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Article: Mass Spectrometry-Based Methods for Immunoglobulin G N-Glycosylation Analysis.

Habazin, Siniša / Štambuk, Jerko / Šimunović, Jelena / Keser, Toma / Razdorov, Genadij / Novokmet, Mislav

Experientia supplementum (2012)

2021 Volume 112, Page(s) 73–135

Abstract: Mass spectrometry and its hyphenated techniques enabled by the improvements in liquid chromatography, capillary electrophoresis, novel ionization, and fragmentation modes are truly a cornerstone of robust and reliable protein glycosylation analysis. ... ...

Abstract	Mass spectrometry and its hyphenated techniques enabled by the improvements in liquid chromatography, capillary electrophoresis, novel ionization, and fragmentation modes are truly a cornerstone of robust and reliable protein glycosylation analysis. Boost in immunoglobulin G (IgG) glycan and glycopeptide profiling demands for both applied biomedical and research applications has brought many new advances in the field in terms of technical innovations, sample preparation, improved throughput, and confidence in glycan structural characterization. This chapter summarizes mass spectrometry basics, focusing on IgG and monoclonal antibody N-glycosylation analysis on several complexity levels. Different approaches, including antibody enrichment, glycan release, labeling, and glycopeptide preparation and purification, are covered and illustrated with recent breakthroughs and examples from the literature omitting excessive theoretical frameworks. Finally, selected highly popular methodologies in IgG glycoanalytics such as liquid chromatography-mass spectrometry and matrix-assisted laser desorption ionization are discussed more thoroughly yet in simple terms making this text a practical starting point either for the beginner in the field or an experienced clinician trying to make sense out of the IgG glycomic or glycoproteomic dataset.
MeSH term(s)	Chromatography, Liquid ; Glycopeptides ; Glycosylation ; Immunoglobulin G/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Chemical Substances	Glycopeptides ; Immunoglobulin G
Language	English
Publishing date	2021-10-22
Publishing country	Switzerland
Document type	Journal Article
ISSN	1664-431X
ISSN	1664-431X
DOI	10.1007/978-3-030-76912-3_3
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Article ; Online: BPM1 regulates RdDM-mediated DNA methylation via a cullin 3 independent mechanism

Jagić, Mateja / Vuk, Tamara / Škiljaica, Andreja / Markulin, Lucija / Vičić Bočkor, Vedrana / Tokić, Mirta / Miškec, Karlo / Razdorov, Genadij / Habazin, Siniša / Šoštar, Marko / Weber, Igor / Bauer, Nataša / Leljak Levanić, Dunja

Plant Cell Rep. 2022 Nov., v. 41, no. 11 p.2139-2157

2022

Abstract: KEY MESSAGE: BPM1 interacts with components of the DDR complex and stimulates DNA methylation at CHH sites, suggesting its involvement in the RdDM methylation pathway. The best-known function of MATH-BTB proteins, including Arabidopsis BPM proteins, is ... ...

Abstract	KEY MESSAGE: BPM1 interacts with components of the DDR complex and stimulates DNA methylation at CHH sites, suggesting its involvement in the RdDM methylation pathway. The best-known function of MATH-BTB proteins, including Arabidopsis BPM proteins, is their role as substrate-specific adaptors of CUL3-based E3 ligases in the ubiquitin-proteasome pathway. This paper reports a new CUL3-independent role of BPM1 in RNA-directed DNA methylation (RdDM). Using quantitative and qualitative Y2H, pull down, microscale thermophoresis and FRET-FLIM, we demonstrate that BPM1 interacts with DMS3 and RDM1, components of the chromatin remodeling DDR complex involved in the recruitment of the RdDM methylation machinery. All three proteins colocalized predominantly in the nucleus. The MATH domain, which specifically binds proteins destined for degradation, was not essential for interactions with DMS3 and RDM1. In plants overexpressing BPM1, endogenous DMS3 protein levels were stable, indicating that BPM1 does not induce proteasomal degradation. In RDM1-overexpressing plants, RDM1 was not ubiquitinated. Together, these results suggest that BPM1 does not mediate the degradation of DMS3 and RDM1. Additionally, overexpression of BPM1 caused increased global methylation levels as well as CHH methylation in promoters of two RdDM-regulated genes, FWA and CML41. Overall, BPM1 seems to have a stimulating effect on RdDM activity, and this role appears to be unrelated to its known function as a Cul3-based E3 ligase adaptor.
Keywords	Arabidopsis ; DNA methylation ; chromatin ; ubiquitin-protein ligase
Language	English
Dates of publication	2022-11
Size	p. 2139-2157.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	8397-5
ISSN	1432-203X ; 0721-085X ; 0721-7714
ISSN (online)	1432-203X
ISSN	0721-085X ; 0721-7714
DOI	10.1007/s00299-022-02911-9
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Article ; Online: Developments and perspectives in high-throughput protein glycomics: enabling the analysis of thousands of samples.

