A semi-automated, high throughput approach for O-glycosylation profiling of in vitro established cancer cell lines by MALDI-FT-ICR MS.

The study of protein O-glycosylation is important in biological research as O-glycans have been reported to regulate a multitude of molecular and cell biology processes occurring in cancer. It is known that alterations in O-glycosylation are involved in the development and progression of cancer. Their easy accessibility makes in vitro established cell lines suitable and useful models for studying biological mechanisms in disease. However, the O-glycosylation analysis of large numbers of samples, as required in systems biology and biomarker discovery studies, is often challenging. In the present study, O-glycans from three human colorectal cancer cell lines and two human pancreatic cancer cell lines were released by semi-automated, high throughput reductive ß-elimination and analysed using ultrahigh resolution MALDI-FT-ICR MS. Automated data integration and processing was performed using MassyTools, where the analyte was automatically included for relative quantitation based on a range of selection criteria including signal-to-noise ratio, mass error and isotopic pattern quality scores. A total of 126 O-glycan compositions, ranging from a single monosaccharide to large oligosaccharides exhibiting complex glycan motifs, were detected. The use of ultrahigh resolution MALDI-FTICR MS enabled glycan identification and quantitation in the matrix region of the spectrum. This approach has the potential to be used for O-glycosylation analysis of large numbers of samples, such as patient sample cohorts.

Interlaboratory evaluation of plasma N-glycan antennary fucosylation as a clinical biomarker for HNF1A-MODY using liquid chromatography methods.

Antennary fucosylation alterations in plasma glycoproteins have been previously proposed and tested as a biomarker for differentiation of maturity onset diabetes of the young (MODY) patients carrying a functional mutation in the HNF1A gene. Here, we developed a novel LC-based workflow to analyze blood plasma N-glycan fucosylation in 320 diabetes cases with clinical features matching those at risk of HNF1A-MODY. Fucosylation levels measured in two independent research centers by using similar LC-based methods were correlated to evaluate the interlaboratory performance of the biomarker. The interlaboratory study showed good correlation between fucosylation levels measured for the 320 cases in the two centers with the correlation coefficient (r) of up to 0.88 for a single trait A3FG3S2. The improved chromatographic separation allowed the identification of six single glycan traits and a derived antennary fucosylation trait that were able to differentiate individuals carrying pathogenic mutations from benign or no HNF1A mutation cases, as determined by the area under the curve (AUC) of up to 0.94. The excellent (r = 0.88) interlaboratory performance of the glycan biomarker for HNF1A-MODY further supports the development of a clinically relevant diagnostic test measuring antennary fucosylation levels.

Hinge-Region O-Glycosylation of Human Immunoglobulin G3 (IgG3).

Immunoglobulin G (IgG) is one of the most abundant proteins present in human serum and a fundamental component of the immune system. IgG3 represents ∼8% of the total amount of IgG in human serum and stands out from the other IgG subclasses because of its elongated hinge region and enhanced effector functions. This study reports partial O-glycosylation of the IgG3 hinge region, observed with nanoLC-ESI-IT-MS(/MS) analysis after proteolytic digestion. The repeat regions within the IgG3 hinge were found to be in part O-glycosylated at the threonine in the triple repeat motif. Non-, mono- and disialylated core 1-type O-glycans were detected in various IgG3 samples, both poly- and monoclonal. NanoLC-ESI-IT-MS/MS with electron transfer dissociation fragmentation and CE-MS/MS with CID fragmentation were used to determine the site of IgG3 O-glycosylation. The O-glycosylation site was further confirmed by the recombinant production of mutant IgG3 in which potential O-glycosylation sites had been knocked out. For IgG3 samples from six donors we found similar O-glycan structures and site occupancies, whereas for the same samples the conserved N-glycosylation of the Fc CH2 domain showed considerable interindividual variation. The occupancy of each of the three O-glycosylation sites was found to be ∼10% in six serum-derived IgG3 samples and ∼13% in two monoclonal IgG3 allotypes.

