PXD023278

PXD023278 is an original dataset announced via ProteomeXchange.

Title	Targeted Quantification of the Lysosomal Proteome in Complex Samples
Description	The lysosome, as the main degradative organelle of eukaryotic cells, is involved in numerous cellular processes. A defect in one of its proteins often results in lysosomal storage diseases (LSDs). For the study of lysosomal proteins, mass spectrometry (MS) has emerged as the method of choice. Lysosomal proteins are, however, low-abundant, restricting the analysis of lysosomal proteins in unbiased approaches to the investigation of lysosome-enriched fractions. The use of targeted MS provides an attractive alternative to analyze lysosomal proteins in a complex background. In this study, the two targeted MS approaches data-independent acquisition (DIA) and parallel reaction monitoring (PRM) were compared with regard to their ability to analyse lysosomal proteins. These experiments were conducted with samples of different complexity: low-complex lysosome-enriched fractions, medium-complex mouse embryonic fibroblasts (MEF), and high-complex liver whole tissue lysate. While both MS approaches were able to identify and quantify lysosomal proteins, PRM outperformed DIA, especially in high-complex samples.
HostingRepository	PRIDE
AnnounceDate	2021-03-08
AnnouncementXML	Submission_2021-03-08_05:11:42.173.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Peter Robert Mosen
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	S-carboxamidoethyl-L-cysteine; monohydroxylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-22 09:59:30	ID requested
1	2021-03-08 02:37:47	announced
⏵ 2	2021-03-08 05:11:42	announced	2021-03-08: Updated project metadata.

Mosen P, Sanner A, Singh J, Winter D, Targeted Quantification of the Lysosomal Proteome in Complex Samples. Proteomes, 9(1):(2021) [pubmed]

10.3390/PROTEOMES9010004;

submitter keyword: targeted proteomics, lysosomes, parallel reaction monitoring, data-independent acquisition, label-free quantification

Dominic Winter
contact affiliation	Institute for Biochemistry and Molecular Biology Medical Faculty Rheinische Friedrich-Wilhelms-University of Bonn, Germany
contact email	dominic.winter@uni-bonn.de
lab head
Peter Robert Mosen
contact affiliation	Institute of Biochemistry and Molecular Biology, University of Bonn
contact email	pmos@uni-bonn.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD023278
     1. Label: PRIDE project
     2. Name: Targeted Quantification of the Lysosomal Proteome in Complex Samples