Dataset of a comparative proteomics experiment in a methylmalonyl-CoA mutase knockout HEK 293 cell model.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33195772", "kind": "science-record", "revision": 6, "content_hash": "sha256:03484bd222b7e3104c4d406175f053346a5472ad9da6983977cd9d01723a4cd9", "created_at": "2026-11-01T15:41:16Z", "updated_at": "2026-11-01T21:24:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dataset of a comparative proteomics experiment in a methylmalonyl-CoA mutase knockout HEK 293 cell model.", "doi": "10.1016/j.dib.2020.106453", "pmid": "33195772", "authors": ["Michele Costanzo", "Marianna Caterino", "Armando Cevenini", "Vincent Jung", "Cerina Chhuon", "Joanna Lipecka", "Roberta Fedele", "Ida Chiara Guerrera", "Margherita Ruoppolo"], "journal": "Data in brief", "year": 2020, "abstract": "Methylmalonic acidemia is a rare inborn error of metabolism with severe clinical complications and poor outcome. The present data article is related to a proteomic investigation conducted on a HEK 293 cell line which has been genetically modified using CRISPR-CAS9 system to knockout the methylmalonyl-CoA mutase enzyme (MUT-KO). Thus, the generated cell model for methylmalonic acidemia was used for a proteomic comparison with respect to HEK 293 wild type cells performing a label-free quantification (LFQ) experiment. A comparison between FASP and S-Trap digestion methods was performed on protein extracts before to proceed with the proteomic analysis of the samples. Four biological replicates were employed for LC-MS/MS analysis and each was run in technical triplicates. MaxQuant and Perseus platforms were used to perform the LFQ of the proteomes and carry out statistical analysis, respectively. Globally, 4341 proteins were identified, and 243 as differentially regulated, of which 150 down-regulated and 93 up-regulated in the MUT-KO condition. MS proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD017977. The information provided in this dataset shed new light on the cellular mechanisms altered in this rare metabolic disorder, highlighting quantitative unbalances in proteins acting in cell structure and architecture organization and response to the stress. This article can be used as a new source of protein actors to be validated and a starting point for the identification of clinically relevant therapeutic targets.", "claims": [{"id": "claim-method", "statement": "MaxQuant software (version 1.5.8.3) was employed to perform the LFQ analysis of the proteomes, while the Perseus platform (version 1.6.0.7) to carry out data visualization and statistical analysis [2].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33195772", "locator": "sections[7] \"Data processing\" paragraph 2", "quote": "MaxQuant software (version 1.5.8.3) was employed to perform the LFQ analysis of the proteomes, while the Perseus platform (version 1.6.0.7) to carry out data visualization and statistical analysis [2]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw MS proteomics data have been deposited to the ProteomeXchange Consortium (available at http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD017977", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33195772", "locator": "sections[1] \"Specifications Table\" paragraph 2", "quote": "Raw MS proteomics data have been deposited to the ProteomeXchange Consortium (available at http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD017977"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33195772"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD017977"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD017977"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33195772", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2020.106453", "sha256": "sha256:a1f587df309b01c30597181f4b28328fb30b0d37d179f4e76beb53bbd597fb39", "bytes": 10866, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2020.106453", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7644733", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD017977", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD017977", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD017977", "version": null, "note": "Raw MS proteomics data have been deposited to the ProteomeXchange Consortium (available at http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD017977", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw MS proteomics data have been deposited to the ProteomeXchange Consortium (available at http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD017977", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomics cell model with gene MUT KO", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33195772:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e62b191e29706e76953fc02c15c193242f599647c93d3cc74c7045919d12ffca", "bytes": 1712, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#utbl0001", "version": null, "note": null, "structure": {"pmcid": "PMC7644733", "section_index": 1, "section_title": "Specifications Table", "row_count": 10, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject", "Biochemistry"], ["Specific subject area", "Proteomics, inborn errors of metabolism"], ["Type of data", "FiguresTable"], ["How data were acquired", "LC-MS/MS analysis on a nanoRSLC-Q Exactive PLUS (RSLC Ultimate 3000) (Thermo Scientific)"], ["Data format", "AnalyzedFiltered"], ["Parameters for data collection", "Total proteins were extracted from two different HEK 293 cell lines. One was a wild type (WT) cell line. The second one was a cell line developed as cellular model for methylmalonic acidemia after knockout of methylmalonyl-CoA mutase enzyme (MUT-KO)."], ["Description of data collection", "The knockout of methylmalonyl-CoA mutase was tested to ensure it was stable over the time. MUT-KO and WT cells were cultured for the same time and in the same conditions before to be collected for proteome extraction. 4 biological replicates per condition were cultured independently."], ["Data source location", "CEINGE – Biotecnologie Avanzate s.c.ar.l., Naples, ItalyProteomics Platform Necker, Paris, France"], ["Data accessibility", "Raw MS proteomics data have been deposited to the ProteomeXchange Consortium (available at http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD017977"], ["Related research article", "Costanzo M, Caterino M, Cevenini A, Jung V, Chhuon C, Lipecka J, Fedele R, Guerrera IC, Ruoppolo M. Proteomics Reveals that Methylmalonyl-CoA Mutase Modulates Cell Architecture and Increases Susceptibility to Stress. Int J Mol Sci. 2020 Jul 15;21(14):E4998. https://doi.org/10.3390/ijms21144998"]], "row_count": 10, "column_count": 2, "numeric_cells": 5, "header_rows": 0, "locator": "section[1]/table-wrap[1]#utbl0001"}}], "gaps": ["asset:data:geo:PXD017977 not downloaded", "asset:data:geo:PXD017977 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson's correlation"}}, {"id": "method-2", "family": null, "specific": null, "label": "Label-free quantification (LFQ)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "MaxQuant software (version 1.5.8.3) was employed to perform the LFQ analysis of the proteomes, while the Perseus platform (version 1.6.0.7) to carry out data visualization and statistical analysis [2]."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD017977"], "resolved_accessions": ["PXD017977"], "statements": ["Raw MS proteomics data have been deposited to the ProteomeXchange Consortium (available at http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD017977"], "basis": "The paper names PXD017977 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pearson_r"], "assets": ["source:pmid:33195772", "data:geo:PXD017977", "asset:table:pmid:33195772:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD017977"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:16Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 9777, "completion_tokens": 1418, "cached_tokens": 792}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33195772", "type": "paper", "label": "pmid:33195772"}, {"id": "source:pmid:33195772", "type": "manuscript", "label": "PMID 33195772 full text"}, {"id": "data:geo:PXD017977", "type": "dataset", "label": "GEO PXD017977"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33195772", "type": "paper", "label": "pmid:33195772"}, {"id": "source:pmid:33195772", "type": "manuscript", "label": "PMID 33195772 full text"}, {"id": "data:geo:PXD017977", "type": "dataset", "label": "GEO PXD017977"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33195772", "type": "extraction", "used": ["source:pmid:33195772"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD017977", "type": "accession_resolution", "used": ["data:geo:PXD017977"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33195772", "parent_hash": "sha256:0477162a4ab2f63b03f50e873f75e69b442673d4fb4b11b8ce40baba5067677a", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD017977 licence not read", "asset:data:geo:PXD017977 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["ne which has been genetically modified using CRISPR-CAS9 system to knockout the methylmalonyl-Co"], "order_basis": "paper_text_order:314", "id": "assay:1"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Pearson's correlation"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}