ChipFilter: Microfluidic-Based Comprehensive Sample Preparation Methodology for Microbial Consortia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38353246", "kind": "science-record", "revision": 3, "content_hash": "sha256:0083f9eddf955a263ee87a721823ada26ec2e36615486c7780ee3775a7886d29", "created_at": "2026-11-01T19:20:17Z", "updated_at": "2026-11-01T22:11:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "ChipFilter: Microfluidic-Based Comprehensive Sample Preparation Methodology for Microbial Consortia.", "doi": "10.1021/acs.jproteome.3c00288", "pmid": "38353246", "authors": ["Ranjith Kumar Ravi Kumar", "Massamba Mbacke Ndiaye", "Iman Haddad", "Joelle Vinh", "Yann Verdier"], "journal": "Journal of proteome research", "year": 2024, "abstract": "The metaproteomic approach is an attractive way to describe a microbiome at the functional level, allowing the identification and quantification of proteins across a broad dynamic range as well as the detection of post-translational modifications. However, it remains relatively underutilized, mainly due to technical challenges that should be addressed, including the complexity of extracting proteins from heterogeneous microbial communities. Here, we show that a ChipFilter microfluidic device coupled to a liquid chromatography tandem mass spectrometry (LC-MS/MS) setup can be successfully used for the identification of microbial proteins. Using cultures of Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae, we have shown that it is possible to directly lyse the cells and digest the proteins in the ChipFilter to allow the identification of a higher number of proteins and peptides than that by standard protocols, even at low cell density. The peptides produced are overall longer after ChipFilter digestion but show no change in their degree of hydrophobicity. Analysis of a more complex mixture of 17 species from the gut microbiome showed that the ChipFilter preparation was able to identify and estimate the amounts of 16 of these species. These results show that ChipFilter can be used for the proteomic study of microbiomes, particularly in the case of a low volume or cell density. The mass spectrometry data have been deposited on the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD039581.", "claims": [{"id": "claim-method", "statement": "Statistical tests to identify significance (unpaired t-test) were performed, and values shown always represent mean ± standard error of the mean.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38353246", "locator": "sections[9] \"Data Analysis\" paragraph 5", "quote": "Statistical tests to identify significance (unpaired t-test) were performed, and values shown always represent mean ± standard error of the mean."}], "state": "complete"}, {"id": "claim-target-result", "statement": "ChipFilter can be used for the proteomic study of microbiomes, particularly in the case of a low volume or cell density.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38353246", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "These results show that ChipFilter can be used for the proteomic study of microbiomes, particularly in the case of a low volume or cell density."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "ChipFilter can be used for the proteomic study of microbiomes, particularly in the case of a low volume or cell density.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38353246"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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The mass spectrometry data have been deposited on the ProteomeXcha", "uid chromatography tandem mass spectrometry (LC-MS/MS) setup can be successfully used for the iden", "chased from Fisher Scientific. Trypsin Gold, mass spectrometry grade, was provided by Promega, and lysozyme"], "order_basis": "paper_text_order:595", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["0.01 to 0.0009% considering the cell number. Murine feces were collected from healthy female mur", "ine feces were collected from healthy female murine housed in the Brain Plasticity Laboratory, E", "s compatible with the use of the ChipFilter, mouse feces samples were analyzed in the device. 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