PXD039883

PXD039883 is an original dataset announced via ProteomeXchange.

Title	Combination of digital microfluidics and magnetic bead-based intact proteoform elution for top-down nanoproteomics of single C. elegans
Description	While most nanoproteomics approaches for the analysis of low-input samples are based on bottom-up LC-MS workflows, top-down approaches enabling proteoform characterization are still underrepresented. Using mammalian cell proteomes, we here established a facile one-pot sample preparation protocol based on protein aggregation on magnetic beads and intact proteoform elution using 40% v/v formic acid. Performed on a digital microfluidics device, the workflow enabled sensitive analysis of single Caenorhabditis elegans nematodes, increasing the number of proteoform identifications compared to in-tube sample preparation by 46%. Label-free quantification of single nematodes grown under different conditions allowed to identify changes in abundance of proteoforms not distinguishable by bottom-up proteomics. The workflow presented here will help to elucidate cellular changes on the proteoform level in other samples of limited availability.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_06:44:26.538.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andreas Tholey
SpeciesList	scientific name: Caenorhabditis elegans; NCBI TaxID: 6239;
ModificationList	acetylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-06 05:33:43	ID requested
1	2023-06-19 06:22:30	announced
⏵ 2	2023-11-14 06:44:26	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Top-down Proteomics

Nanoproteomics

Caenorhabditis elegans

Digital Microfluidics

Andreas Tholey
contact affiliation	Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
contact email	a.tholey@iem.uni-kiel.de
lab head
Andreas Tholey
contact affiliation	Systematic Proteome Research & Bioanalytics, University of Kiel
contact email	a.tholey@iem.uni-kiel.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/2023/06/PXD039883

PRIDE project URI

• PRIDE
  1. PXD039883
     1. Label: PRIDE project
     2. Name: Combination of digital microfluidics and magnetic bead-based intact proteoform elution for top-down nanoproteomics of single C. elegans