PXD020600

PXD020600 is an original dataset announced via ProteomeXchange.

Title	Multi cell line comparison of lysosome enriched fractions reveals cell type specific features and novel lysosomal proteins
Description	Lysosomes are the main degradative organelles of mammalian cells and are responsible for the breakdown of the majority of cellular macromolecules and the recycling of their building blocks. To accomplish this task, lysosomes contain ~60 hydrolases. Malfunction of these proteins, as well as other proteins responsible for the transport of small molecules or proteins, lead to the accumulation of their respective substrates. This accumulation of substrates results in heavy impairment of lysosomal function leading to ~70 lysosomal storage disorders (LSDs). A better understanding of lysosomal composition is of high importance not only for a better understanding of LSDs, but also for cellular function. Analysis of lysosomes by mass spectrometry-based proteomics presents an attractive approach to allow for a better characterization of lysosomes. In the current study, we investigated the lysosomal proteome from six different cell lines (HEK293, HeLa, HuH-7, SH-SY5Y, MEF and NIH3T3) by lysosome enrichment using SPIONs (superparamagnetic iron oxide nanoparticles) combined with mass spectrometry-based proteomics. Comparison of the individual proteomes revealed cell type specific characteristics in lysosomal protein expression. To allow for the discrimination of lysosomal from unspecific enriched proteins, we included a differentially SILAC (stable isotope labelling by amino acids in cell culture) labelled control sample. Afterwards, lysosomal proteins were identified using a bimodal distribution model. By combination of data from several cell lines, we were able to generate a high confidence list of putative novel lysosomal proteins of which several were confirmed by immunostaining.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:19:29.414.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fatema Akter
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidoethyl-L-cysteine; acetylated residue; monohydroxylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-28 01:27:50	ID requested
1	2023-02-21 06:34:19	announced
⏵ 2	2023-11-14 07:19:30	announced	2023-11-14: Updated project metadata.

Akter F, Bonini S, Ponnaiyan S, K, ö, gler-Mohrbacher B, Bleibaum F, Damme M, Renard BY, Winter D, Multi-Cell Line Analysis of Lysosomal Proteomes Reveals Unique Features and Novel Lysosomal Proteins. Mol Cell Proteomics, 22(3):100509(2023) [pubmed]

submitter keyword: isolated lysosomes, DIA, human, SILAC, LFQ, mouse, IBAQ,lysosome, cell line comparison

Dominic Winter
contact affiliation	Institute for Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
contact email	dwin@uni-bonn.de
lab head
Fatema Akter
contact affiliation	Postdoctoral Researcher
contact email	fatemapoly@uni-bonn.de
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/2023/02/PXD020600

PRIDE project URI

• PRIDE
  1. PXD020600
     1. Label: PRIDE project
     2. Name: Multi cell line comparison of lysosome enriched fractions reveals cell type specific features and novel lysosomal proteins