de Haan, Noortje / Pučić-Baković, Maja / Novokmet, Mislav / Falck, David / Lageveen-Kammeijer, Guinevere / Razdorov, Genadij / Vučković, Frano / Trbojević-Akmačić, Irena / Gornik, Olga / Hanić, Maja / Wuhrer, Manfred / Lauc, Gordan

Glycobiology

2022 Volume 32, Issue 8, Page(s) 651–663

Abstract: Glycans expand the structural complexity of proteins by several orders of magnitude, resulting in a tremendous analytical challenge when including them in biomedical research. Recent glycobiological research is painting a picture in which glycans ... ...

Abstract	Glycans expand the structural complexity of proteins by several orders of magnitude, resulting in a tremendous analytical challenge when including them in biomedical research. Recent glycobiological research is painting a picture in which glycans represent a crucial structural and functional component of the majority of proteins, with alternative glycosylation of proteins and lipids being an important regulatory mechanism in many biological and pathological processes. Since interindividual differences in glycosylation are extensive, large studies are needed to map the structures and to understand the role of glycosylation in human (patho)physiology. Driven by these challenges, methods have emerged, which can tackle the complexity of glycosylation in thousands of samples, also known as high-throughput (HT) glycomics. For facile dissemination and implementation of HT glycomics technology, the sample preparation, analysis, as well as data mining, need to be stable over a long period of time (months/years), amenable to automation, and available to non-specialized laboratories. Current HT glycomics methods mainly focus on protein N-glycosylation and allow to extensively characterize this subset of the human glycome in large numbers of various biological samples. The ultimate goal in HT glycomics is to gain better knowledge and understanding of the complete human glycome using methods that are easy to adapt and implement in (basic) biomedical research. Aiming to promote wider use and development of HT glycomics, here, we present currently available, emerging, and prospective methods and some of their applications, revealing a largely unexplored molecular layer of the complexity of life.
MeSH term(s)	Glycomics/methods ; Glycosylation ; Humans ; Polysaccharides/chemistry ; Proteins/metabolism
Chemical Substances	Polysaccharides ; Proteins
Language	English
Publishing date	2022-04-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1067689-2
ISSN	1460-2423 ; 0959-6658
ISSN (online)	1460-2423
ISSN	0959-6658
DOI	10.1093/glycob/cwac026
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Article ; Online: BPM1 regulates RdDM-mediated DNA methylation via a cullin 3 independent mechanism.

Plant cell reports

2022 Volume 41, Issue 11, Page(s) 2139–2157

Abstract: Key message: BPM1 interacts with components of the DDR complex and stimulates DNA methylation at CHH sites, suggesting its involvement in the RdDM methylation pathway. The best-known function of MATH-BTB proteins, including Arabidopsis BPM proteins, is ... ...

Abstract	Key message: BPM1 interacts with components of the DDR complex and stimulates DNA methylation at CHH sites, suggesting its involvement in the RdDM methylation pathway. The best-known function of MATH-BTB proteins, including Arabidopsis BPM proteins, is their role as substrate-specific adaptors of CUL3-based E3 ligases in the ubiquitin-proteasome pathway. This paper reports a new CUL3-independent role of BPM1 in RNA-directed DNA methylation (RdDM). Using quantitative and qualitative Y2H, pull down, microscale thermophoresis and FRET-FLIM, we demonstrate that BPM1 interacts with DMS3 and RDM1, components of the chromatin remodeling DDR complex involved in the recruitment of the RdDM methylation machinery. All three proteins colocalized predominantly in the nucleus. The MATH domain, which specifically binds proteins destined for degradation, was not essential for interactions with DMS3 and RDM1. In plants overexpressing BPM1, endogenous DMS3 protein levels were stable, indicating that BPM1 does not induce proteasomal degradation. In RDM1-overexpressing plants, RDM1 was not ubiquitinated. Together, these results suggest that BPM1 does not mediate the degradation of DMS3 and RDM1. Additionally, overexpression of BPM1 caused increased global methylation levels as well as CHH methylation in promoters of two RdDM-regulated genes, FWA and CML41. Overall, BPM1 seems to have a stimulating effect on RdDM activity, and this role appears to be unrelated to its known function as a Cul3-based E3 ligase adaptor.
MeSH term(s)	DNA Methylation/genetics ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Cullin Proteins/genetics ; Cullin Proteins/metabolism ; RNA/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Transcription Factors/genetics ; Homeodomain Proteins/genetics
Chemical Substances	Cullin Proteins ; RNA (63231-63-0) ; Arabidopsis Proteins ; FWA protein, Arabidopsis ; Transcription Factors ; Homeodomain Proteins ; BPM1 protein, Arabidopsis
Language	English
Publishing date	2022-09-06
Publishing country	Germany
Document type	Journal Article
ZDB-ID	8397-5
ISSN	1432-203X ; 0721-085X ; 0721-7714
ISSN (online)	1432-203X
ISSN	0721-085X ; 0721-7714
DOI	10.1007/s00299-022-02911-9
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Article ; Online: High-throughput immunoaffinity enrichment and N-glycan analysis of human plasma haptoglobin.

