biostudies-literatureSimopoulos CMAGouvernement du Canada | Natural Sciences and Engineering Research Council of CanadaOntario GenomicsOntario Ministry of Economic Development and InnovationGenome Canadae0038122https://www.ebi.ac.uk/biostudies/studies/S-EPMC9426440biostudies-literatureUnknown7(4)Metaproteomics is used to explore the functional dynamics of microbial communities. However, acquiring metaproteomic data by tandem mass spectrometry (MS/MS) is time-consuming and resource-intensive, and there is a demand for computational methods that can be used to reduce these resource requirements. We present MetaProClust-MS1, a computational framework for microbiome feature screening developed to prioritize samples for follow-up MS/MS. In this proof-of-concept study, we tested and compared MetaProClust-MS1 results on gut microbiome data, from fecal samples, acquired using short 15-min MS1-only chromatographic gradients and MS1 spectra from longer 60-min gradients to MS/MS-acquired data. We found that MetaProClust-MS1 identified robust gut microbiome responses caused by xenobiotics witmSystemsMetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening.PMC9426440OGI-149ORF-DIG 14405OGI-156CREATE in Technologies for Microbiome Science and Engineering (TECHNOMISE)210034Discovery GrantSimopoulos CMAKhamis MMFigeys DZhang XLavallee-Adam MNing ZLi LfalseMetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening.Metaproteomics is used to explore the functional dynamics of microbial communities. However, acquiring metaproteomic data by tandem mass spectrometry (MS/MS) is time-consuming and resource-intensive, and there is a demand for computational methods that can be used to reduce these resource requirements. We present MetaProClust-MS1, a computational framework for microbiome feature screening developed to prioritize samples for follow-up MS/MS. In this proof-of-concept study, we tested and compared MetaProClust-MS1 results on gut microbiome data, from fecal samples, acquired using short 15-min MS1-only chromatographic gradients and MS1 spectra from longer 60-min gradients to MS/MS-acquired data. We found that MetaProClust-MS1 identified robust gut microbiome responses caused by xenobiotics wit2022-01-01T00:00:00Z2022 Aug2026-06-13T06:03:45.225Z2025-02-19T03:28:56.604ZS-EPMC94264403595076210.1128/msystems.00381-22