PXD049366

PXD049366 is an original dataset announced via ProteomeXchange.

Title	Refinement of Protein Extraction Protocols for Human Peripheral Nerve Tissue
Description	Our aim was to establish an effective method for protein extraction from freshly frozen human peripheral nerves and determine the minimum amount required for consistent protein extraction outcomes. Five extraction methods were compared using 8 M Urea and Ripa buffer, using either the Bullet Blender or Bioruptor. Out of the total 2619 identified proteins, protein extraction using Ripa buffer combined with either Bioruptor or the Bullet Blender resulted in the identification of 1582 (60%) and 1615 (62%) proteins, respectively. In contrast, using 8 M Urea and Bioruptor for protein extraction resulted in 1022 proteins (39%), whereas employing the Bullet Blender yielded 1446 proteins (55%). Sample amount, ranging from 0.6 to 10 mg, were prepared with consistent protein extraction outcome obtained for samples ≥ 1.2 mg. Combining Ripa and 8M Urea with Bullet Blender increased protein identification to 2126 (81%). Proteins were classified by their cell components, molecular functions, and biological processes. Furthermore, a subclassification of proteins involved in the extracellular matrix (ECM) was introduced. We recommend the use of Ripa buffer, in combination with 8 M Urea and Bullet Blender for extracting proteins from fresh-frozen human nerves weighing ≥ 1.2 mg.
HostingRepository	PRIDE
AnnounceDate	2025-02-21
AnnouncementXML	Submission_2025-02-21_01:04:31.936.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Charlotte Welinder
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-14 05:21:59	ID requested
⏵ 1	2025-02-21 01:04:32	announced

Frostadottir D, Welinder C, Perez R, Dahlin LB, Refinement of Protein Extraction Protocols for Human Peripheral Nerve Tissue. ACS Omega, 10(5):5111-5118(2025) [pubmed]

10.1021/acsomega.4c11373;

submitter keyword: Sural nerve, human,Extracellular proteins, Nerve regeneration, Proteomics, LC-MS/MS

Drifa Frostadottir
contact affiliation	Department of Translational Medicine – Hand Surgery, Lund University, Malmö, Sweden
contact email	drifa.frostadottir@med.lu.se
lab head
Charlotte Welinder
contact affiliation	Dept. of Oncology, Clinical Sciences, Lund University, 221 85 Lund, Sweden
contact email	charlotte.welinder@med.lu.se
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/2025/02/PXD049366

PRIDE project URI

• PRIDE
  1. PXD049366
     1. Label: PRIDE project
     2. Name: Refinement of Protein Extraction Protocols for Human Peripheral Nerve Tissue