PXD033143

PXD033143 is an original dataset announced via ProteomeXchange.

Title	Microproteomics workflows for quantitative proteome analysis of single Caenorhabditis elegans nematodes
Description	Miniaturization of sample preparation including omissible manual sample handling steps is key for reproducible nanoproteomics as material is often restricted to only hundreds of cells or single model organisms. Here, we demonstrate a highly sensitive digital microfluidics (DMF)-based sample preparation workflow making use of single-pot solid-phase enhanced sample preparation (SP3) in combination with high-field asymmetric-waveform ion mobility spectrometry (FAIMS), and fast and sensitive ion trap detection on an Orbitrap tribrid MS system. Compared to a manual in-tube SP3-supported sample preparation, the number of peptides identified, the achievable standard deviations between replicates, and the number of proteins identified as differentially abundant were markedly increased. We identified up to 5,000 proteins from single nematodes. Moreover, label-free quantification of protein changes in single Caenorhabditis elegans treated with a heat stimulus yielded 45 differentially abundant proteins when compared to the untreated control, demonstrating the potential of this technology for low-input proteomics studies.
HostingRepository	PRIDE
AnnounceDate	2022-08-12
AnnouncementXML	Submission_2022-08-12_01:21:52.526.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	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-11 02:26:29	ID requested
⏵ 1	2022-08-12 01:21:53	announced

Steinbach MK, Leipert J, Blurton C, Leippe M, Tholey A, Nematodes. J Proteome Res, 21(8):1986-1996(2022) [pubmed]

submitter keyword: Caenorhabditis elegans, ion trap, low-input proteomics, microproteomics, nanoproteomics, FAIMS

Andreas Tholey
contact affiliation	Institute for Experimental Medicine, Kiel University, 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

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PRIDE project URI

• PRIDE
  1. PXD033143
     1. Label: PRIDE project
     2. Name: Microproteomics workflows for quantitative proteome analysis of single Caenorhabditis elegans nematodes