Fig. 2: Highly efficient and platform-independent MS data access.
From: AlphaPept: a modern and open framework for MS-based proteomics
a MS data from different vendors is imported into an HDF5 container for fast and platform-independent data access. To read Thermo data, we provide a Python application programming interface. Bruker data is accessed via Bruker’s proprietary DLL. Additionally, generic data can be imported using the Pyteomics package. b The output of each processing step is appended to the HDF5, allowing processing in a modular way. c To efficiently store MS spectra, multiple spectra of variable length are concatenated, and start indices are saved in a lookup table. d HDF5 Accessing times. Loading data from HDF5 into memory takes less than 1 s for a typical 2 h full proteome analysis of a HeLa sample acquired on a Thermo Orbitrap mass spectrometer.
