PXD065022-1

PXD065022 is an original dataset announced via ProteomeXchange.

Title	Proteome analysis of seven Treponema pallidum subsp. pallidum strains grown in vitro: a limited number of quantitative differences in the proteomes
Description	In this work, proteomes of seven Treponema pallidum subsp. pallidum (TPA) strains including Nichols-like strains (DAL-1, Haiti B, Madras) and SS14-like strains (SS14, Philadelphia 1, Grady, Mexico A), grown under in vitro conditions, were analyzed in biological triplicates. Digestion peptides during proteome analyses (LC-MS/MS) were detected with different annotation algorithms (DFAST, PGAP, Prodigal, Prokka, RAST, GeneMarkS, and a manual GenBank annotation) of the corresponding genomes. In addition, ORFfinder was used to predict all ORFs encoding polypeptides longer than 50 amino acid residues. Altogether, 10,823 unique peptides of treponemal origin were detected during analyses. The number of detected peptides per strain varied between 2117 and 7455 with the highest number of detected peptides found for TPA DAL-1 strain. To determine the extent of detected proteins, seven different annotations of seven TPA strains were combined together and only unique protein annotations were kept. Altogether, 1216 predicted protein sequences were searched in the database of detected peptides and 911 individual proteins were identified (74.9%). From individual annotation algorithms, the highest percentage coverage of annotated proteins was detected by GeneMarkS algorithm reaching up to 88.9% of detected proteins out of GeneMarkS-annotated proteins in TPA Haiti B. The support for detected proteins was quite robust with 85.5% of detected proteins identified by two or more peptides and almost three quarters of proteins identified by three and more peptides (72.4%). Altogether, a set of 51 proteins out of 1,053 RAST-annotated proteins (4.8%) showed statistically significant quantitative differences in the proteome signals among different TPA strains. Despite the previously found differences in the growth rates of several TPA strains, proteome analysis revealed only a limited number of detectable quantitative differences in the proteomes.
HostingRepository	PRIDE
AnnounceDate	2025-11-02
AnnouncementXML	Submission_2025-11-02_03:09:13.168.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Katerina Hanakova
SpeciesList	scientific name: Treponema pallidum subsp. pallidum; NCBI TaxID: NEWT:161;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-14 15:09:22	ID requested
⏵ 1	2025-11-02 03:09:13	announced

10.1021/ACS.JPROTEOME.5C00624;

submitter keyword: Treponema pallidum, LC-MS/MS

Zbynek Zdrahal
contact affiliation	Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic
contact email	zdrahal@sci.muni.cz
lab head
Katerina Hanakova
contact affiliation	CEITEC MU
contact email	katerina.hanak@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/11/PXD065022

PRIDE project URI

• PRIDE
  1. PXD065022
     1. Label: PRIDE project
     2. Name: Proteome analysis of seven Treponema pallidum subsp. pallidum strains grown in vitro: a limited number of quantitative differences in the proteomes