PXD073367-1

PXD073367 is an original dataset announced via ProteomeXchange.

Title	Evaluation of deep and dynamic proteomic screening strategies at sub-50Hz scan rate and without automation
Description	In this study, we systematically evaluate sample preparation strategies, data acquisition modes and data-analysis approaches for both labeled and label-free proteomics, with the explicit goal of maximizing throughput and quantitative depth using Orbitrap-based instruments operating below 50Hz scan rates and without reliance on automation. Our central objective is to define realistic, accessible proteomics workflows that can be implemented within standard cell and molecular biology laboratories, enabling high-throughput deep and dynamic proteome measurements akin to cell screening platforms. Specifically, we first assess high-throughput sample preparation strategies compatible with 96-well cell culture formats, comparing in-solution (adapted from Simplit17 i.e. Simplit2), filter-based (STrap18), and on bead aggregation (SP319) based enzymatic digestion. Next we benchmarked TMT-based approaches (MS2,SPS-MS3 and real time search assisted SPS-MS3) and DIA appraoches on three species peptide mix. Similar benchmarking of dynamic SILAC-DIA and SILAC-TMT can be found in associated submissions.
HostingRepository	PRIDE
AnnounceDate	2026-03-30
AnnouncementXML	Submission_2026-03-30_05:10:36.868.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Münch
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Escherichia coli; NCBI TaxID: NEWT:562; scientific name: Staphylococcus aureus; NCBI TaxID: NEWT:1280;
ModificationList	Acetyl:2H(3); Oxidation; Carbamidomethyl
Instrument	Q Exactive HF; Orbitrap Fusion Lumos; Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2026-01-21 14:49:45	ID requested
⏵ 1	2026-03-30 05:10:37	announced

10.5281/ZENODO.18925014;

submitter keyword: None

Christian Münch
contact affiliation	Institute of Molecular Systems Medicine, Goethe University, Frankfurt Germany
contact email	ch.muench@em.uni-frankfurt.de
lab head
Christian Münch
contact affiliation	Goethe University Frankfurt
contact email	ch.muench@em.uni-frankfurt.de
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/2026/03/PXD073367

PRIDE project URI

• PRIDE
  1. PXD073367
     1. Label: PRIDE project
     2. Name: Evaluation of deep and dynamic proteomic screening strategies at sub-50Hz scan rate and without automation