Documentation for AlphaTims.

With the introduction of the Bruker TimsTOF and Parallel Accumulation–Serial Fragmentation (PASEF), the inclusion of trapped ion mobility separation (TIMS) between liquid chromatography (LC) and tandem mass spectrometry (MSMS) instruments has gained popularity for both DDA and DIA. However, detection of such five dimensional points (chromatographic retention time (rt), ion mobility, quadrupole mass to charge (m/z), time-of-flight (TOF) m/z and intensity) at GHz results in an increased amount of data and complexity. Efficient accession, analysis and visualisation of Bruker TimsTOF data are therefore imperative. AlphaTims is freely available, open-source and available on all major Operating Systems. It can be used with a graphical user interface (GUI), a command-line interface (CLI) or as a regular Python package.

This documentation is intended as an API for direct Python use. For more information, see AlphaTims on GitHub.

• alphatims.utils
• alphatims.bruker
• alphatims.plotting