PXD015622-1

PXD015622 is an original dataset announced via ProteomeXchange.

Title	N-linked Glycopeptides in Human Serum and Standard Glycoprotein(HRP,Ovalbumin and Serotransferrin) LC-MS/MS analysis
Description	Large-scale identification of N-linked glycopeptides by liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) in human serum is challenging due to the wide dynamic range of serum protein abundances, the lack of a complete serum N-Glycan database, and the existence of non-specifically digested peptides and numerous modifications. In this regard, we present a spectral-library search method for serum N-linked glycopeptide identification with target-decoy and motif-specific false discovery rate (FDR) control. Low-abundant glycoproteins were firstly separated from high-abundant proteins by acetonitrile precipitation. After digestion, the N-linked glycopeptides were enriched by hydrophilic interaction liquid chromatography (HILIC) column and processed by Glycopeptidase F (PNGase F) to generate de-glycopeptides, the spectra of which were utilized for library construction. From the de-glycopeptide datasets, 618 glycoproteins with 1,302 N-linked glycosites and 3,000 unique de-glycopeptides were identified. Four types of N-glycosylation motifs were used to recognize the de-glycopeptides, and two different N-Glycan mass databases including 27 modified N-Glycan masses and 712 unmodified N-Glycan masses were utilized during library search. In total, 439 glycoproteins, 851 occupied N-linked glycosites, 24,317 unique glycopeptides and 738 N-Glycan masses were identified under 1% FDR, representing the most in-depth serum N-glycoproteome identified by LC-MS/MS method at glycopeptide level.
HostingRepository	PRIDE
AnnounceDate	2020-01-10
AnnouncementXML	Submission_2020-01-10_06:49:35.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lian Shu
SpeciesList	scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Armoracia rusticana; NCBI TaxID: 3704;
ModificationList	dihydroxylated residue; monohydroxylated residue; complex glycosylation; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-09-27 07:45:20	ID requested
⏵ 1	2020-01-10 06:49:36	announced
2	2020-04-27 00:48:28	announced	2020-04-27: Updated publication reference for PubMed record(s): 32102970.
3	2024-10-22 05:02:23	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Human,Serum,LC-MS/MS,Glycopeptides,HRP,Ovalbumin,Serotransferrin

Fuquan Yang
contact affiliation	Institute of Biophysics, Chinese Academy of Sciences
contact email	fqyang@ibp.ac.cn
lab head
Lian Shu
contact affiliation	Institute of Biophysics,Chinese Academy of Sciences
contact email	shulian13@mails.ucas.edu.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD015622
     1. Label: PRIDE project
     2. Name: N-linked Glycopeptides in Human Serum and Standard Glycoprotein(HRP,Ovalbumin and Serotransferrin) LC-MS/MS analysis