PXD035292

PXD035292 is an original dataset announced via ProteomeXchange.

Title	Artificial Intelligence in proteomic profiling of Cerebrospinal fluid from extraventricular drainage in child Medulloblastoma
Description	Medulloblastoma (MB) is the most common pediatric malignant central nervous system tumor. Overall survival in MB depends on treatment tuning. There is the need for biomarkers of residual disease, and recurrence. We analysed the proteome of waste cerebrospinal fluid (CSF) from extraventricular drainage (EVD) from 6 children bearing various subtypes of MB and 6 controls needing EVD insertion for unrelated causes. Samples included total CSF, Microvesicles, Exosomes, and proteins captured by combinatorial peptide ligand library (CPLL). Liquid Chromatography-Coupled Tandem Mass Spectrometry proteomics identified 3560 proteins in CSF from control and MB patients, 2412 (67.7%) of which were overlapping, and 346 (9.7%) and 805 (22.6%) exclusive. Multidimensional scaling analysis discriminated samples. The weighted gene co-expression network analysis (WGCNA) identified those modules functionally associated with the samples. A ranked core of 192 proteins allowed distinguishing between control and MB samples. Machine learning highlighted long-chain fatty acid transport protein 4 (SLC27A4), and laminin B-type (LMNB1) as proteins that maximize the discrimination between control and MB samples, respectively. Artificial intelligence was able to distinguish between MB vs non-tumor/hemorrhagic controls. The two potential protein biomarkers for the discrimination between control and MB may guide therapy and predict recurrences, improving the MB patients quality of life.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:39:39.369.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martina Bartolucci
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-13 06:05:50	ID requested
1	2022-10-14 04:26:07	announced
⏵ 2	2023-11-14 07:39:41	announced	2023-11-14: Updated project metadata.

Bruschi M, Kajana X, Petretto A, Bartolucci M, Pavanello M, Ghiggeri GM, Panfoli I, Candiano G, Weighted Gene Co-Expression Network Analysis and Support Vector Machine Learning in the Proteomic Profiling of Cerebrospinal Fluid from Extraventricular Drainage in Child Medulloblastoma. Metabolites, 12(8):(2022) [pubmed]

submitter keyword: cerebrospinal fluid, central nervous system, Mass Spectrometry, proteomics,Medulloblastoma

Andrea Petretto
contact affiliation	IRCCS Istituto Giannina Gaslini
contact email	a.petretto@gmail.com
lab head
Martina Bartolucci
contact affiliation	IRCCS Gaslini
contact email	smartibartolucci@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/2022/10/PXD035292

PRIDE project URI

• PRIDE
  1. PXD035292
     1. Label: PRIDE project
     2. Name: Artificial Intelligence in proteomic profiling of Cerebrospinal fluid from extraventricular drainage in child Medulloblastoma