PXD013764

PXD013764 is an original dataset announced via ProteomeXchange.

Title	Human Milk Site-specific N-Glycoproteome Changes Across Lactation
Description	N-glycosylation is an essential post-translational modification (PTM) of human milk proteins for the promotion of infant health. N-glycosylation is relevant regarding proteolytic susceptibility and functions as a competitive inhibitor of pathogen binding and immunomodulators. Due to the individual uniqueness of human milk, the overall complexity and temporal changes of N-glycosylation, the analysis for site-specific information of this PTM must take these factors into consideration. Here we demonstrate, by adapting the automated platform and hydrophilic-interaction chromatography (HILIC)-based cartridge with 150 μg of milk protein digestion, that proteome-wide N-glycopeptides can be reproducibly enriched in technical triplicates and biological samples across lactation. With higher energy c-trap dissociation (HCD) triggered electron-transfer/higher-energy collision dissociation (EThcD), we were able to map, to our knowledge, the most comprehensive human milk N-glycoproteome to date. We found 1697 glycopeptides from 110 glycoproteins and 191 glycosites of which 43 novel sites were not yet reported in experimental evidence. We next quantified the glycopeptides in targeted monitoring mode with scheduled selective ion monitoring (SIM) and parallel reaction monitoring (PRM). Co-trending HCD fragment ions enabled us to pinpoint the MS1 extracted ion chromatogram (XIC) of intact glycopeptide. In a 90 min gradient, we could measure 318 glycopeptides from 51 glycoproteins, catching at least 10 data points in their chromatographic peaks. We observed distinctive quantitative site-specific glycosylation trends, indicating the potential of specific temporal changes associated with functions that support the developing infant’s health.
HostingRepository	PRIDE
AnnounceDate	2024-10-08
AnnouncementXML	Submission_2024-10-08_11:37:13.711.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD013764
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	yuhsien lin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl; HexNAc(2)
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-05-08 01:46:31	ID requested
⏵ 1	2024-10-08 11:37:14	announced

10.1021/acs.jproteome.9b00753;

Zhu J, Lin YH, Dingess KA, Mank M, Stahl B, Heck AJR, -Glycoproteome of Human Milk from a Single Donor Reveals the Highly Variable Repertoire and Dynamic Site-Specific Changes. J Proteome Res, 19(5):1941-1952(2020) [pubmed]

10.6019/PXD013764;

submitter keyword: glycosylation, HILIC, glycoproteomics,Human Milk, Mass spectrometry, Parallel reaction monitoring

Albert J R Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands ( lab head )
contact email	A.J.R.Heck@uu.nl
lab head
yuhsien lin
contact affiliation	Utrecht University
contact email	y.lin1@uu.nl
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/2021/09/PXD013764

PRIDE project URI

• PRIDE
  1. PXD013764
     1. Label: PRIDE project
     2. Name: Human Milk Site-specific N-Glycoproteome Changes Across Lactation