raw2mzDB

raw2mzDB converts raw or XML mass spectrometry files into the mzDB SQLite-based format to enable efficient storage, three-dimensional indexing, and rapid retrieval of LC-MS, LC-MS/MS, and SWATH-MS datasets.

Key Features:

• SQLite-based mzDB: mzDB is a server-less, single-file database built on SQLite for portable storage of mass spectrometry data.
• Reduced storage: Conversion to mzDB reduces storage requirements by approximately 25% compared to standard XML-based formats.
• Three-dimensional indexing: Uses optimized three-dimensional indexing based on LC-MS coordinates—retention time, m/z, and precursor m/z for SWATH-MS—to organize spectra.
• Accelerated access times: Provides access time improvements ranging from twofold to 2000-fold versus XML formats and reports superior performance to mz5 for many access patterns.
• Implementations for conversion: Implements conversion in C++ and Java as an extension of the ProteoWizard framework to produce mzDB files from raw or XML inputs.
• Cross-language access: mzDB files can be accessed via the SQLite C library and drivers for major programming languages.

Scientific Applications:

• Proteomics and SWATH-MS data management: Supports large-scale proteomics datasets and SWATH-MS workflows by reducing storage footprint and enabling rapid data extraction for identification of target peptides.
• High-throughput MS pipelines: Improves performance of mass spectrometry analysis pipelines and facilitates high-throughput proteomics workflows through faster data retrieval.

Methodology:

Conversion of raw or XML files is implemented in C++ and Java as an extension of the ProteoWizard framework; mzDB is a server-less SQLite single-file database using three-dimensional LC-MS coordinate indexing (retention time, m/z, precursor m/z) to optimize storage and accelerate data retrieval.