Šimunović, Jelena / Gašperšič, Jernej / Černigoj, Urh / Vidič, Jana / Štrancar, Aleš / Novokmet, Mislav / Razdorov, Genadij / Pezer, Marija / Lauc, Gordan / Trbojević-Akmačić, Irena

Biotechnology and bioengineering

2022 Volume 120, Issue 2, Page(s) 491–502

Abstract: Haptoglobin (Hp) is a positive acute phase protein, synthesized in the liver, with four N-glycosylation sites carrying mainly complex type N-glycans. Its glycosylation is altered in different types of diseases but still has not been extensively studied ... ...

Abstract	Haptoglobin (Hp) is a positive acute phase protein, synthesized in the liver, with four N-glycosylation sites carrying mainly complex type N-glycans. Its glycosylation is altered in different types of diseases but still has not been extensively studied mainly due to analytical challenges, especially the lack of a fast, efficient, and robust high-throughput Hp isolation procedure. Here, we describe the development of a high-throughput method for Hp enrichment from human plasma, based on monolithic chromatographic support in immunoaffinity mode and downstream Hp N-glycome analysis by hydrophilic interaction ultrahigh-performance liquid chromatography with fluorescent detection (HILIC-UHPLC-FLR). Chromatographic monolithic supports in a 96-well format enable fast, efficient, and robust Hp enrichment directly from diluted plasma samples. The N-glycome analysis demonstrated that a degree of Hp deglycosylation differs depending on the conditions used for N-glycan release and on the specific glycosylation site, with Asn 241 being the most resistant to deglycosylation under tested conditions. HILIC-UHPLC-FLR analysis enables robust quantification of 28 individual chromatographic peaks, in which N-glycan compositions were determined by UHPLC coupled to electrospray ionization quadrupole time of flight mass spectrometry. The developed analytical approach enables fast evaluation of total Hp N-glycosylation and is applicable in large-scale studies.
MeSH term(s)	Humans ; Haptoglobins ; Chromatography, Liquid ; Glycosylation ; Spectrometry, Mass, Electrospray Ionization ; Polysaccharides/chemistry
Chemical Substances	Haptoglobins ; Polysaccharides
Language	English
Publishing date	2022-11-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	280318-5
ISSN	1097-0290 ; 0006-3592
ISSN (online)	1097-0290
ISSN	0006-3592
DOI	10.1002/bit.28280
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Article ; Online: Blood plasma/IgG N-glycome biosignatures associated with major depressive disorder symptom severity and the antidepressant response.

Park, Dong Ik / Štambuk, Jerko / Razdorov, Genadij / Pučić-Baković, Maja / Martins-de-Souza, Daniel / Lauc, Gordan / Turck, Christoph W

Scientific reports

2018 Volume 8, Issue 1, Page(s) 179

Abstract: While N-linked glycosylation has been extensively studied in the context of inflammatory and metabolic disorders, its relationship with major depressive disorder (MDD) and antidepressant treatment response has not been investigated. In our exploratory ... ...

