PXD048325

PXD048325 is an original dataset announced via ProteomeXchange.

Title	Fully automated workflow for integrated sample digestion and Evotip loading enabling high-throughput clinical proteomics
Description	Protein identification and quantification is an important tool for biomarker discovery. With the increased sensitivity and speed of modern mass spectrometers, sample-preparation remains a bottleneck for studying large cohorts. To address this issue, we prepared and evaluated a simple and efficient workflow on the Opentrons OT-2 (OT-2) robot that combines sample digestion, cleanup and Evotip loading in a fully automated manner, allowing the processing of up to 192 samples in 6 hours. Our results demonstrate a highly sensitive workflow yielding both reproducibility and stability even at low sample inputs. The workflow is optimized for minimal sample starting amount to reduce the costs for reagents needed for sample preparation, which is critical when analyzing large biological cohorts. Building on the digesting workflow, we incorporated an automated phosphopeptide enrichment step using magnetic Ti-IMAC beads. This allows for a fully automated proteome and phosphoproteome sample preparation in a single step with high sensitivity. Using the integrated workflow, we evaluated the effects of cancer immune therapy on the plasma proteome in metastatic melanoma patients.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:44:39.398.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anders Kverneland
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-08 17:07:46	ID requested
1	2024-06-12 06:00:29	announced
⏵ 2	2024-10-22 06:44:40	announced	2024-10-22: Updated project metadata.

10.1016/j.mcpro.2024.100790;

Kverneland AH, Harking F, Vej-Nielsen JM, Huusfeldt M, Bekker-Jensen DB, Svane IM, Bache N, Olsen JV, Fully Automated Workflow for Integrated Sample Digestion and Evotip Loading Enabling High-Throughput Clinical Proteomics. Mol Cell Proteomics, 23(7):100790(2024) [pubmed]

submitter keyword: Automation, Plasma proteomics, DIA, biomarkers

Jesper Velgaard Olsen
contact affiliation	NNF Center for Protein Research, University of Copenhagen
contact email	jesper.olsen@cpr.ku.dk
lab head
Anders Kverneland
contact affiliation	NNF Center for Protein Research, University of Copenhagen
contact email	akverneland@sund.ku.dk
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/2024/06/PXD048325

PRIDE project URI

• PRIDE
  1. PXD048325
     1. Label: PRIDE project
     2. Name: Fully automated workflow for integrated sample digestion and Evotip loading enabling high-throughput clinical proteomics