PXD054603

PXD054603 is an original dataset announced via ProteomeXchange.

Title	Revisiting the effect of trypsin digestion buffers on artificial deamidation
Description	Deamidation of asparagine and glutamine residues occurs spontaneously, accelerated by adjacent amino acid residues and influenced by pH, temperature, and incubation time. Standard proteolytic digestion induces significant deamidation, which is especially problematic in bottom-up proteomic studies. Trypsin digestion protocol modifications, including shorter incubation times and specific lysis buffers are shown to minimize deamidation. Herein, HEPES is proven to be most optimal due to reduced deamidation coupled with its compatibility for both proteins and trypsin digestion, highlighting its suitability for maintaining sample integrity in biological research contexts.
HostingRepository	PRIDE
AnnounceDate	2025-03-11
AnnouncementXML	Submission_2025-03-11_07:14:58.991.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Emmajay Sutherland
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-05 09:22:14	ID requested
⏵ 1	2025-03-11 07:14:59	announced

10.1021/jasms.4c00389;

Sutherland E, Veth TS, Riley NM, Revisiting the Effect of Trypsin Digestion Buffers on Artificial Deamidation. J Am Soc Mass Spectrom, 36(3):457-462(2025) [pubmed]

submitter keyword: de-glycopeptides,Chemical deamidation, de-glycoproteomics

Nicholas M. Riley
contact affiliation	Department of Chemistry University of Washington, Seattle, WA, USA
contact email	nmriley@uw.edu
lab head
Emmajay Sutherland
contact affiliation	University of Washington
contact email	emmajay.sutherland@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/2025/03/PXD054603

PRIDE project URI

• PRIDE
  1. PXD054603
     1. Label: PRIDE project
     2. Name: Revisiting the effect of trypsin digestion buffers on artificial deamidation