Abstract	While N-linked glycosylation has been extensively studied in the context of inflammatory and metabolic disorders, its relationship with major depressive disorder (MDD) and antidepressant treatment response has not been investigated. In our exploratory study, we analysed N-glycan profiles in blood plasma samples collected from MDD patients (n = 18) and found gender-dependent correlations with severity of depressive symptoms prior to initiating antidepressant treatment. In addition, several N-glycosylation traits showed gender-dependent associations with clinical antidepressant response. Follow up proteomics analysis in peripheral blood mononuclear cells (PBMCs) collected from MDD patients (n = 20) identified baseline and post-antidepressant treatment pathway differences between responder and non-responder patients. Reactome data analysis further delineated potential biological reaction differences between responder and non-responder patients. Our preliminary results suggest that specific glycosylation traits are associated with depressive symptom severity and antidepressant response and may be of use as biomarkers.
MeSH term(s)	Adult ; Aged ; Antidepressive Agents/therapeutic use ; Biomarkers/blood ; Depressive Disorder, Major/blood ; Depressive Disorder, Major/drug therapy ; Female ; Glycosylation ; Humans ; Immunoglobulin G/blood ; Immunoglobulin G/metabolism ; Male ; Middle Aged ; Monocytes/metabolism ; Polysaccharides/blood ; Protein Processing, Post-Translational
Chemical Substances	Antidepressive Agents ; Biomarkers ; Immunoglobulin G ; Polysaccharides
Language	English
Publishing date	2018-01-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-017-17500-0
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Article: LaCyTools: A Targeted Liquid Chromatography–Mass Spectrometry Data Processing Package for Relative Quantitation of Glycopeptides

Jansen, Bas C / Falck David / de Haan Noortje / Hipgrave Ederveen AgnesL / Razdorov Genadij / Lauc Gordan / Wuhrer Manfred

Journal of Proteome Research. 2016 July 01, v. 15, no. 7

2016

Abstract: Bottom-up glycoproteomics by liquid chromatography–mass spectrometry (LC–MS) is an established approach for assessing glycosylation in a protein- and site-specific manner. Consequently, tools are needed to automatically align, calibrate, and integrate LC– ...

Abstract	Bottom-up glycoproteomics by liquid chromatography–mass spectrometry (LC–MS) is an established approach for assessing glycosylation in a protein- and site-specific manner. Consequently, tools are needed to automatically align, calibrate, and integrate LC–MS glycoproteomics data. We developed a modular software package designed to tackle the individual aspects of an LC–MS experiment, called LaCyTools. Targeted alignment is performed using user defined m/z and retention time (tᵣ) combinations. Subsequently, sum spectra are created for each user defined analyte group. Quantitation is performed on the sum spectra, where each user defined analyte can have its own tᵣ, minimum, and maximum charge states. Consequently, LaCyTools deals with multiple charge states, which gives an output per charge state if desired, and offers various analyte and spectra quality criteria. We compared throughput and performance of LaCyTools to combinations of available tools that deal with individual processing steps. LaCyTools yielded relative quantitation of equal precision (relative standard deviation <0.5%) and higher trueness due to the use of MS peak area instead of MS peak intensity. In conclusion, LaCyTools is an accurate automated data processing tool for high-throughput analysis of LC–MS glycoproteomics data. Released under the Apache 2.0 license, it is freely available on GitHub (https://github.com/Tarskin/LaCyTools).
Keywords	computer software ; glycopeptides ; glycoproteomics ; glycosylation ; information processing ; liquid chromatography ; mass spectrometry ; proteome ; statistical analysis
Language	English
Dates of publication	2016-0701
Size	p. 2198-2210.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021%2Facs.jproteome.6b00171
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Article: The MATH-BTB Protein TaMAB2 Accumulates in Ubiquitin-Containing Foci and Interacts With the Translation Initiation Machinery in

Bauer, Nataša / Škiljaica, Andreja / Malenica, Nenad / Razdorov, Genadij / Klasić, Marija / Juranić, Martina / Močibob, Marko / Sprunck, Stefanie / Dresselhaus, Thomas / Leljak Levanić, Dunja

Frontiers in plant science

2019 Volume 10, Page(s) 1469

Abstract: MATH-BTB proteins are known to act as substrate-specific adaptors of CUL3-based E3 ligases in the ubiquitin proteasome pathway. Their BTB domain binds to CUL3 scaffold proteins and the less conserved MATH domain targets a highly diverse collection of ... ...

Abstract	MATH-BTB proteins are known to act as substrate-specific adaptors of CUL3-based E3 ligases in the ubiquitin proteasome pathway. Their BTB domain binds to CUL3 scaffold proteins and the less conserved MATH domain targets a highly diverse collection of substrate proteins to promote their ubiquitination and subsequent degradation. In plants, a significant expansion of the MATH-BTB family occurred in the grasses. Here, we report analysis of TaMAB2, a MATH-BTB protein transiently expressed at the onset of embryogenesis in wheat. Due to difficulties in studying its role in zygotes and early embryos, we have overexpressed
Language	English
Publishing date	2019-11-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2019.01469
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Article ; Online: LaCyTools: A Targeted Liquid Chromatography-Mass Spectrometry Data Processing Package for Relative Quantitation of Glycopeptides.

