{"doi":"10.3389/fmicb.2024.1505893","title":"Proteomic analysis of the Treponema pallidum subsp. pallidum SS14 strain: coverage and comparison with the Nichols strain proteome","abstract":"Introduction: , group into one of two deep-branching clades: the Nichols clade or the globally dominant Street Strain 14 (SS14) clade. To date, in-depth proteome-wide analyses have focused on Nichols clade strains. Methods: SS14 clade reference strain (SS14) proteome was characterized via protein detection and quantification analyses using mass spectrometry, and comparison was made to the Nichols clade reference strain (Nichols) proteome. Results: SS14 were detected and quantitated, allowing confirmation of expression of 259 proteins for the first time in this strain, including 11 known/putative outer membrane proteins (OMPs). SS14 and Nichols proteome comparative analyses demonstrated similar protein expression/quantification profiles between the two strains, and showed that inter-strain amino acid sequence differences are located primarily within predicted surface-exposed regions in 16 known/putative OMPs. Discussion: SS14 and Nichols strains. The findings inform syphilis vaccine design by confirming the expression of known/predicted OMP vaccine candidates in SS14 treponemes, and via the finding that most inter-strain variable residues found in OMPs are predicted to be located in surface-exposed, host-facing regions of these proteins.","journal":"Frontiers in Microbiology","year":2024,"id":482592,"datarank":0.12921046749934026,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.02523839041534846,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.02523839041534846,"corpus_percentile":29.12508702715247,"corpus_rank":9162,"citation_count":1,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8929,"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":58.3333,"fair_percentile":72.8829104249465,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":594792,"name":"Steven H. Marshall","orcid":"0009-0003-1811-2633","position":1,"is_corresponding":false},{"id":464701,"name":"Alloysius Gomez","orcid":null,"position":2,"is_corresponding":false},{"id":463851,"name":"Caroline E. Cameron","orcid":"0000-0002-8786-4359","position":3,"is_corresponding":false},{"id":463849,"name":"Simon Houston","orcid":"0000-0001-5961-5227","position":0,"is_corresponding":true}],"reference_count":52,"raw_metadata":null,"created_at":"2026-07-19T02:07:18.280369Z","pmid":"39723147","pmcid":"PMC11668736","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":83.3333,"fair_a":62.5,"fair_i":20.0,"fair_r":25.0,"fair_zscore":0.9454,"fair_rationale":{"fair_score":58.33,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The data presented in the study are deposited in the MassIVE repository, accession number MSV000095818 (ProteomeXchange identifier PXD055753).","grounded":true,"rationale":"A ProteomeXchange identifier (PXD055753) is a persistent identifier scheme. [majority verdict 'yes' (4/5 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":"MassIVE repository","grounded":true,"rationale":"MassIVE is a curated data repository listed in re3data.","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":1.0,"verdict":"yes","evidence":"The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.","grounded":true,"rationale":"The statement points to a repository record (MassIVE) with accession, fitting Colavizza category 3.","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":0.5,"verdict":"partial","evidence":"In the present study, 7,163 unique T. pallidum peptides were identified which allowed for the detection of 607 of 987 proteins within treponemes from the SS14 strain, representing 61.5% of the total proteome","grounded":true,"rationale":"The dataset's content is described in running prose only, without an itemised inventory.","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 data presented in the study are deposited in the MassIVE repository, accession number MSV000095818 (ProteomeXchange identifier PXD055753).","grounded":true,"rationale":"The dataset identifier appears in the body text (Data availability statement), not in the reference list.","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":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The data presented in the study are deposited in the MassIVE repository, accession number MSV000095818 (ProteomeXchange identifier PXD055753).","grounded":true,"rationale":"The text gives a route to the data (MassIVE repository with accession) with no stated precondition.","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":"The data presented in the study are deposited in the MassIVE repository, accession number MSV000095818 (ProteomeXchange identifier PXD055753).","grounded":true,"rationale":"The paper does not explicitly label the access level of the data (e.g. 'open access'), but describes the access action of depositing in a public repository, from which the level must be inferred. [majority verdict 'partial' (4/5 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 not sensitive or human-subject, so no gatekeeper is named.","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":null,"grounded":false,"rationale":"No sentence addresses when the data become available or how long they persist.","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":20.0,"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 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 data or metadata community standard (e.g. MIAPE, MIAME) is named for the data. 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'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":"No licence is named for the data; the CC BY licence on the article does not apply to the data.","gain":16.67,"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. 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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 data presented in the study are deposited in the MassIVE repository, accession number MSV000095818 (ProteomeXchange identifier PXD055753).","why":"The dataset identifier appears in the body text (Data availability statement), not in the reference list.","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). 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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":"The data presented in the study are deposited in the MassIVE repository, accession number MSV000095818 (ProteomeXchange identifier PXD055753).","why":"The paper does not explicitly label the access level of the data (e.g. 'open access'), but describes the access action of depositing in a public repository, from which the level must be inferred. [majority verdict 'partial' (4/5 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 data or metadata community standard (e.g. MIAPE, MIAME) is named for the data. [majority verdict 'no' (4/5 passes agreed)]","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":null,"why":"No documentation object (README, codebook) is said to accompany the data. 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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).","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.","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."],"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":"2026-07-20T13:48:29.694512Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}