PXD016148

PXD016148 is an original dataset announced via ProteomeXchange.

Title	Fast and robust proteome screening platform identifies neutrophil extracellular trap formation in the lung in response to cobalt ferrite nanoparticles
Description	The goal of this study was to investigate the effects of magnetic iron cobalt oxide nanoparticles (cobalt doped Fe3O4 nanoparticles with increasing amounts of cobalt) after pulmonary exposure while in parallel presenting a proteomics platform that is easily transferable to large-scale nanotoxicology screening as part of an integrated assessment and testing approach for regulation of nanoparticles. Bronchoalveolar lavage fluid (BALF) is a proximal biofluid that can be used to monitor airway inflammation and toxic responses in the lung. It is routinely sampled for differential lung diagnostics and has been discussed as a source for early detection of lung cancer. In order to assess effects of metal oxide nanoparticles upon inhalation, bronchoalveolar lavage fluid from mice dosed by single intratracheal instillation was collected and subjected to classical biocompatibility assays as well as proteome analysis. Magnetic oxide nanoparticles with iron and cobalt oxide (Fe3-xCoxO4) at different ratios (1:0, 3:1, 1:1, 1:3, 0:1) were tested at two concentrations (54 µg, 162 µg per animal) and two time points after instillation (day 1, day 3). As a positive control carbon black nanomaterial known to induce lung inflammation was included for both time points, but only at the high dosage (162 µg per animal). Proteomics experiments were divided into three parts – test of reproducibility, discovery and screening phase. The reproducibility of the newly introduced Evosep One LC system was evaluated by re-measuring of technical replicates (n=16). During the discovery phase, selected representative samples with 3 biological replicates per group (total n=9) including pure iron oxide nanoparticles, pure cobalt oxide nanoparticles and vehicle controls were subjected to in-depth proteome profiling by extensive pre-fractionation and including isobaric tandem mass tag (TMT) labeling following a classical LC-MS/MS setup. This step allowed us to identify affected pathways and generate hypotheses regarding mechanisms of the effects of nanoparticles. During screening, all samples of the study were measured label-free as single-shot injections separated on short gradients of 21 min using the robust, high-throughput Evosep One LC system. This step allowed a fast screening of the 5 different types of magnetic metal oxide nanoparticles on BALF, at two concentrations and two time points together with their representative controls (total n=166). All screening measurements were completed in only 2.7 days.
HostingRepository	PRIDE
AnnounceDate	2020-03-26
AnnouncementXML	Submission_2020-03-26_02:38:33.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anja Billing
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-05 07:55:04	ID requested
⏵ 1	2020-03-26 02:38:34	announced

Billing AM, Knudsen KB, Chetwynd AJ, Ellis LA, Tang SVY, Berthing T, Wallin H, Lynch I, Vogel U, Kjeldsen F, Fast and Robust Proteome Screening Platform Identifies Neutrophil Extracellular Trap Formation in the Lung in Response to Cobalt Ferrite Nanoparticles. ACS Nano, 14(4):4096-4110(2020) [pubmed]

submitter keyword: BALF, bronchoalveolar lavage fluid, nanoparticles, murine, mouse, iron cobalt oxide nanoparticles, metal oxide nanoparticles, lung, label-free, TMT, clinical proteomics

Frank Kjeldsen
contact affiliation	Professor Department of Biochemistry and Molecular Biology University of Southern Denmark
contact email	frankk@bmb.sdu.dk
lab head
Anja Billing
contact affiliation	University of Southern Denmark
contact email	anjabilling@gmail.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/2020/03/PXD016148

PRIDE project URI

• PRIDE
  1. PXD016148
     1. Label: PRIDE project
     2. Name: Fast and robust proteome screening platform identifies neutrophil extracellular trap formation in the lung in response to cobalt ferrite nanoparticles