Do Not Waste Time─Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38294351", "kind": "science-record", "revision": 2, "content_hash": "sha256:8a2b76723a2abb4bea62eed318d102dc76557bde0393e3c96aeece6fe6111643", "created_at": "2026-11-01T19:20:13Z", "updated_at": "2026-11-01T21:32:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Do Not Waste Time─Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin.", "doi": "10.1021/acs.analchem.3c04682", "pmid": "38294351", "authors": ["Lucienne Nouchikian", "David Fernandez-Martinez", "Pierre-Yves Renard", "Cyrille Sabot", "Guillaume Duménil", "Martial Rey", "Julia Chamot-Rooke"], "journal": "Analytical chemistry", "year": 2024, "abstract": "Cross-linking mass spectrometry (XL-MS) has become a very useful tool for studying protein complexes and interactions in living systems. It enables the investigation of many large and dynamic assemblies in their native state, providing an unbiased view of their protein interactions and restraints for integrative modeling. More researchers are turning toward trying XL-MS to probe their complexes of interest, especially in their native environments. However, due to the presence of other potentially higher abundant proteins, sufficient cross-links on a system of interest may not be reached to achieve satisfactory structural and interaction information. There are currently no rules for predicting whether XL-MS experiments are likely to work or not; in other words, if a protein complex of interest will lead to useful XL-MS data. Here, we show that a simple iBAQ (intensity-based absolute quantification) analysis performed from trypsin digest data can provide a good understanding of whether proteins of interest are abundant enough to achieve successful cross-linking data. Comparing our findings to large-scale data on diverse systems from several other groups, we show that proteins of interest should be at least in the top 20% abundance range to expect more than one cross-link found per protein. We foresee that this guideline is a good starting point for researchers who would like to use XL-MS to study their protein of interest and help ensure a successful cross-linking experiment from the beginning. Data are available via ProteomeXchange with identifier PXD045792.", "claims": [{"id": "claim-method", "statement": "Here, we show that a simple iBAQ (intensity-based absolute quantification) analysis performed from trypsin digest data can provide a good understanding of whether proteins of interest are abundant enough to achieve successful cross-linking data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38294351", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we show that a simple iBAQ (intensity-based absolute quantification) analysis performed from trypsin digest data can provide a good understanding of whether proteins of interest are abundant enough to achieve successful cross-linking data."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All raw data, parameter files, and processed data have been deposited to the ProteomeXchange Consortium via the PRIDE35 partner repository with the data set identifier PXD045792.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38294351", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "All raw data, parameter files, and processed data have been deposited to the ProteomeXchange Consortium via the PRIDE35 partner repository with the data set identifier PXD045792."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Comparing our findings to large-scale data on diverse systems from several other groups, we show that proteins of interest should be at least in the top 20% abundance range to expect more than one cross-link found per protein.", "kind": "quantitative", "target": {"value": 20.0, "unit": "per cent", "tolerance": null, "source": "Comparing our findings to large-scale data on diverse systems from several other groups, we show that proteins of interest should be at least in the top 20% abundance range to expect more than one cross-link found per protein."}, "evidence": [{"asset": "source:pmid:38294351", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Comparing our findings to large-scale data on diverse systems from several other groups, we show that proteins of interest should be at least in the top 20% abundance range to expect more than one cross-link found per protein."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Comparing our findings to large-scale data on diverse systems from several other groups, we show that proteins of interest should be at least in the top 20% abundance range to expect more than one cross-link found per protein.", "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:38294351"], "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:PXD021553"], "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:PXD021553"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38294351", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1021/acs.analchem.3c04682", "sha256": "sha256:7f16ffdd19c10640fec0ceabb60d2f6785cd121c6e4c750d29b91d1fb51b2d42", "bytes": 38244, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1021/acs.analchem.3c04682", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10867798", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD021553", "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=PXD021553", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD021553", "version": null, "note": "All raw data, parameter files, and processed data have been deposited to the ProteomeXchange Consortium via the PRIDE35 partner repository with the data set identifier PXD045792.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All raw data, parameter files, and processed data have been deposited to the ProteomeXchange Consortium via the PRIDE35 partner repository with the data set identifier PXD045792.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "A simplified in vivo cross-linking mass spectrometry strategy for proteome-wide studies.", "resolution_checked_at": "2026-11-01T19:09:50Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD045792", "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=PXD045792", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD045792", "version": null, "note": "All raw data, parameter files, and processed data have been deposited to the ProteomeXchange Consortium via the PRIDE35 partner repository with the data set identifier PXD045792.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All raw data, parameter files, and processed data have been deposited to the ProteomeXchange Consortium via the PRIDE35 partner repository with the data set identifier PXD045792.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Don’t Waste Time – Ensure Success in Your Cross-Linking Mass Spectrometry Experiments Before You Begin.", "resolution_checked_at": "2026-11-01T19:09:50Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD021553 not downloaded", "asset:data:geo:PXD021553 licence not read", "asset:data:geo:PXD045792 not downloaded", "asset:data:geo:PXD045792 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "iBAQ (intensity-based absolute quantification) analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Here, we show that a simple iBAQ (intensity-based absolute quantification) analysis performed from trypsin digest data can provide a good understanding of whether proteins of interest are abundant enough to achieve successful cross-linking data."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 20.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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 (iBAQ (intensity-based absolute quantification) analysis), 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": ["PXD045792", "PXD021553"], "resolved_accessions": ["PXD045792", "PXD021553"], "statements": ["All raw data, parameter files, and processed data have been deposited to the ProteomeXchange Consortium via the PRIDE35 partner repository with the data set identifier PXD045792."], "basis": "The paper names PXD045792, PXD021553 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:38294351", "data:geo:PXD021553"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD021553"]}, "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": "2026-11-01T19:07:04Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10280, "completion_tokens": 1444, "cached_tokens": 128}}, "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:38294351", "type": "paper", "label": "pmid:38294351"}, {"id": "source:pmid:38294351", "type": "manuscript", "label": "PMID 38294351 full text"}, {"id": "data:geo:PXD021553", "type": "dataset", "label": "GEO PXD021553"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38294351", "type": "paper", "label": "pmid:38294351"}, {"id": "source:pmid:38294351", "type": "manuscript", "label": "PMID 38294351 full text"}, {"id": "data:geo:PXD021553", "type": "dataset", "label": "GEO PXD021553"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38294351", "type": "extraction", "used": ["source:pmid:38294351"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD021553", "type": "accession_resolution", "used": ["data:geo:PXD021553"], "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:38294351", "parent_hash": "sha256:488e99304b2f0111c1cfd64090f90428a96ac1714c36c27225fc5f503724f05b", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:PXD021553 licence not read", "asset:data:geo:PXD021553 not downloaded", "asset:data:geo:PXD045792 licence not read", "asset:data:geo:PXD045792 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["te Time─Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin.", "Cross-linking mass spectrometry (XL-MS) has become a very useful tool for st"], "order_basis": "paper_text_order:10", "id": "assay:1"}]}