PXD054730

PXD054730 is an original dataset announced via ProteomeXchange.

Title	Removal of NHS-labelling by-products in proteomic samples
Description	N-Hydroxysuccinimide (NHS) chemistry is used extensively across proteomics sample preparation. One of the most popular applications is its use in isobaric reagent based quantitation; specifically both the iTRAQ and TMT approaches. The labels are introduced onto primary Serines, tyrosines, and threonines can be labelled during TMT labelling reactions in addition to the desired amides. These peptides are typically classed as over-labelled and are disregarded for quantification. Their presence also unnecessarily increases sample complexity, which reduces identification rates. In this study, we developed a robust method to remove over-labelled peptides through systematic screening of nucleophilic aminolysis reagents and reaction conditions. The new method reduces the proportion of over-labelled peptides in the sample to less than 1% without affecting the labelling rate or introducing other modifications, leading to superior identification rates and quantitation precision.
HostingRepository	PRIDE
AnnounceDate	2025-03-14
AnnouncementXML	Submission_2025-03-14_06:58:25.565.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yana Demyanenko
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex reporter+balance reagent acylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-08 15:51:34	ID requested
⏵ 1	2025-03-14 06:58:26	announced

10.1016/J.MCPRO.2025.100948;

submitter keyword: NHS, methylamine, hydroxylamine,N-hydroxysuccinimide, O-acylation

Shabaz Mohammed
contact affiliation	The Rosalind Franklon Institute, University of Oxford
contact email	shabaz.mohammed@rfi.ac.uk
lab head
Yana Demyanenko
contact affiliation	Rosalind Franklin Institute
contact email	yana.demyanenko@rfi.ac.uk
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/PXD054730

PRIDE project URI

• PRIDE
  1. PXD054730
     1. Label: PRIDE project
     2. Name: Removal of NHS-labelling by-products in proteomic samples