MSMS-Chooser

MSMS-Chooser facilitates community-driven creation and submission of MS/MS reference spectra to the GNPS public library to improve spectral annotation and chemical identification.

Key Features:

• Community contribution: Enables generation and submission of MS/MS reference spectra to the GNPS public MS/MS reference library.
• Template and sequence table generation: Uses an MSMS-Chooser sample template and programmatic generation of sequence tables to organize data collection.
• Data acquisition modes: Acquires MS/MS spectra using LC-MS/MS with data-dependent acquisition in positive and negative electrospray ionization (ESI) modes from chemical standards dissolved in methanol–water.
• Automatic spectral annotation: Uploads data to GNPS via MSMS-Chooser for automatic spectral annotation, with 99.2% of manually validated scans correctly annotated in proof-of-concept experiments.
• Output and integration: Produces a table formatted for potential inclusion in the GNPS library and can directly initiate Molecular Annotation Search System Tool (MASST) searches.
• Processing time: Demonstrated end-to-end processing—from acquisition and processing to upload and annotation—in approximately two hours for proof-of-concept scenarios.

Scientific Applications:

• Compound identification: Expands reference MS/MS spectra available for identification of unknown compounds in mass spectrometry experiments.
• Library expansion: Supports growth of the GNPS public MS/MS reference library through community-contributed spectra.
• Chemical annotation improvement: Improves accuracy and breadth of chemical annotations in mass spectrometry-based studies via automated annotation and integrated searches.
• Relevant fields: Applicable to metabolomics, proteomics, and natural products research where precise compound identification is required.

Methodology:

Complete an MSMS-Chooser sample template, generate sequence tables programmatically, upload acquired MS/MS data to GNPS via MSMS-Chooser for automatic spectral annotation, and output a GNPS-formatted table with the option to launch MASST searches.