LaCyTools: A Targeted Liquid Chromatography-Mass Spectrometry Data Processing Package for Relative Quantitation of Glycopeptides.

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 ).

Dopant Enriched Nitrogen Gas Combined with Sheathless Capillary Electrophoresis-Electrospray Ionization-Mass Spectrometry for Improved Sensitivity and Repeatability in Glycopeptide Analysis.

Over the last years, numerous strategies have been proposed to enhance both ionization efficiency and spray stability in electrospray ionization (ESI), in particular for nanospray applications. In nano-liquid chromatography-mass spectrometry (nano-LC-ESI-MS), a better ESI performance has been observed when a coaxial gas flow is added around the ESI emitter. Moreover, enrichment of the gas with an organic dopant has led to an improved desolvation and ionization efficiency with an overall enhanced sensitivity. In this study, the use of a dopant enriched nitrogen (DEN)-gas combined with sheathless capillary electrophoresis (CE)-ESI-MS was evaluated for glycopeptide analysis. Using acetonitrile as a dopant, an increased sensitivity was observed compared to conventional sheathless CE-ESI-MS. Up to 25-fold higher sensitivities for model glycopeptides were obtained, allowing for limits of detection unachieved by state-of-the-art nano-LC-ESI-MS. The effect of DEN-gas on the repeatability and intermediate precision was also investigated. When compared to previously reported nano-LC-ESI-MS measurements, similar values were found for CE-ESI-MS with DEN-gas. The enhanced repeatability fosters the use of DEN-gas sheathless CE-ESI-MS in protein glycosylation analysis, where precision is essential. The use of DEN-gas opens new avenues for highly sensitive sheathless CE-ESI-MS approaches in glycoproteomics research, by significantly improving sensitivity and precision.

Human plasma protein N-glycosylation.

Glycosylation is the most abundant and complex protein modification, and can have a profound structural and functional effect on the conjugate. The oligosaccharide fraction is recognized to be involved in multiple biological processes, and to affect proteins physical properties, and has consequentially been labeled a critical quality attribute of biopharmaceuticals. Additionally, due to recent advances in analytical methods and analysis software, glycosylation is targeted in the search for disease biomarkers for early diagnosis and patient stratification. Biofluids such as saliva, serum or plasma are of great use in this regard, as they are easily accessible and can provide relevant glycosylation information. Thus, as the assessment of protein glycosylation is becoming a major element in clinical and biopharmaceutical research, this review aims to convey the current state of knowledge on the N-glycosylation of the major plasma glycoproteins alpha-1-acid glycoprotein, alpha-1-antitrypsin, alpha-1B-glycoprotein, alpha-2-HS-glycoprotein, alpha-2-macroglobulin, antithrombin-III, apolipoprotein B-100, apolipoprotein D, apolipoprotein F, beta-2-glycoprotein 1, ceruloplasmin, fibrinogen, immunoglobulin (Ig) A, IgG, IgM, haptoglobin, hemopexin, histidine-rich glycoprotein, kininogen-1, serotransferrin, vitronectin, and zinc-alpha-2-glycoprotein. In addition, the less abundant immunoglobulins D and E are included because of their major relevance in immunology and biopharmaceutical research. Where available, the glycosylation is described in a site-specific manner. In the discussion, we put the glycosylation of individual proteins into perspective and speculate how the individual proteins may contribute to a total plasma N-glycosylation profile determined at the released glycan level.

Acute phase inflammation is characterized by rapid changes in plasma/peritoneal fluid N-glycosylation in mice.

