Benchmark of site- and structure-specific quantitative tissue N-glycoproteomics for discovery of potential N-glycoprotein markers: a case study of pancreatic cancer

Pancreatic cancer is a highly malignant tumor of the digestive tract that is difficult to diagnose and treat. It is more common in developed countries and has become one of the main causes of death in some countries and regions. Currently, pancreatic cancer generally has a poor prognosis, partly due...

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Bibliographic Details
Published in:Glycoconjugate journal 2021-04, Vol.38 (2), p.213-231
Main Authors: Lu, Haoran, Xiao, Kaijie, Tian, Zhixin
Format: Article
Language:English
Subjects:
Antibiotics
Benchmarking
Biochemistry
Biomarkers, Tumor - metabolism
Biomedical and Life Sciences
Databases, Protein
Gastrointestinal tract
Glycopeptides
Glycoproteins
Glycoproteins - analysis
Glycoproteins - chemistry
Glycoproteins - metabolism
Humans
Isotope Labeling
Life Sciences
Mass Spectrometry and the Analysis of Glycoconjugates
Mass spectroscopy
Monosaccharides
Original Article
Pancreatic cancer
Pancreatic Neoplasms - metabolism
Pathology
Proteomics - methods
Search Engine
Tandem Mass Spectrometry - methods
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Summary:Pancreatic cancer is a highly malignant tumor of the digestive tract that is difficult to diagnose and treat. It is more common in developed countries and has become one of the main causes of death in some countries and regions. Currently, pancreatic cancer generally has a poor prognosis, partly due to the lack of symptoms in the early stages of pancreatic cancer. Therefore, most cases are diagnosed at advanced stage. With the continuous in-depth research of glycoproteomics in precision medical diagnosis, there have been some reports on quantitative analysis of cancer-related cells, plasma or tissues to find specific biomarkers for targeted therapy. This research is based on the developed complete N-linked glycopeptide database search engine GPSeeker, combined with liquid-mass spectrometry and stable diethyl isotope labeling, providing a benchmark of site- and structure-specific quantitative tissue N-glycoproteomics for discovery of potential N-glycoprotein markers. With spectrum-level FDR ≤1%, 20,038 intact N-Glycopeptides corresponding to 4518 peptide backbones, 228 N-glycan monosaccharide compositions 1026 N-glycan putative structures, 4460 N-glycosites and 3437 intact N-glycoproteins were identified. With the criteria of ≥1.5-fold change and p value
ISSN:0282-0080
1573-4986
DOI:10.1007/s10719-021-09994-8