MassBase

MassBase provides a repository of mass spectrometry metabolomics datasets to support non-targeted detection and comparative analysis of low-molecular-weight metabolites.

Key Features:

• Diverse Data Collection: MassBase contains 46,493 datasets (as of August 1, 2020) covering biological samples analyzed by gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and capillary electrophoresis-mass spectrometry (CE-MS).
• Raw Data Conversion: Raw vendor-specific binary MS files are converted into text file formats to enable downstream data extraction.
• Chromatogram Peak Extraction: Chromatograph peak information is extracted from converted text files to support metabolite detection.
• High-Accuracy LC-MS Processing: Mass chromatograms from 90 plant species acquired by LC-Fourier transform ion cyclotron resonance MS or Orbitrap MS were processed with PowerGet for high-accuracy detection and annotation of ionized molecules.
• Chemical Annotation: Extracted peaks receive chemical annotation to provide putative chemical identities and compositional information.
• Data Deposition: Annotated datasets are deposited in the associated KomicMarket2 database for chemical analysis.

Scientific Applications:

• Comparative Metabolomics: Enables large-scale comparison of metabolite profiles across samples and conditions.
• Functional Genomics: Supports linking metabolite data to genomic and pathway analyses for gene-function inference.
• Cross-Species Profiling: Facilitates metabolomic investigations across plants, microorganisms, animals, and foods.

Methodology:

Computational methods include conversion of raw binary MS files to text formats, extraction of chromatogram peak information, processing of LC-FTICR and Orbitrap mass chromatograms with PowerGet, and chemical annotation of detected peaks.