Murine zymosan-induced peritonitis is a widely used model for studying the molecular and cellular events responsible for the initiation, persistence and/or resolution of inflammation. Among these events, it is becoming increasingly evident that changes in glycosylation of proteins, especially in the plasma and at the site of inflammation, play an important role in the inflammatory response. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS)-based glycosylation profiling, we investigated the qualitative and quantitative effect of zymosan-induced peritonitis on N-glycosylation in mouse plasma and peritoneal fluid. Our results show that both N-glycomes exhibit highly similar glycosylation patterns, consisting mainly of diantennary and triantennary complex type N-glycans with high levels (>95 %) of galactosylation and sialylation (mostly NeuGc) and a medium degree of core fucosylation (30 %). Moreover, MS/MS structural analysis, assisted by linkage-specific derivatization of sialic acids, revealed the presence of O-acetylated sialic acids as well as disialylated antennae ("branching sialylation") characterized by the presence of α2-6-linked NeuGc on the GlcNAc of the NeuGcα2-3-Galß1-3-GlcNAc terminal motif. A significant decrease of (core) fucosylation together with an increase of both α2-3-linked NeuGc and "branching sialylation" were observed in N-glycomes of mice challenged with zymosan, but not in control mice injected with PBS. Importantly, substantial changes in glycosylation were already observed 12 h after induction of peritonitis, thereby demonstrating an unexpected velocity of the biological mechanisms involved.

Glycoforms of Immunoglobulin G Based Biopharmaceuticals Are Differentially Cleaved by Trypsin Due to the Glycoform Influence on Higher-Order Structure.

It has been reported that glycosylation can influence the proteolytic cleavage of proteins. A thorough investigation of this phenomenon was conducted for the serine protease trypsin, which is essential in many proteomics workflows. Monoclonal and polyclonal immunoglobulin G biopharmaceuticals were employed as model substances, which are highly relevant for the bioanalytical applications. Relative quantitation of glycopeptides derived from the conserved Fc-glycosylation site allowed resolution of biases on the level of individual glycan compositions. As a result, a strong preferential digestion of high mannose, hybrid, alpha2-3-sialylated and bisected glycoforms was observed over the most abundant neutral, fucosylated glycoforms. Interestingly, this bias was, to a large extent, dependent on the intact higher order structure of the antibodies and, consequently, was drastically reduced in denatured versus intact antibodies. In addition, a cleavage protocol with acidic denaturation was tested, which featured reduced hands-on time and toxicity while showing highly comparable results to a published denaturation, reduction, and alkylation based protocol.

MassyTools: A High-Throughput Targeted Data Processing Tool for Relative Quantitation and Quality Control Developed for Glycomic and Glycoproteomic MALDI-MS.

The study of N-linked glycosylation has long been complicated by a lack of bioinformatics tools. In particular, there is still a lack of fast and robust data processing tools for targeted (relative) quantitation. We have developed modular, high-throughput data processing software, MassyTools, that is capable of calibrating spectra, extracting data, and performing quality control calculations based on a user-defined list of glycan or glycopeptide compositions. Typical examples of output include relative areas after background subtraction, isotopic pattern-based quality scores, spectral quality scores, and signal-to-noise ratios. We demonstrated MassyTools' performance on MALDI-TOF-MS glycan and glycopeptide data from different samples. MassyTools yielded better calibration than the commercial software flexAnalysis, generally showing 2-fold better ppm errors after internal calibration. Relative quantitation using MassyTools and flexAnalysis gave similar results, yielding a relative standard deviation (RSD) of the main glycan of ~6%. However, MassyTools yielded 2- to 5-fold lower RSD values for low-abundant analytes than flexAnalysis. Additionally, feature curation based on the computed quality criteria improved the data quality. In conclusion, we show that MassyTools is a robust automated data processing tool for high-throughput, high-performance glycosylation analysis. The package is released under the Apache 2.0 license and is freely available on GitHub ( https://github.com/Tarskin/MassyTools ).

A Comparison of Inertial Measurement Units and Overnight Videography to Assess Sleep Biomechanics.

