ms-data-core-api

ms-data-core-api provides a Java API that supplies a pluggable programming interface and a common data model for reading and representing proteomics spectra, peptide and protein identifications, and quantitative data to support development of computational proteomics tools and workflows.

Key Features:

• Common data model: Represents raw spectra, peptide and protein identifications, and quantitative assessments for proteomics analyses.
• Controlled vocabularies and ontologies: Constructs the data model using controlled vocabularies and ontologies to ensure consistency and interoperability.
• Pluggable programming interface: Exposes a Java API that enables programmatic access and extensibility for proteomics applications.
• Supported file formats: Includes native readers for PSI standards mzML, mzIdentML, mzTab and additional formats dta, ms2, mgf, pkl, apl, mzXML, and mzData.
• PRIDE XML processing: Processes PRIDE XML files for compatibility with datasets from the PRIDE database.

Scientific Applications:

• Development of proteomics tools and pipelines: Implements core data representations and readers used to build computational proteomics applications.
• Integration of heterogeneous proteomics data: Enables integration and analysis of spectra, identification, and quantitative results across multiple file formats including PSI standards and legacy formats.
• Processing PRIDE datasets: Facilitates processing and reanalysis of datasets exported from the PRIDE database via PRIDE XML.

Methodology:

Implemented in Java; employs a common data model constructed from controlled vocabularies and ontologies and provides native readers for mzML, mzIdentML, mzTab, dta, ms2, mgf, pkl, apl, mzXML, mzData, and PRIDE XML.