Reversible Click Chemistry Tag for Universal Proteome Sample Preparation for Top-Down and Bottom-Up Analysis.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34524823", "kind": "science-record", "revision": 3, "content_hash": "sha256:d45d9e77b9001a558c5a5d978514682a778700d365904ce5565f14828d585395", "created_at": "2026-11-01T17:36:06Z", "updated_at": "2026-11-01T21:26:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Reversible Click Chemistry Tag for Universal Proteome Sample Preparation for Top-Down and Bottom-Up Analysis.", "doi": "10.1021/acs.jproteome.1c00443", "pmid": "34524823", "authors": ["Stephanie Biedka", "Brigitte F Schmidt", "Nolan M Frey", "Sarah M Boothman", "Jonathan S Minden", "Amber Lee Wilson"], "journal": "Journal of proteome research", "year": 2021, "abstract": "Successful proteome analysis requires reliable sample preparation beginning with protein solubilization and ending with a sample free of contaminants, ready for downstream analysis. Most proteome sample preparation technologies utilize precipitation or filter-based separation, both of which have significant disadvantages. None of the current technologies are able to prepare both intact proteins or digested peptides. Here, we introduce a reversible protein tag, ProMTag, that enables whole proteome capture, cleanup, and release of intact proteins for top-down analysis. Alternatively, the addition of a novel Trypsin derivative to the workflow generates peptides for bottom-up analysis. We show that the ProMTag workflow yields >90% for intact proteins and >85% for proteome digests. For top-down analysis, ProMTag cleanup improves resolution on 2D gels; for bottom-up exploration, this methodology produced reproducible mass spectrometry results, demonstrating that the ProMTag method is a truly universal approach that produces high-quality proteome samples compatible with multiple downstream analytical techniques. Data are available via ProteomeXchange with identifier PXD027799.", "claims": [{"id": "claim-method", "statement": "Proteins were held to a false discovery rate of 1%, using standard approaches described previously.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34524823", "locator": "sections[14] \"MS Analysis of Peptides after Precipitation/in-Solution Digestion or ProMTag Cleanup\" paragraph 5", "quote": "Proteins were held to a false discovery rate of 1%, using standard approaches described previously."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD027799.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34524823", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD027799."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We show that the ProMTag workflow yields >90% for intact proteins and >85% for proteome digests.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34524823", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We show that the ProMTag workflow yields >90% for intact proteins and >85% for proteome digests."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We show that the ProMTag workflow yields >90% for intact proteins and >85% for proteome digests.", "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:34524823"], "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:PXD027799"], "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:PXD027799"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34524823", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1021/acs.jproteome.1c00443", "sha256": "sha256:8e0a40499f39fc52e720367bf06edaf1cb8f7b7c3a6bebe75c0b910d00f0de0f", "bytes": 53605, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1021/acs.jproteome.1c00443", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9392872", "source": "ncbi_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD027799", "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=PXD027799", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD027799", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD027799.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD027799.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Reversible Click Chemistry Tag for Universal Proteome Sample Preparation", "resolution_checked_at": "2026-11-01T17:30:50Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD027799 not downloaded", "asset:data:geo:PXD027799 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "False discovery rate control at 1%", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Proteins were held to a false discovery rate of 1%, using standard approaches described previously."}}], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (False discovery rate control at 1%), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["PXD027799"], "resolved_accessions": ["PXD027799"], "statements": ["Data are available via ProteomeXchange with identifier PXD027799."], "basis": "The paper names PXD027799 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:34524823", "data:geo:PXD027799"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD027799"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:02:49Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15321, "completion_tokens": 1012, "cached_tokens": 256}}, "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:34524823", "type": "paper", "label": "pmid:34524823"}, {"id": "source:pmid:34524823", "type": "manuscript", "label": "PMID 34524823 full text"}, {"id": "data:geo:PXD027799", "type": "dataset", "label": "GEO PXD027799"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34524823", "type": "paper", "label": "pmid:34524823"}, {"id": "source:pmid:34524823", "type": "manuscript", "label": "PMID 34524823 full text"}, {"id": "data:geo:PXD027799", "type": "dataset", "label": "GEO PXD027799"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34524823", "type": "extraction", "used": ["source:pmid:34524823"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD027799", "type": "accession_resolution", "used": ["data:geo:PXD027799"], "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:34524823", "parent_hash": "sha256:01eb2ada5de5c98c3df9b576b4c7b22be594225a29fb575f28cd19e6aae5da42", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD027799 licence not read", "asset:data:geo:PXD027799 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}