PXD015622-3

PXD015622 is an original dataset announced via ProteomeXchange.

Title	Human serum N-linked intact glycopeptides LC-MS/MS
Description	Large-scale identification of N-linked intact 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, a spectral library search method was presented for serum N-linked intact glycopeptides identification with target-decoy and motif-specific false discovery rate (FDR) control. Low-abundant glycoproteins were firstly separated from high-abundant proteins by acetonitrile (ACN) precipitation. After digestion, the N-linked intact glycopeptides were enriched by hydrophilic interaction liquid chromatography (HILIC) column and a portion of the enriched N-linked intact glycopeptides were processed by N-Glycosidase F (PNGase F) to generate de-glycopeptides. Both N-linked intact glycopeptides and de-glycopeptides were analyzed by LC-MS/MS. From N-linked de-glycopeptides datasets, 764 N-linked glycoproteins, 1,699 N-linked glycosites and 3,328 unique N-linked de-glycopeptides were identified. The spectra of these N-linked de-glycopeptides were utilized for N-linked de-glycopeptides library construction and identification of N-linked intact glycopeptides. Four types of N-linked glycosylation motifs (NXS/T/C/V, X≠P) were used to recognize the N-linked de-glycopeptides, and two different N-Glycan mass databases including 27 modified N-Glycan masses and 712 unmodified N-Glycan masses were combined and utilized during spectral library search for identification of N-linked intact glycopeptides. In total, from the N-linked intact glycopeptides datasets, 526 N-linked glycoproteins, 1,036 N-linked glycosites, 22,677 N-linked intact glycopeptides and 738 N-Glycan masses were identified under 1% FDR, representing the most in-depth serum N-glycoproteome identified by LC-MS/MS at N-linked intact glycopeptide level and N-linked de-glycopeptides level.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:02:15.813.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	2-pyrrolidone-5-carboxylic acid (Gln); 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.

Shu Q, Li M, Shu L, An Z, Wang J, Lv H, Yang M, Cai T, Hu T, Fu Y, Yang F, Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search. Mol Cell Proteomics, 19(4):672-689(2020) [pubmed]

10.1074/mcp.RA119.001791;

submitter keyword: N-linked intact glycopeptide, co-elution, spectral library search, human serum, isotopic distribution

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: Human serum N-linked intact glycopeptides LC-MS/MS