{"doi":"10.1016/j.mcpro.2021.100139","title":"IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics","abstract":"Proteomics methodology has expanded to include protein structural analysis, primarily through cross-linking mass spectrometry (XL-MS) and hydrogen-deuterium exchange mass spectrometry (HX-MS). However, while the structural proteomics community has effective tools for primary data analysis, there is a need for structure modeling pipelines that are accessible to the proteomics specialist. Integrative structural biology requires the aggregation of multiple distinct types of data to generate models that satisfy all inputs. Here, we describe IMProv, an app in the Mass Spec Studio that combines XL-MS data with other structural data, such as cryo-EM densities and crystallographic structures, for integrative structure modeling on high-performance computing platforms. The resource provides an easily deployed bundle that includes the open-source Integrative Modeling Platform program (IMP) and its dependencies. IMProv also provides functionality to adjust cross-link distance restraints according to the underlying dynamics of cross-linked sites, as characterized by HX-MS. A dynamics-driven conditioning of restraint values can improve structure modeling precision, as illustrated by an integrative structure of the five-membered Polycomb Repressive Complex 2. IMProv is extensible to additional types of data.","journal":"Molecular & Cellular Proteomics","year":2021,"id":179680,"datarank":0.7203389049239035,"base_score":2.9444389791664403,"endowment":2.9444389791664403,"self_citation_contribution":0.44166584687496613,"citation_network_contribution":0.27867305804893744,"self_endowment_contribution":0.44166584687496613,"citer_contribution":0.27867305804893744,"corpus_percentile":72.14357546221088,"corpus_rank":3602,"citation_count":18,"citer_count":15,"citers_with_citation_signal":12,"citers_with_endowment":12,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6846,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":50.0,"fair_percentile":62.702537450321,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":103663,"name":"Daniel J. Saltzberg","orcid":"0000-0001-8641-6194","position":1,"is_corresponding":false},{"id":727351,"name":"Troy J. Pells","orcid":"0000-0002-2340-5356","position":2,"is_corresponding":false},{"id":727352,"name":"D. Alex Crowder","orcid":"0000-0001-6833-5542","position":3,"is_corresponding":false},{"id":727353,"name":"Christoph U. Schräder","orcid":"0000-0002-0461-3782","position":4,"is_corresponding":false},{"id":727354,"name":"Morgan Hepburn","orcid":"0000-0002-0611-4004","position":5,"is_corresponding":false},{"id":91660,"name":"Andrej Săli","orcid":"0000-0003-0435-6197","position":6,"is_corresponding":false},{"id":727355,"name":"David C. Schriemer","orcid":"0000-0002-5202-1618","position":7,"is_corresponding":false},{"id":727350,"name":"Daniel S. Ziemianowicz","orcid":"0000-0002-6164-2723","position":0,"is_corresponding":true}],"reference_count":77,"raw_metadata":null,"created_at":"2026-07-18T23:47:48.974996Z","pmid":"34418567","pmcid":"PMC8452774","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":55.5556,"fair_a":25.0,"fair_i":0.0,"fair_r":33.3333,"fair_zscore":0.6155,"fair_rationale":{"fair_score":50.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":55.56,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"PXD022861","grounded":true,"rationale":"The paper provides the PRIDE accession PXD022861, which is a persistent identifier scheme accepted in the FAIR data maturity model.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"PRIDE partner repository","grounded":true,"rationale":"The paper names the PRIDE partner repository as the holder of the data, which is a proper noun that is a repository.","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Data Availability All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","grounded":false,"rationale":"The statement points to a repository record (PRIDE with accession PXD022861), which is Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","grounded":false,"rationale":"The dataset is described in a single sentence in running prose; no itemised inventory (section, table, or list) is provided. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","grounded":false,"rationale":"The dataset identifier PXD022861 appears only in the body text (Data Availability section) and not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":25.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","grounded":false,"rationale":"The data are deposited in a public repository (PRIDE) with no stated precondition such as embargo, registration, or application. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","grounded":false,"rationale":"The paper describes the access action of depositing data to PRIDE, but does not apply an explicit access-level label such as 'open access' to the data themselves. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are proteomics data, not sensitive human-subject data, and no gatekeeper is named; the paper does not discuss access restrictions.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","grounded":false,"rationale":"The paper states that the data have been deposited (availability timing) but does not specify how long they will persist. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":0.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format token is named for the released data.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No community standard checklist, ontology, or metadata schema from FAIRsharing is named for the data.","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"6C23","grounded":false,"rationale":"The paper references PDB IDs (6C23, 5WAI, etc.) for structures used in the study. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":33.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not state any licence for the data; the CC BY license applies to the article, not the data.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Orbitrap Fusion Lumos (Thermo Scientific)","grounded":true,"rationale":"The paper names specific instruments and software used to produce the data, such as the Orbitrap Fusion Lumos mass spectrometer.","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","grounded":false,"rationale":"The paper does not name a documentation object like a README or codebook that travels with the data; variable/field definitions are provided inside the article (e.g., Table 1). [downgraded to 'no' — no verifiable quote from the paper]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No version token or date is provided for the dataset; the accession PXD022861 does not carry a version suffix.","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"www.msstudio.ca","grounded":true,"rationale":"The code is available at a project website (www.msstudio.ca), which is a non-authoritative location (not a code repository or archive DOI).","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"RGPIN-2017-04879","grounded":true,"rationale":"The paper includes award/grant numbers for the funding agencies, such as NSERC RGPIN-2017-04879.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not state any licence for the data; the CC BY license applies to the article, not the data.","gain":16.67,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","why":"The data are deposited in a public repository (PRIDE) with no stated precondition such as embargo, registration, or application. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","why":"The dataset identifier PXD022861 appears only in the body text (Data Availability section) and not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open proteomics formats such as mzML or mzIdentML.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format token is named for the released data.","gain":8.33,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"www.msstudio.ca","why":"The code is available at a project website (www.msstudio.ca), which is a non-authoritative location (not a code repository or archive DOI).","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No version token or date is provided for the dataset; the accession PXD022861 does not carry a version suffix.","gain":4.17,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data Availability All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","why":"The statement points to a repository record (PRIDE with accession PXD022861), which is Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","why":"The dataset is described in a single sentence in running prose; no itemised inventory (section, table, or list) is provided. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","why":"The paper describes the access action of depositing data to PRIDE, but does not apply an explicit access-level label such as 'open access' to the data themselves. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In proteomics, describe the data with mzML or MIAPE.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No community standard checklist, ontology, or metadata schema from FAIRsharing is named for the data.","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","why":"The paper does not name a documentation object like a README or codebook that travels with the data; variable/field definitions are provided inside the article (e.g., Table 1). [downgraded to 'no' — no verifiable quote from the paper]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are proteomics data, not sensitive human-subject data, and no gatekeeper is named; the paper does not discuss access restrictions.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"6C23","why":"The paper references PDB IDs (6C23, 5WAI, etc.) for structures used in the study. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All LC-MS and LC-MS/MS data generated to support the findings of this study (including all cross-links identified and their categorization, as well as tables supporting the HX-MS analysis) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (75) with the dataset identifier PXD022861.","why":"The paper states that the data have been deposited (availability timing) but does not specify how long they will persist. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open proteomics formats such as mzML or mzIdentML.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI)."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:59:03.167648Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}