PXD058138-1

PXD058138 is an original dataset announced via ProteomeXchange.

Title	SIMPLEX enriches hydrophobic and lipidated proteins in membrane proteomics experiments
Description	Synaptosome (Syn) and synaptic junctions (SJ) are widely used in omics experiments to investigate protein content and networks of synapses. Synapses are a neuronal compartment wit a high lipid content. Liquid-liquid extraction (LLE), typically used in lipidomics, shows great potential for multiomics experiments, where data is generated from the same sample, due to its ability to integrate different molecule classes in one extraction. However, the influence of liquid-liquid extraction on protein and phospho-proteins analysis of membrane-enriched samples has not been investigated nor compared to one-phase extraction. In this study, we compared the suitability of SIMPLEX (Simultaneous Metabolite, Protein, Lipid Extraction)- an example of LLE- for mass-spectrometry based protein identification to a commonly used acetone protein precipitation.
HostingRepository	PRIDE
AnnounceDate	2025-09-08
AnnouncementXML	Submission_2025-09-07_21:26:59.485.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tingting Li
SpeciesList	scientific name: Rattus rattus (Black rat); NCBI TaxID: 10117;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-21 06:39:05	ID requested
⏵ 1	2025-09-07 21:27:00	announced

Li T, Wenger A, Coman C, Borutzki C, Kreutz MR, Ahrends R, SIMPLEX Enriches Hydrophobic and Lipidated Proteins in Membrane Proteomics Experiments. Proteomics, 25(16):28-39(2025) [pubmed]

10.1002/pmic.70016;

submitter keyword: Liquid-liquid extraction, synaptosomes, domains, synaptic junctions, membrane-enriched sample, transmembrane proteins

Robert Ahrends
contact affiliation	University of Vienna Department of Chemistry Institute of Analytical Chemistry
contact email	robert.ahrends@univie.ac.at
lab head
Tingting Li
contact affiliation	University of Vienna
contact email	tingting_li0804@163.com
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/2025/09/PXD058138

PRIDE project URI

• PRIDE
  1. PXD058138
     1. Label: PRIDE project
     2. Name: SIMPLEX enriches hydrophobic and lipidated proteins in membrane proteomics experiments