MetaProClust-MS1

MetaProClust-MS1 performs high-throughput MS1-only profiling and clustering to prioritize microbiome and proteome samples for downstream MS/MS-based metaproteomic analysis.

Key Features:

• MS1-Only Profiling: Uses short 15-minute MS1-only chromatographic gradients to screen proteomic features, reducing acquisition time relative to long liquid chromatography (LC)-MS/MS methods.
• Robust Sample Prioritization: Clusters samples based on MS1 profiles to identify robust microbial community responses and prioritize specimens for in-depth metaproteomic characterization.
• Comparative Analysis Capability: Validated on data acquired with both short and long chromatographic gradients and produces cluster topologies that correlate significantly with MS/MS-acquired data.
• Clinical Diagnostic Potential: Differentiates ulcerative colitis and Crohn's disease using mucosal luminal interface samples and detects proteome shifts in Alzheimer’s disease mouse models following small-molecule treatment.
• Generalizability: Applicable to single-species proteomes and broader proteomics experiments beyond microbiome studies.

Scientific Applications:

• Large-scale metaproteomic screening: Rapidly screens complex microbial communities using MS1-only profiles to prioritize samples for follow-up MS/MS.
• Gut microbiome research: Enables prioritization of samples for LC-MS/MS to study associations between microbiome composition/function and health or disease states.
• Clinical diagnostics and therapeutic evaluation: Supports differentiation of inflammatory bowel disease diagnoses and evaluation of proteome responses to small-molecule treatment in Alzheimer’s disease models.
• Single-species proteome screening: Applies the same MS1-based screening approach to single-species proteomes for broad proteomics applications.

Methodology:

Performs MS1-only profiling using short 15-minute chromatographic gradients and clusters samples based on their MS1 profiles, with validation by comparing cluster topologies to MS/MS-acquired data from short and long chromatographic gradients.