Multistage mass spectrometry with intelligent precursor selection for N-glycan branching pattern analysis.

Biological functions of N-glycans are frequently related to their unique branching patterns. Multistage mass spectrometry (MSn) has become the primary method for glycan structural analysis. However, selection of the best fragment as the precursor for the next round of product-ion scanning is important but difficult. We have previously proposed the concept and designed the approach of glycan intelligent precursor selection (GIPS) to guide MSn experiments, but its use in N-glycans is not straightforward as some N-glycans are of high similarity in branching patterns. In the present work we introduced new elements to GIPS to improve its performance in N-glycan branching pattern analysis. These include a hypothesis and significance test, based on Bayes factor, and DPbiased as a new precursor selection strategy. The improved GIPS was successfully applied to identification of individual N-glycans, and incorporated into MALDI-MS N-glycan profiling for assignment of N-glycans obtained from glycoproteins and complex human serum.

[1]  Matthew P. Campbell,et al.  Quantitative profiling of glycans and glycopeptides: an informatics' perspective. , 2016, Current opinion in structural biology.

[2]  A. Carvalho,et al.  Unravelling Glucan Recognition Systems by Glycome Microarrays Using the Designer Approach and Mass Spectrometry , 2015, Molecular & Cellular Proteomics.

[3]  René Ranzinger,et al.  “Glyco‐peakfinder” – de novo composition analysis of glycoconjugates , 2007, Proteomics.

[4]  David J. Harvey,et al.  N-glycan microheterogeneity regulates interactions of plasma proteins , 2018, Proceedings of the National Academy of Sciences.

[5]  Martin Frank,et al.  EUROCarbDB: An open-access platform for glycoinformatics , 2010, Glycobiology.

[6]  R. Dwek,et al.  Structural and quantitative analysis of N-linked glycans by matrix-assisted laser desorption ionization and negative ion nanospray mass spectrometry. , 2008, Analytical biochemistry.

[7]  Philip G. Evans,et al.  Analysis of chain and blood group type and branching pattern of sialylated oligosaccharides by negative ion electrospray tandem mass spectrometry. , 2006, Analytical chemistry.

[8]  Oliver Horlacher,et al.  Towards a standardized bioinformatics infrastructure for N- and O-glycomics , 2019, Nature Communications.

[9]  S. Todo,et al.  Age- and gender-related differences in carbohydrate concentrations of α1-acid glycoprotein variants and the effects of glycoforms on their drug-binding capacities , 2002, European Journal of Clinical Pharmacology.

[10]  Congjian Xu,et al.  Distribution of IgG galactosylation as a promising biomarker for cancer screening in multiple cancer types , 2016, Cell Research.

[11]  P. Albersheim,et al.  Letter to the Glyco-Forum , 1991 .

[12]  Kiyoko F. Aoki-Kinoshita,et al.  GlyTouCan: an accessible glycan structure repository. , 2017, Glycobiology.

[13]  James C Paulson,et al.  Sweet spots in functional glycomics , 2006, Nature chemical biology.

[14]  M. Longtine,et al.  Evidence for Differential Glycosylation of Trophoblast Cell Types* , 2016, Molecular & Cellular Proteomics.

[15]  M. Tarlov,et al.  Selective binding of RNase B glycoforms by polydopamine-immobilized concanavalin A. , 2009, Analytical chemistry.

[16]  Qi Zhang,et al.  Best-first search guided multistage mass spectrometry-based glycan identification , 2019, Bioinform..

[17]  A. Rizzi,et al.  Quantitative isomer-specific N-glycan fingerprinting using isotope coded labeling and high performance liquid chromatography-electrospray ionization-mass spectrometry with graphitic carbon stationary phase. , 2015, Journal of chromatography. A.

[18]  W. Chai,et al.  Negative-Ion Electrospray Tandem Mass Spectrometry and Microarray Analyses of Developmentally Regulated Antigens Based on Type 1 and Type 2 Backbone Sequences. , 2015, Analytical chemistry.

[19]  J. Paulson,et al.  Glycomics: an integrated systems approach to structure-function relationships of glycans , 2005, Nature Methods.

[20]  D. Ashline,et al.  Isomeric complexity of glycosylation documented by MSn , 2016, Analytical and Bioanalytical Chemistry.

[21]  David J. Harvey,et al.  Electrospray mass spectrometry and fragmentation of N-linked carbohydrates derivatized at the reducing terminus , 2000, Journal of the American Society for Mass Spectrometry.

[22]  Martin Frank,et al.  GlycomeDB—a unified database for carbohydrate structures , 2010, Nucleic Acids Res..

