PXD063636

PXD063636 is an original dataset announced via ProteomeXchange.

Title	A flexible end-to-end automated sample preparation workflow enables reproducible large-scale bottom-up proteomics - Part 2
Description	Bottom-up proteomics holds significant promise for clinical applications due to its high sensitivity and precision, but is limited by labor-intensive, low-throughput sample preparation meth-ods. Advanced automation is essential to enhance throughput, reproducibility, and accuracy and to allow standardization, thus making bottom-up proteomics amenable for large-scale studies. We developed a fully integrated, automated sample preparation platform that covers the entire process from biological sample input to mass spectrometry-ready peptide output and can be applied on a multitude of biological samples. With this end-to-end solution, we achieved high intra- and interplate reproducibility, as well as longitudinal consistency, result-ing in precise and reproducible workflows. We showed that our automated workflow surpass-es established manual and semi-automated workflows, while improving time efficiency. Finally, we demonstrated the suitability of our automated sample preparation platform for drug development by performing a high-content compound characterization for targeted pro-tein degradation . For this, we coupled application-specific workflows to perform high-content compound characterization by proteome profiling and confirm target degra-dation by precise and reliable protein quantification. Thus, the automated sample preparation platform facilitates rapid adaptation to emerging developments in proteomics sample prepara-tion, combining standardization, flexibility, and high-throughput capabilities to drive significant advancements in clinical assays and proteomics research.
HostingRepository	PRIDE
AnnounceDate	2025-10-17
AnnouncementXML	Submission_2025-10-17_12:23:46.865.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sandra Schär
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-06 04:03:07	ID requested
⏵ 1	2025-10-17 12:23:47	announced

10.1021/ACS.ANALCHEM.5C03829;

submitter keyword: Automated sample preparation, end-to-end

Roland Bruderer
contact affiliation	Biognosys AG
contact email	roland.bruderer@biognosys.com
lab head
Sandra Schär
contact affiliation	Biognosys AG
contact email	sandra.schaer@biognosys.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/2025/10/PXD063636

PRIDE project URI

• PRIDE
  1. PXD063636
     1. Label: PRIDE project
     2. Name: A flexible end-to-end automated sample preparation workflow enables reproducible large-scale bottom-up proteomics - Part 2