PXD042958

PXD042958 is an original dataset announced via ProteomeXchange.

Title	Large-scale proteogenomics characterization of the Mycobacterium tuberculosis hidden proteome
Description	Traditional genome annotation methods exclude Open Reading Frames shorter than 300 codons (smORFs), which leaves a substantial portion of the proteome overlooked. Proteogenomics is a multi-omics approach that merges genomics, transcriptomics and proteomics to identify proteoforms and unannotated proteins from Mass Spectrometry data. Here, we employed our recently developed proteogenomics pipeline to aid genome annotation and identify hundreds of novel microproteins encoded by smORFs in the genome of Mycobacterium tuberculosis (Mtb). To avoid limitations regarding sensitivity, we used 680 Mass Spectrometry experiments in a large-scale approach, which let us classify the findings by different degrees of confidence using our machine learning model. After integrating the results with RNA-Seq datasets, we explore the biological relevance of the novel sequences and show they are differentially expressed upon starvation and antibiotic treatment, and are co-expressed with many annotated genes that are vital for bacterial virulence. Moreover, some smORFs are located inside essential genomic segments and could be attractive targets for the development of new drugs. Altogether, our results should improve the current annotation of the proteome of Mtb and guide the following studies focusing on studying these microproteins thoroughly.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_10:59:18.981.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eduardo Vieira de Souza
SpeciesList	scientific name: Mycobacterium tuberculosis H37Rv; NCBI TaxID: 83332;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-13 13:46:54	ID requested
⏵ 1	2025-05-06 10:59:19	announced

10.1038/s41598-024-82465-w;

de Souza EV, Dalberto PF, Miranda AC, Saghatelian A, Pinto AM, Basso LA, Machado P, Bizarro CV, Large-scale proteogenomics characterization of microproteins in Mycobacterium tuberculosis. Sci Rep, 14(1):31186(2024) [pubmed]

submitter keyword: proteogenomics, microproteins, tuberculosis,small orfs

Cristiano Valim Bizarro
contact affiliation	Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Programa de Pós-Graduação em Biologia Celular e Molecular - Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
contact email	cristiano.bizarro@pucrs.br
lab head
Eduardo Vieira de Souza
contact affiliation	Salk Institute for Biological Studies
contact email	vdseduardo@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/2025/05/PXD042958

PRIDE project URI

• PRIDE
  1. PXD042958
     1. Label: PRIDE project
     2. Name: Large-scale proteogenomics characterization of the Mycobacterium tuberculosis hidden proteome