PXD042574

PXD042574 is an original dataset announced via ProteomeXchange.

Title	Limited proteolysis-mass spectrometry of saliva maps proteome-wide structural changes associated with oral cancer aggressiveness.
Description	Considering that these potential diagnostic and prognostic targets may be regulated by events that do not imply variation in protein abundance levels, we investigated the hypothesis that changes in protein conformation can be associated with diagnosis and prognosis, revealing biological processes and novel targets of clinical relevance. For this, we employed LiP-MS in saliva samples to explore structural alterations comparing the proteome of healthy control and squamous cell carcinoma (OSCC) patients, with and without lymph node metastasis (N0 and N+, respectively). Our LiP strategy revealed 311 proteins with structural rearrangements when comparing among control and OSCC patients and 15 unique enriched biological processes, in contrast to 66 and 11 processes enriched in traditional proteomics workflow, mostly associated with immunity events. Moreover, 51 proteins with potential structural rearrangements were associated with clinical patient features, indicating conformotypic peptides associated with lymph node metastasis.
HostingRepository	PRIDE
AnnounceDate	2025-03-11
AnnouncementXML	Submission_2025-03-11_07:09:59.422.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Adriana Franco Paes Leme
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-31 05:35:41	ID requested
⏵ 1	2025-03-11 07:10:00	announced

Granato DC, Carnielli CM, Trino LD, Busso-Lopes AF, C, â, mara GA, Normando AGC, Filho HVR, Domingues RR, Yokoo S, Pauletti BA, Patroni FM, Santos-Silva AR, Lopes MA, Brand, ã, o TB, Prado-Ribeiro AC, Lopes-de Oliveira PS, Telles GP, Paes Leme AF, Mapping Conformational Changes in the Saliva Proteome Potentially Associated with Oral Cancer Aggressiveness. J Proteome Res, 23(6):2148-2159(2024) [pubmed]

10.1021/acs.jproteome.4c00093;

submitter keyword: Oral cance, Limited proteolysis, Saliva,Functional proteomics, Mass spectrometry, Structural proteomic,Protein post-translational modification, Prognosis

Adriana Franco Paes Leme
contact affiliation	Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, 13083-970, Brazil
contact email	adriana.paesleme@lnbio.cnpem.br
lab head
Adriana Franco Paes Leme
contact affiliation	CNPEM
contact email	adriana.paesleme@lnbio.cnpem.br
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/2025/03/PXD042574

PRIDE project URI

• PRIDE
  1. PXD042574
     1. Label: PRIDE project
     2. Name: Limited proteolysis-mass spectrometry of saliva maps proteome-wide structural changes associated with oral cancer aggressiveness.