[23]  Joseph Zaia,et al.  Algorithms and design strategies towards automated glycoproteomics analysis. , 2017, Mass spectrometry reviews.

[24]  Joseph Zaia,et al.  Mass spectrometry and the emerging field of glycomics. , 2008, Chemistry & biology.

[25]  André M Deelder,et al.  IgG glycosylation analysis , 2009, Proteomics.

[26]  Serge Perez,et al.  Databases of Conformations and NMR Structures of Glycan Determinants. , 2015, Glycobiology.

[27]  L. Dijkhuizen,et al.  Large-scale quantitative isolation of pure protein N-linked glycans. , 2019, Carbohydrate research.

[28]  Akiyasu C. Yoshizawa,et al.  GlycanAnalysis Plug-in: a database search tool for N-glycan structures using mass spectrometry , 2015, Bioinform..

[29]  Manfred Wuhrer,et al.  Comparison of methods for the analysis of therapeutic immunoglobulin G Fc-glycosylation profiles—Part 1: Separation-based methods , 2014, mAbs.

[30]  B Leijnse,et al.  Alterations in carbohydrate composition of serum IgG from patients with rheumatoid arthritis and from pregnant women. , 1988, Annals of the rheumatic diseases.

[31]  K. Khoo,et al.  Mass spectrometry of carbohydrate-containing biopolymers. , 1994, Methods in enzymology.

[32]  H. Kuwano,et al.  Fucosylated Glycans in α1-Acid Glycoprotein for Monitoring Treatment Outcomes and Prognosis of Cancer Patients , 2016, PloS one.

[33]  Niclas G Karlsson,et al.  Development of a mass fingerprinting tool for automated interpretation of oligosaccharide fragmentation data , 2004, Proteomics.

[34]  C. Lebrilla,et al.  Annotation of a serum N-glycan library for rapid identification of structures. , 2012, Journal of proteome research.

[35]  Kiyoko F. Aoki-Kinoshita,et al.  GlyTouCan 1.0 – The international glycan structure repository , 2015, Nucleic Acids Res..

[36]  Hailong Zhang,et al.  Toward a Platform for Comprehensive Glycan Sequencing* , 2013, Molecular & Cellular Proteomics.

[37]  Chuncui Huang,et al.  Distribution of abnormal IgG glycosylation patterns from rheumatoid arthritis and osteoarthritis patients by MALDI-TOF-MSn. , 2019, The Analyst.

[38]  M. Anugraham,et al.  Specific Glycosylation of Membrane Proteins in Epithelial Ovarian Cancer Cell Lines: Glycan Structures Reflect Gene Expression and DNA Methylation Status * , 2014, Molecular & Cellular Proteomics.

[39]  Kiyoko F. Aoki-Kinoshita,et al.  KEGG as a glycome informatics resource. , 2006, Glycobiology.

[40]  J. Marth,et al.  Mammalian glycosylation in immunity , 2008, Nature Reviews Immunology.

[41]  Dongbo Bu,et al.  De novo glycan structural identification from mass spectra using tree merging strategy , 2019, Comput. Biol. Chem..

[42]  Andrew G McDonald,et al.  Databases and tools in glycobiology. , 2012, Methods in molecular biology.

[43]  N. Packer,et al.  N-glycan MALDI Imaging Mass Spectrometry on Formalin-Fixed Paraffin-Embedded Tissue Enables the Delineation of Ovarian Cancer Tissues * , 2016, Molecular & Cellular Proteomics.

[44]  T. Fournier,et al.  Alpha-1-acid glycoprotein. , 2000, Biochimica et biophysica acta.

[45]  K Bock,et al.  The Complex Carbohydrate Structure Database. , 1989, Trends in biochemical sciences.

[46]  D. Bu,et al.  Identification of glycan branching patterns using multistage mass spectrometry with spectra tree analysis. , 2020, Journal of proteomics.

[47]  D. Ashline,et al.  Congruent strategies for carbohydrate sequencing. 1. Mining structural details by MSn. , 2005, Analytical chemistry.

[48]  D. Ashline,et al.  Carbohydrate structural isomers analyzed by sequential mass spectrometry. , 2007, Analytical chemistry.

[49]  D. Bu,et al.  Toward Automated Identification of Glycan Branching Patterns Using Multistage Mass Spectrometry with Intelligent Precursor Selection. , 2018, Analytical chemistry.

[50]  N. Taniguchi,et al.  Enzymes for N-Glycan Branching and Their Genetic and Nongenetic Regulation in Cancer , 2016, Biomolecules.

[51]  N. Edwards,et al.  Site-specific Glycoforms of Haptoglobin in Liver Cirrhosis and Hepatocellular Carcinoma* , 2013, Molecular & Cellular Proteomics.