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Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search
Shu, Qingbo1,2,3; Li, Mengjie3,4; Shu, Lian1,3,5; An, Zhiwu3,4; Wang, Jifeng1; Lv, Hao3,4,6; Yang, Ming1,3; Cai, Tanxi1,3; Hu, Tony2; Fu, Yan3,4; Yang, Fuquan1,5
2020-04-01
Source PublicationMOLECULAR & CELLULAR PROTEOMICS
ISSN1535-9476
Volume19Issue:4Pages:672-689
AbstractLarge-scale identification of N-linked intact glycopeptides by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) in human serum is challenging because of the wide dynamic range of serum protein abundances, the lack of a complete serum N-glycan database and the existence of proteoforms. In this regard, a spectral library search method was presented for the identification of N-linked intact glycopeptides from N-linked glycoproteins in human serum with target-decoy and motif-specific false discovery rate (FDR) control. Serum proteins were firstly separated into low-abundance and high-abundance proteins by acetonitrile (ACN) precipitation. After digestion, the N-linked intact glycopeptides were enriched by hydrophilic interaction liquid chromatography (HILIC) and a portion of the enriched N-linked intact glycopeptides were processed by Peptide-N-Glycosidase F (PNGase F) to generate N-linked deglycopeptides. Both N-linked intact glycopeptides and deglycopeptides were analyzed by LC-MS/MS. From N-linked deglycopeptides data sets, 764 N-linked glycoproteins, 1699 N-linked glycosites and 3328 unique N-linked deglycopeptides were identified. Four types of N-linked glycosylation motifs (NXS/T/C/V, X not equal P) were used to recognize the N-linked deglycopeptides. The spectra of these N-linked deglycopeptides were utilized for N-linked deglycopeptides library construction and identification of N-linked intact glycopeptides. A database containing 739 N-glycan masses was constructed and utilized during spectral library search for the identification of N-linked intact glycopeptides. In total, 526 N-linked glycoproteins, 1036 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.
DOI10.1074/mcp.RA119.001791
Indexed BySCI
Language英语
Funding ProjectNational Key R&D Program of China[2018YFA0507801] ; National Key R&D Program of China[2018YFA0507103] ; National Natural Science Foundation of China[91640112] ; National Natural Science Foundation of China[21607170] ; National Natural Science Foundation of China[31670185] ; Strategic Priority Research Programs of the Chinese Academy of Sciences[XDA12030202] ; NCMIS CAS
WOS Research AreaBiochemistry & Molecular Biology
WOS SubjectBiochemical Research Methods
WOS IDWOS:000524532100010
PublisherAMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
Citation statistics
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/51179
Collection中国科学院数学与系统科学研究院
Corresponding AuthorFu, Yan; Yang, Fuquan
Affiliation1.Chinese Acad Sci, Inst Biophys, Lab Prot & Peptide Pharmaceut & Prote Lab, Beijing 100101, Peoples R China
2.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Key Lab Random Complex Struct & Data Sci, Beijing 100190, Peoples R China
3.Tulane Univ, Ctr Cellular & Mol Diagnost, Sch Med, Dept Biochem & Mol Biol, New Orleans, LA 70112 USA
4.Chinese Acad Sci, Comp Network Informat Ctr, Beijing 100101, Peoples R China
5.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
6.Guizhou Med Univ, Basic Med Coll, Res Ctr Basic Sci Med, Guiyang 550025, Peoples R China
Recommended Citation
GB/T 7714
Shu, Qingbo,Li, Mengjie,Shu, Lian,et al. Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search[J]. MOLECULAR & CELLULAR PROTEOMICS,2020,19(4):672-689.
APA Shu, Qingbo.,Li, Mengjie.,Shu, Lian.,An, Zhiwu.,Wang, Jifeng.,...&Yang, Fuquan.(2020).Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search.MOLECULAR & CELLULAR PROTEOMICS,19(4),672-689.
MLA Shu, Qingbo,et al."Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search".MOLECULAR & CELLULAR PROTEOMICS 19.4(2020):672-689.
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