMS-MS datasets: Processing and downstream analysis of large-scale LC-TIMS-MS data files.

Methodology:

OpenTIMS reads Bruker TDF files via a C++ library, provides Python (TimsPy) and R (TimsR) bindings, converts TDF to HDF5, and enables downstream analysis with tools such as vaex.