{"doi":"10.1038/s41597-024-04047-9","title":"Borrelia PeptideAtlas: A proteome resource of common Borrelia burgdorferi isolates for Lyme research","abstract":"Lyme disease is caused by an infection with the spirochete Borrelia burgdorferi, and is the most common vector-borne disease in North America. B. burgdorferi isolates harbor extensive genomic and proteomic variability and further comparison of isolates is key to understanding the infectivity of the spirochetes and biological impacts of identified sequence variants. Here, we applied both transcriptome analysis and mass spectrometry-based proteomics to assemble peptide datasets of B. burgdorferi laboratory isolates B31, MM1, and the infective isolate B31-5A4, to provide a publicly available Borrelia PeptideAtlas. Included are total proteome, secretome, and membrane proteome identifications of the individual isolates. Proteomic data collected from 35 different experiment datasets, totaling 386 mass spectrometry runs, have identified 81,967 distinct peptides, which map to 1,113 proteins. The Borrelia PeptideAtlas covers 86% of the total B31 proteome of 1,291 protein sequences. The Borrelia PeptideAtlas is an extensible comprehensive peptide repository with proteomic information from B. burgdorferi isolates useful for Lyme disease research.","journal":"Scientific Data","year":2024,"id":492516,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":22.178386323199504,"corpus_rank":9377,"citation_count":1,"citer_count":1,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5654,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":45.8333,"fair_percentile":59.49250993579945,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":557232,"name":"Zhi Sun","orcid":"0000-0003-3324-6851","position":1,"is_corresponding":false},{"id":667930,"name":"Helisa H. Wippel","orcid":"0000-0002-9811-6700","position":2,"is_corresponding":false},{"id":1066863,"name":"David Baxter","orcid":"0000-0003-4468-2069","position":3,"is_corresponding":false},{"id":237003,"name":"Kristian E. Swearingen","orcid":"0000-0002-6756-4471","position":4,"is_corresponding":false},{"id":432655,"name":"David Shteynberg","orcid":"0000-0001-7982-0498","position":5,"is_corresponding":false},{"id":146014,"name":"Mukul K. Midha","orcid":"0000-0003-4053-0682","position":6,"is_corresponding":false},{"id":344003,"name":"Melissa J. Caimano","orcid":"0000-0003-1170-4102","position":7,"is_corresponding":false},{"id":482773,"name":"Klemen Strle","orcid":"0000-0002-0109-6791","position":8,"is_corresponding":false},{"id":323624,"name":"Yongwook Choi","orcid":"0000-0003-4017-9669","position":9,"is_corresponding":false},{"id":18785,"name":"Agnes P. Chan","orcid":"0000-0003-2373-9580","position":10,"is_corresponding":false},{"id":51360,"name":"Nicholas J. Schork","orcid":"0000-0003-0920-5013","position":11,"is_corresponding":false},{"id":778654,"name":"Andrea S. Varela‐Stokes","orcid":"0000-0002-3991-9730","position":12,"is_corresponding":false},{"id":78845,"name":"Robert L. Moritz","orcid":"0000-0002-3216-9447","position":13,"is_corresponding":false},{"id":627756,"name":"Panga Jaipal Reddy","orcid":"0000-0002-4481-3631","position":0,"is_corresponding":true}],"reference_count":66,"raw_metadata":null,"created_at":"2026-07-19T02:08:56.210382Z","pmid":"39622905","pmcid":"PMC11612207","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":50.0,"fair_a":37.5,"fair_i":0.0,"fair_r":50.0,"fair_zscore":0.4506,"fair_rationale":{"fair_score":45.83,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All MS data and Supplementary Tables for the Borrelia PeptideAtlas is available and deposited at the EBI PRIDE repository at https://www.ebi.ac.uk/pride/archive/projects/PXD046281 and https://doi.org/10.6019/PXD046281.","grounded":false,"rationale":"The paper gives a DOI (10.6019/PXD046281) and a PRIDE accession, both persistent identifiers, for the dataset. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","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":"deposited to the ProteomeXchange Consortium via the PRIDE40 partner repository","grounded":true,"rationale":"PRIDE is a named data repository listed in re3data/FAIRsharing. [majority verdict 'yes' (3/5 passes agreed)]","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":"All MS data and Supplementary Tables for the Borrelia PeptideAtlas is available and deposited at the EBI PRIDE repository at https://www.ebi.ac.uk/pride/archive/projects/PXD046281 and https://doi.org/10.6019/PXD046281.","grounded":false,"rationale":"The data-availability statement points to a repository record with a DOI/link, corresponding to Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","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":"Mass spectrometry data from 35 different experiments using laboratory isolates B31 and MM1, and infective B31-5A4, with a total of 358 DDA- and 28 DIA-MS runs (Thermo Scientific instrument .raw files, Bruker instruments.d files), were uniformly analyzed through the TPP pipeline (see Methods) and deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046281.","grounded":false,"rationale":"The Data Records section describes the dataset in running prose; there is no itemised inventory of files or variables. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 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":0.5,"verdict":"partial","evidence":"The mass spectrometry data was deposited to the ProteomeXchange Consortium via the PRIDE40 partner repository with the dataset identifier PXD04628141.","grounded":true,"rationale":"The dataset identifier appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (4/5 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":37.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All MS data and Supplementary Tables for the Borrelia PeptideAtlas is available and deposited at the EBI PRIDE repository at https://www.ebi.ac.uk/pride/archive/projects/PXD046281 and https://doi.org/10.6019/PXD046281.","grounded":false,"rationale":"The data are freely and openly accessible via a public repository with no stated precondition. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":0.5,"verdict":"partial","evidence":null,"grounded":false,"rationale":"The paper labels the data as 'publicly available' in the abstract, which is a natural-language equivalent of 'open access'. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":"All MS data and Supplementary Tables for the Borrelia PeptideAtlas is available and deposited at the EBI PRIDE repository at https://www.ebi.ac.uk/pride/archive/projects/PXD046281 and https://doi.org/10.6019/PXD046281.","grounded":false,"rationale":"The data are not human-subject or sensitive, and no gatekeeper of any kind is named; the data are openly available with no access control.","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":"deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046281","grounded":false,"rationale":"The paper states the data are deposited and available now, but does not commit to any retention period or permanent archival claim. [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":"The paper does not name the file format of the released data; it mentions raw formats (.raw, .d, .wiff) but these are proprietary and not stated as the deposit format. [majority verdict 'no' (3/5 passes agreed)]","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":"adhering to FAIR (Findability, Accessibility, Interoperability, and Reusability) principles","grounded":true,"rationale":"The paper does not name a specific data or metadata community standard (e.g., MIAME, ISA-Tab, an ontology); FAIR principles are not a standard.","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":"For isolate B31, the UniProt proteome (ProteomeID UP0000018079)","grounded":false,"rationale":"The paper provides a UniProt proteome identifier (UP0000018079) for an external reference database used in the analysis. [downgraded to 'no' — no verifiable quote from the paper]","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":50.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License","grounded":true,"rationale":"The only license mentioned is for the article itself, not for the data; no license artefact is attached to the dataset.","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":"Q-Exactive HF mass spectrometer (Thermo Fisher Scientific)","grounded":true,"rationale":"The paper names specific instruments (e.g., Q-Exactive HF) and software used to produce the data. [majority verdict 'yes' (4/5 passes agreed)]","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":1.0,"verdict":"yes","evidence":"Supplementary Tables 1–6 are also deposited in the same PRIDE dataset.","grounded":true,"rationale":"The paper states that supplementary tables (which likely contain definitions) are deposited alongside the data, serving as documentation objects. [majority verdict 'yes' (4/5 passes agreed)]","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":1.0,"verdict":"yes","evidence":"All results collated in the Borrelia PeptideAtlas are made available at http://www.peptideatlas.org/builds/borrelia/, build 2024-03.","grounded":true,"rationale":"The paper identifies the PeptideAtlas build with a version token 'build 2024-03'. [majority verdict 'yes' (4/5 passes agreed)]","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":0.0,"verdict":"no","evidence":"Code availability The authors do not have code specific to this work to disclose.","grounded":true,"rationale":"The paper explicitly states that no code was written for this work, so no locator is provided.","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":"National Institutes of Health grants from the National Institutes of Health, National Institute of Allergy and Infectious Diseases (NIAID) R21AI142302","grounded":true,"rationale":"The paper includes specific grant numbers (e.g., R21AI142302) for the funding. [majority verdict 'yes' (4/5 passes agreed)]","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":"Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License","why":"The only license mentioned is for the article itself, not for the data; no license artefact is attached to the dataset.","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All MS data and Supplementary Tables for the Borrelia PeptideAtlas is available and deposited at the EBI PRIDE repository at https://www.ebi.ac.uk/pride/archive/projects/PXD046281 and https://doi.org/10.6019/PXD046281.","why":"The paper gives a DOI (10.6019/PXD046281) and a PRIDE accession, both persistent identifiers, for the dataset. