PXD039885

PXD039885 is an original dataset announced via ProteomeXchange.

Title	A mouse model of Fragile X Syndrome analyzed by quantitative proteomics: a comparison of methods
Description	We have compared the performance of seven different strategies in the analysis of a mouse model of Fragile X Syndrome, involving the knockout of the fmr1 gene that is the leading cause of autism spectrum disorder. Focusing on the cerebellum, we show that Data-Independent Acquisition (DIA) and the TMT-based Real-time Search method (RTS) generated the most informative profiles, generating 334 and 329 significantly altered proteins respectively, although the latter still suffered from ratio compression. Label-free methods such as BoxCar and a conventional Data-Dependent Acquisition were too noisy to generate a reliable profile, while TMT methods that do not invoke RTS showed a suppressed dynamic range. The TMT method based on complementary ions (ProC) overcomes ratio compression, but current limitations in ion detection reduces sensitivity. Overall, both DIA and RTS uncovered known regulators of the syndrome and detected alterations in calcium signalling pathways that are consistent with calcium deregulation recently observed in imaging studies.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:04:50.022.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ruzena Filandrova
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-06 05:34:35	ID requested
1	2023-08-21 11:30:23	announced
⏵ 2	2023-11-14 09:04:58	announced	2023-11-14: Updated project metadata.

Filandrova R, Douglas P, Zhan X, Verhey TB, Morrissy S, Turner RW, Schriemer DC, Mouse Model of Fragile X Syndrome Analyzed by Quantitative Proteomics: A Comparison of Methods. J Proteome Res, 22(9):3054-3067(2023) [pubmed]

submitter keyword: Quantitative proteomics, BoxCar, complementary ion quantification, DIA, Method comparison, Label-free, TMT labeling, mouse brain proteomics,Fragile X syndrome

David Christopher Schriemer
contact affiliation	Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
contact email	dschriem@ucalgary.ca
lab head
Ruzena Filandrova
contact affiliation	University of Calgary
contact email	filandrova.ruzena@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/2023/08/PXD039885

PRIDE project URI

• PRIDE
  1. PXD039885
     1. Label: PRIDE project
     2. Name: A mouse model of Fragile X Syndrome analyzed by quantitative proteomics: a comparison of methods