Dataset Information

Data-independent Acquisition - Parallel Reaction Monitoring (DIA-PRM) Acquisition Reveals Alteration of Lysosomal Hydrolases in a Mouse Model of Metachromatic Leukodystrophy

ABSTRACT: 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 .

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain, Cell Culture

DISEASE(S): Metachromatic Leukodystrophy

SUBMITTER: Anne Sanner

LAB HEAD: Dominic Winter

PROVIDER: PXD052313 | Pride | 2025-05-07

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20230503_171234_20230503_DIA-PRM_MEF_Comparison_combined_nonorm.sne	Other
	20230504_124012_20230503_DIA-PRM_MEF_Comparison_combined_nonorm_Report.xls	Xls
	20230727_163854_230222_DIA-PRM_micebrain_no-impute_localnorm.sne	Other
	20230727_164111_230222_DIA-PRM_micebrain_no-impute_localnorm_MSstats_Report.tsv	Tabular
	230124_RH03_22_250ng_MEF01_DIA.raw	Raw

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Publications

Data-Independent Acquisition-Parallel Reaction Monitoring Acquisition Reveals Age-Dependent Alterations of the Lysosomal Proteome in a Mouse Model of Metachromatic Leukodystrophy.

Sanner Anne A Hardt Robert R Matzner Ulrich U Winter Dominic D

Analytical chemistry 20241202 49

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, however, come with distinct advantages and shortcomings. While DIA enables unbiased whole proteome analysis, it shows limitations with respect to dynamic range and the quantification of low-abundant proteins. PRM, on the other hand, is ...[more]

PMID: 39620638

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