PXD052313

PXD052313 is an original dataset announced via ProteomeXchange.

Title	Data-independent Acquisition - Parallel Reaction Monitoring (DIA-PRM) Acquisition Reveals Alteration of Lysosomal Hydrolases in a Mouse Model of Metachromatic Leukodystrophy
Description	For the reproducible analysis of peptides by mass spectrometry-based proteomics, data-independent acquisition (DIA) and parallel/multiple reaction monitoring (PRM/MRM) deliver unrivalled performance with respect to sensitivity and reproducibility. Both approaches come, however, with distinct advantages as well as shortcomings. While DIA enables the unbiased analysis of a large fraction of a sample’s proteome, it shows limitations with respect to dynamic range and the reproducible identification/quantification of low-abundant proteins. PRM, on the other hand, is ideally suited to reproducibly and sensitively quantify selected peptides originating from the proteins of interest, even if they are low-abundant, but no knowledge of the remaining sample is obtained. Here, we combine both methods into a mixed DIA-PRM acquisition approach, thereby merging the benefits of each method, while operating at reduced machine run times and sample amount, relative to individual measurements. We demonstrate the feasibility of the approach by merging a scheduled PRM assay for 59 low-abundant lysosomal hydrolases, covered through 103 peptides, with a DIA data acquisition scheme. After benchmarking DIA-PRM against mouse embryonic fibroblast (MEF) whole cell lysates, we use the approach to investigate disease progression in brain tissues of a mouse model of metachromatic leukodystrophy (MLD). In these tissues, we found a progressive increase in lysosomal hydrolases in MLD as compared to healthy control mice .
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-06_17:24:43.742.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anne Sanner
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-16 05:54:01	ID requested
⏵ 1	2025-05-06 17:24:44	announced

Sanner A, Hardt R, Matzner U, Winter D, Data-Independent Acquisition-Parallel Reaction Monitoring Acquisition Reveals Age-Dependent Alterations of the Lysosomal Proteome in a Mouse Model of Metachromatic Leukodystrophy. Anal Chem, 96(49):19567-19575(2024) [pubmed]

10.1021/acs.analchem.4c04378;

submitter keyword: DIA, PRM, targeted,mass spectrometry, MLD, lysosomes

Dominic Winter
contact affiliation	Institute of Biochemistry and Molecular Biology, University of Bonn, Germany
contact email	dwin@uni-bonn.de
lab head
Anne Sanner
contact affiliation	Institute for Biochemostry and Molecular Biology
contact email	anne.sanner@hotmail.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD052313
     1. Label: PRIDE project
     2. Name: Data-independent Acquisition - Parallel Reaction Monitoring (DIA-PRM) Acquisition Reveals Alteration of Lysosomal Hydrolases in a Mouse Model of Metachromatic Leukodystrophy