PXD037921

PXD037921 is an original dataset announced via ProteomeXchange.

Title	Simultaneous N-deglycosylation and digestion of human and chicken proteins on S-Traps
Description	N-linked glycosylation is an important post-translational modification that is difficult to identify and quantify in traditional bottom-up proteomics experiments. Enzymatic deglycosylation of proteins by peptide:N-glycosidase F (PNGase F) prior to digestion and subsequent mass spectrometry analysis has been shown to improve coverage of various N-linked glycopeptides, but inclusion of this step may add up to a day to an already lengthy sample preparation process. An efficient way to integrate deglycosylation with bottom-up proteomics would be a valuable contribution to the glycoproteomics field. Here, we demonstrate a proteomics workflow in which deglycosylation and proteolytic digestion of samples occurs simultaneously using suspension trapping (S-Trap). This approach adds no additional time to standard digestion protocols. Applying this sample preparation strategy to a human serum sample, we demonstrate improved identification of potential N-glycosylated peptides in deglycosylated samples compared with non-deglycosylated samples, identifying 156 unique peptides that contain the N-glycosylation motif (Asparagine–X–Serine/Threonine), the deamidation modification characteristic of PNGase F, and an increase in peptide intensity over a control sample. We expect that this rapid sample preparation strategy will assist in the identification and quantification of both known and potential glycoproteins.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:58:21.765.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rebecca Whelan
SpeciesList	scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-03 04:51:32	ID requested
1	2023-02-08 17:08:26	announced
⏵ 2	2023-11-14 08:58:22	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Human, deglycosylation, chicken, S-Trap, LC-MS/MS

Rebecca Whelan
contact affiliation	Department of Chemistry, University of Kansas, Lawrence KS, United States
contact email	rwhelan1@ku.edu
lab head
Rebecca Whelan
contact affiliation	Department of Chemistry, University of Kansas
contact email	rwhelan1@ku.edu
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/2023/02/PXD037921

PRIDE project URI

• PRIDE
  1. PXD037921
     1. Label: PRIDE project
     2. Name: Simultaneous N-deglycosylation and digestion of human and chicken proteins on S-Traps