PXD047462-2

PXD047462 is an original dataset announced via ProteomeXchange.

Title	Proteomic workflows for deep phenotypic profiling of 3D organotypic liver models
Description	Organotypic human tissue models constitute promising systems to facilitate drug discovery and development. They allow to maintain native cellular phenotypes and functions, which enables long-term pharmacokinetic and toxicity studies, as well as phenotypic screening. To trace relevant phenotypic changes back to specific targets or signaling pathways, comprehensive proteomic profiling is the gold-standard. A multitude of proteomic workflows have been applied on 3D tissue models to quantify their molecular phenotypes; however, their impact on analytical results and biological conclusions has not been evaluated. Here, we compared the performance of twelve mass spectrometry-based global proteomic workflows that differed in the amount of cellular input, lysis protocols and quantification methods for the analysis of primary human liver spheroids. We find that the different protocols differ majorly in the total number and subcellular compartment bias of identified proteins, which is particularly relevant for the reliable quantification of transporters and drug metabolizing enzymes. However, using a model of non-alcoholic fatty liver disease, we show that critical disease pathways are robustly identified using a standardized high throughput-compatible workflow based on thermal lysis, even using only individual spheroids (1,500 cells) as input. The results increase the applicability of proteomic profiling to phenotypic screens in organotypic microtissues and provides a scalable platform for deep phenotyping from limited biological material.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:37:41.002.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akos Vegvari
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-02 09:37:13	ID requested
1	2024-04-29 05:37:35	announced
⏵ 2	2024-10-22 06:37:41	announced	2024-10-22: Updated project metadata.

10.1002/biot.202300684;

Koutsilieri S, Mickols E, V, é, gv, á, ri Á, Lauschke VM, Proteomic workflows for deep phenotypic profiling of 3D organotypic liver models. Biotechnol J, 19(3):e2300684(2024) [pubmed]

submitter keyword: proteomics,hepatocyte, mass spectrometry, organoid

Akos Vegvari
contact affiliation	Karolinska Institutet, Stockholm, Sweden
contact email	akos.vegvari@ki.se
lab head
Akos Vegvari
contact affiliation	Karolinska Institutet
contact email	akos.vegvari@ki.se
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/2024/04/PXD047462

PRIDE project URI

• PRIDE
  1. PXD047462
     1. Label: PRIDE project
     2. Name: Proteomic workflows for deep phenotypic profiling of 3D organotypic liver models