toffee

toffee provides a lossless, HDF5-backed file format and random I/O access for mass spectrometry proteomics data to enable efficient storage, fast retrieval, and compatibility with mzML-based workflows.

Key Features:

• Open Format: An open, non-proprietary HDF5-based file format for mass spectrometry (MS) data.
• Efficient File Size Management: Uses lossless compression to produce file sizes comparable to vendor formats and avoid the large size increases observed with mzML.
• Random I/O Access Patterns: HDF5 backing enables random input/output access patterns in contrast to the largely sequential I/O of mzML.
• Lossless Data Conversion: Supports lossless conversion back to mzML without information loss, maintaining compatibility with workflows and algorithms such as OpenSWATH.

Scientific Applications:

• High-Throughput Proteomics: Enables efficient storage and rapid retrieval for large-scale proteomics datasets.
• Peptide-Centric Deep-Learning Pipelines: Facilitates deep-learning pipelines for peptide identification by providing efficient data handling and access.
• Enhanced Data Processing: Preserves equivalence in processing outcomes compared to mzML while improving access and performance characteristics.

Methodology:

Built on the HDF5 framework with lossless compression, providing random I/O access patterns and reversible conversion to mzML.