Expanding the MR1 ligandome using chemical class-specific fragmentation and molecular networking

Area of Science:

• Analytical Chemistry
• Immunology
• Biochemistry

Background:

• Identifying unknown analytes via mass spectrometry is challenging, especially for low-abundance compounds absent in databases.
• The MR1 receptor's ligandome, particularly non-nucleoside ligands, remains incompletely characterized.

Purpose of the Study:

• To develop and apply a data analysis workflow for identifying novel small molecule classes binding to the MR1 receptor.
• To reanalyze existing mass spectrometry data to expand the known MR1 ligandome.

Main Methods:

• Utilized Compound Discoverer software for metabolomic analysis.
• Employed fragmentation filtering, molecular networking, and spectral database searching.
• Reanalyzed mass spectrometry data from MR1-presented antigen studies.

Main Results:

• Identified two novel compound classes binding to the MR1 receptor.
• Discovered riboflavin-like compounds with a ribityl substructure.
• Characterized an adenosine monophosphate isomer and larger covalently bound nucleotide complexes.

Conclusions:

• The developed workflow effectively identifies novel compound classes within complex biological samples.
• This approach significantly enhances the characterization of receptor ligandomes, including the MR1 ligandome.
• Highlights the utility of combining fragmentation, networking, and database searching for discovering unknown molecules.