PXD045031

PXD045031 is an original dataset announced via ProteomeXchange.

Title	Arabidopsis thaliana peptide SP2 and ethyl acetate extraction clean up.
Description	The success of bottom-up proteomic analysis frequently depends on the efficient removal of contaminants from protein or peptide samples before LC-MS/MS. For a peptide clean-up workflow, the single-pot solid-phase-enhanced peptide sample preparation on carboxylate-modified paramagnetic beads (termed SP2) was evaluated for sodium dodecyl sulfate or polyethylene glycol removal from Arabidopsis thaliana tryptic peptides. The robust and efficient 40-min SP2 protocol, tested for a 10 ng, 250ng and 10µg peptide sample, was proposed and benchmarked thoroughly against the ethyl acetate extraction protocol. The SP2 protocol on carboxylated magnetic beads proved to be the robust approach even for simultaneous removal of massive sodium dodecyl sulfate (SDS) and polyethylene glycol (PEG) contaminations from AT peptide samples in respect of the LC-MS/MS data outperforming ethyl acetate extraction.
HostingRepository	PRIDE
AnnounceDate	2024-01-04
AnnouncementXML	Submission_2024-01-04_11:27:41.545.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Petra Martinková
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-01 07:05:03	ID requested
⏵ 1	2024-01-04 11:27:41	announced

10.3390/IJMS242417347;

submitter keyword: Arabidopsis thaliana,peptide clean-up, ethyl acetate extraction, SP2, polyethylene glycol, sodium dodecyl sulfate, magnetic beads, LC-MS/MS

Zbynek Zdrahal
contact affiliation	Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (lab head)
contact email	zdrahal@sci.muni.cz
lab head
Petra Martinková
contact affiliation	Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czechia and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
contact email	petra.martinkova@ceitec.muni.cz
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/2024/01/PXD045031

PRIDE project URI

• PRIDE
  1. PXD045031
     1. Label: PRIDE project
     2. Name: Arabidopsis thaliana peptide SP2 and ethyl acetate extraction clean up.