Jansen, Bas C / Falck, David / de Haan, Noortje / Hipgrave Ederveen, Agnes L / Razdorov, Genadij / Lauc, Gordan / Wuhrer, Manfred

Journal of proteome research

2016 Volume 15, Issue 7, Page(s) 2198–2210

Abstract: Bottom-up glycoproteomics by liquid chromatography-mass spectrometry (LC-MS) is an established approach for assessing glycosylation in a protein- and site-specific manner. Consequently, tools are needed to automatically align, calibrate, and integrate LC- ...

Abstract	Bottom-up glycoproteomics by liquid chromatography-mass spectrometry (LC-MS) is an established approach for assessing glycosylation in a protein- and site-specific manner. Consequently, tools are needed to automatically align, calibrate, and integrate LC-MS glycoproteomics data. We developed a modular software package designed to tackle the individual aspects of an LC-MS experiment, called LaCyTools. Targeted alignment is performed using user defined m/z and retention time (tr) combinations. Subsequently, sum spectra are created for each user defined analyte group. Quantitation is performed on the sum spectra, where each user defined analyte can have its own tr, minimum, and maximum charge states. Consequently, LaCyTools deals with multiple charge states, which gives an output per charge state if desired, and offers various analyte and spectra quality criteria. We compared throughput and performance of LaCyTools to combinations of available tools that deal with individual processing steps. LaCyTools yielded relative quantitation of equal precision (relative standard deviation <0.5%) and higher trueness due to the use of MS peak area instead of MS peak intensity. In conclusion, LaCyTools is an accurate automated data processing tool for high-throughput analysis of LC-MS glycoproteomics data. Released under the Apache 2.0 license, it is freely available on GitHub ( https://github.com/Tarskin/LaCyTools ).
MeSH term(s)	Automatic Data Processing/methods ; Chromatography, Liquid ; Glycopeptides/analysis ; Mass Spectrometry ; Proteomics/methods ; Proteomics/standards ; Software
Chemical Substances	Glycopeptides
Language	English
Publishing date	2016-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.6b00171
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Article ; Online: MIgGGly (mouse IgG glycosylation analysis) - a high-throughput method for studying Fc-linked IgG N-glycosylation in mice with nanoUPLC-ESI-MS.

Zaytseva, Olga O / Jansen, Bas C / Hanić, Maja / Mrčela, Mia / Razdorov, Genadij / Stojković, Ranko / Erhardt, Julija / Brizić, Ilija / Jonjić, Stipan / Pezer, Marija / Lauc, Gordan

Scientific reports

2018 Volume 8, Issue 1, Page(s) 13688

Abstract: Immunoglobulin G (IgG) N-glycosylation is crucial for its effector functions. It is a complex trait, and large sample sets are needed to discover multiple genetic factors that underlie it. While in humans such high-throughput studies of IgG N-glycans ... ...

Abstract	Immunoglobulin G (IgG) N-glycosylation is crucial for its effector functions. It is a complex trait, and large sample sets are needed to discover multiple genetic factors that underlie it. While in humans such high-throughput studies of IgG N-glycans became usual, only one has been carried out in mice. Here we describe and validate a method for the relative quantification of IgG Fc-linked N-glycans in a subclass-specific manner using nano-reverse phase liquid chromatography coupled with mass-spectrometry (nanoRP-LC-MS) applied to murine IgG. High-throughput data processing is ensured by the LaCyTools software. We have shown that IgG isolation procedure is the main source of technical variation in the current protocol. The major glycoforms were quantified reliably with coefficients of variation below 6% for all the analytes with relative abundances above 5%. We have applied our method to a sample set of 3 inbred strains: BALB/c, C57BL/6 and C3H and observed differences in subclass-specific and strain-specific N-glycosylation of IgG, suggesting a significant genetic component in the regulation of Fc-linked IgG N-glycosylation.
MeSH term(s)	Animals ; Chromatography, High Pressure Liquid/methods ; Glycosylation ; Immunoglobulin Fc Fragments/blood ; Immunoglobulin G/blood ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C3H ; Mice, Inbred C57BL ; Polysaccharides/blood ; Spectrometry, Mass, Electrospray Ionization/methods
Chemical Substances	Immunoglobulin Fc Fragments ; Immunoglobulin G ; Polysaccharides ; glycosylated IgG
Language	English
Publishing date	2018-09-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-31844-1
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