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"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 MS data and Supplementary Tables for the Borrelia PeptideAtlas is available and deposited at the EBI PRIDE repository at https://www.ebi.ac.uk/pride/archive/projects/PXD046281 and https://doi.org/10.6019/PXD046281.","why":"The data are freely and openly accessible via a public repository with no stated precondition. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","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":"The paper does not name the file format of the released data; it mentions raw formats (.raw, .d, .wiff) but these are proprietary and not stated as the deposit format. [majority verdict 'no' (3/5 passes agreed)]","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":"no","current":0.0,"evidence":"Code availability The authors do not have code specific to this work to disclose.","why":"The paper explicitly states that no code was written for this work, so no locator is provided.","gain":8.33,"priority":"important","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":"partial","current":0.5,"evidence":"The mass spectrometry data was deposited to the ProteomeXchange Consortium via the PRIDE40 partner repository with the dataset identifier PXD04628141.","why":"The dataset identifier appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","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":"All MS data and Supplementary Tables for the Borrelia PeptideAtlas is available and deposited at the EBI PRIDE repository at https://www.ebi.ac.uk/pride/archive/projects/PXD046281 and https://doi.org/10.6019/PXD046281.","why":"The data-availability statement points to a repository record with a DOI/link, corresponding to Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","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":"Mass spectrometry data from 35 different experiments using laboratory isolates B31 and MM1, and infective B31-5A4, with a total of 358 DDA- and 28 DIA-MS runs (Thermo Scientific instrument .raw files, Bruker instruments.d files), were uniformly analyzed through the TPP pipeline (see Methods) and deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046281.","why":"The Data Records section describes the dataset in running prose; there is no itemised inventory of files or variables. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 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":"partial","current":0.5,"evidence":null,"why":"The paper labels the data as 'publicly available' in the abstract, which is a natural-language equivalent of 'open access'. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":"adhering to FAIR (Findability, Accessibility, Interoperability, and Reusability) principles","why":"The paper does not name a specific data or metadata community standard (e.g., MIAME, ISA-Tab, an ontology); FAIR principles are not a standard.","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":"All MS data and Supplementary Tables for the Borrelia PeptideAtlas is available and deposited at the EBI PRIDE repository at https://www.ebi.ac.uk/pride/archive/projects/PXD046281 and https://doi.org/10.6019/PXD046281.","why":"The data are not human-subject or sensitive, and no gatekeeper of any kind is named; the data are openly available with no access control.","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":"For isolate B31, the UniProt proteome (ProteomeID UP0000018079)","why":"The paper provides a UniProt proteome identifier (UP0000018079) for an external reference database used in the analysis. [downgraded to 'no' — no verifiable quote from the paper]","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":"deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046281","why":"The paper states the data are deposited and available now, but does not commit to any retention period or permanent archival claim. [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.","Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","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.","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":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T13:46:43.698573Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}