PXD040003-1

PXD040003 is an original dataset announced via ProteomeXchange.

Title	Proteome profiling of enriched lysosomes obtained from four commercial isolation methodologies.
Description	Lysosomes are membrane-bound cell organelles that can be found in all mammalian cells. They contain digestive enzymes and are involved in multiple processes, including degradation of worn-out cell parts, antigen presentation and induction of programmed cell death. Mass spectrometry studies of lysosomes have been hampered by low sensitivity, since analysis of whole cell proteomes significantly reduce the detection of their relatively low abundant proteins. To overcome this issue, we applied 4 different commercial methods for the enrichment of lysosomes: gradient-based, filter-based, magnetic-bead based and subcellular fractionation, and performed quantitative proteomics analysis on these samples.
HostingRepository	PRIDE
AnnounceDate	2026-02-23
AnnouncementXML	Submission_2026-02-22_17:08:45.139.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Paula Díez
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-09 04:37:06	ID requested
⏵ 1	2026-02-22 17:08:46	announced

de Jager AL, Kassem S, Alesha L, Naber BAE, de Laat IF, de Mooij B, van der Pan K, Bos E, Koning RI, van Dongen JJM, Teodosio C, D, í, ez P, Benchmarking Lysosome Enrichment Methods: A Guide for Research and Clinical Translation. Anal Chem, 98(6):4585-4600(2026) [pubmed]

10.1021/acs.analchem.5c05792;

submitter keyword: TMT,Lysosome, SP3, THP-1, organelle enrichment

Paula Díez
contact affiliation	Leiden University Medical Center (LUMC), Leiden, The Netherlands
contact email	diezgarciapaula@gmail.com
lab head
Paula Díez
contact affiliation	Immune monitoring group - Immunohematology and Blood Transfusion Department Leiden University Medical Center (LUMC=
contact email	p.diez_garcia@lumc.nl
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/2026/02/PXD040003

PRIDE project URI

• PRIDE
  1. PXD040003
     1. Label: PRIDE project
     2. Name: Proteome profiling of enriched lysosomes obtained from four commercial isolation methodologies.