imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging

Area of Science:

• Analytical Chemistry
• Biotechnology
• Data Science

Background:

• Imaging mass spectrometry (MS) generates complex datasets with spatial information on analyte distribution.
• Current data formats are insufficient for comprehensive description of MS imaging experiments.
• Standardization is needed for efficient data exchange and inter-instrument comparability.

Purpose of the Study:

• To introduce imzML, a new data format for imaging mass spectrometry.
• To enable flexible and efficient exchange of MS imaging data.
• To facilitate interoperability between different instruments and data analysis software.

Main Methods:

• Development of the imzML format, separating mass spectral data (binary file) and metadata (XML file).
• Extension of the mzML controlled vocabulary to include imaging-specific parameters (e.g., spatial coordinates, resolution).
• Linking of binary and XML files using offset values and a universally unique identifier.

Main Results:

• imzML provides a standardized, flexible, and efficient format for MS imaging data.
• The format ensures efficient storage and allows for flexible metadata handling.
• Datasets generated using imzML are comparable in size to raw data.

Conclusions:

• imzML supports interoperability, allowing users to choose optimal processing tools and compare data across instruments.
• The adoption of imzML promotes wider accessibility and comparability of MS imaging data.
• The imzML format is supported by several imaging MS software tools, with growing adoption.