PURPOSE: The assessment of sleep biomechanics (comprising movement and position during sleep) is of interest in a wide variety of clinical and research settings. However, there is no standard method by which sleep biomechanics are measured. This study aimed to (1) compare the intra- and inter-rater reliability of the current clinical standard, manually coded overnight videography, and (2) compare sleep position recorded using overnight videography to sleep position recorded using the XSENS DOT wearable sensor platform. METHODS: Ten healthy adult volunteers slept for one night with XSENS DOT units in situ (on their chest, pelvis, and left and right thighs), with three infrared video cameras recording concurrently. Ten clips per participant were edited from the video. Sleeping position in each clip was coded by six experienced allied health professionals using the novel Body Orientation During Sleep (BODS) Framework, comprising 12 sections in a 360-degree circle. Intra-rater reliability was assessed by calculating the differences between the BODS ratings from repeated clips and the percentage who were rated with a maximum of one section of the XSENS DOT value; the same methodology was used to establish the level of agreement between the XSENS DOT and allied health professional ratings of overnight videography. Bennett's S-Score was used to assess inter-rater reliability. RESULTS: High intra-rater reliability (90% of ratings with maximum difference of one section) and moderate inter-rater reliability (Bennett's S-Score 0.466 to 0.632) were demonstrated in the BODS ratings. The raters demonstrated high levels of agreement overall with the XSENS DOT platform, with 90% of ratings from allied health raters being within the range of at least 1 section of the BODS (as compared to the corresponding XSENS DOT produced rating). CONCLUSIONS: The current clinical standard for assessing sleep biomechanics, manually rated overnight videography (as rated using the BODS Framework) demonstrated acceptable intra- and inter-rater reliability. Further, the XSENS DOT platform demonstrated satisfactory levels of agreement as compared to the current clinical standard, providing confidence for its use in future studies of sleep biomechanics.

Serum N-Glycomic Biomarkers Predict Treatment Escalation in Inflammatory Bowel Disease.

Biomarkers to guide clinical decision making at diagnosis of inflammatory bowel disease [IBD] are urgently needed. We investigated a composite serum N-glycomic biomarker to predict future disease course in a discovery cohort of 244 newly diagnosed IBD patients. In all, 47 individual glycan peaks were analysed using ultra-high performance liquid chromatography, identifying 105 glycoforms from which 24 derived glycan traits were calculated. Multivariable logistic regression was performed to determine associations of derived glycan traits with disease. Cox proportional hazard models were used to predict treatment escalation from first-line treatment to biologics or surgery (hazard ratio [HR] 25.9, p = 1.1 × 10-12; 95% confidence interval [CI], 8.52-78.78). Application to an independent replication cohort of 54 IBD patients yielded an HR of 5.1 [p = 1.1 × 10-5; 95% CI, 2.54-10.1]. These data demonstrate the prognostic capacity of serum N-glycan biomarkers and represent a step towards personalised medicine in IBD.

Neutron-encoded diubiquitins to profile linkage selectivity of deubiquitinating enzymes.

Deubiquitinating enzymes are key regulators in the ubiquitin system and an emerging class of drug targets. These proteases disassemble polyubiquitin chains and many deubiquitinases show selectivity for specific polyubiquitin linkages. However, most biochemical insights originate from studies of single diubiquitin linkages in isolation, whereas in cells all linkages coexist. To better mimick this diubiquitin substrate competition, we develop a multiplexed mass spectrometry-based deubiquitinase assay that can probe all ubiquitin linkage types simultaneously to quantify deubiquitinase activity in the presence of all potential diubiquitin substrates. For this, all eight native diubiquitins are generated and each linkage type is designed with a distinct molecular weight by incorporating neutron-encoded amino acids. Overall, 22 deubiquitinases are profiled, providing a three-dimensional overview of deubiquitinase linkage selectivity over time and enzyme concentration.

Discovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha.

Drugs that kill tumors through multiple mechanisms have the potential for broad clinical benefits. Here, we first developed an in silico multiomics approach (BipotentR) to find cancer cell-specific regulators that simultaneously modulate tumor immunity and another oncogenic pathway and then used it to identify 38 candidate immune-metabolic regulators. We show the tumor activities of these regulators stratify patients with melanoma by their response to anti-PD-1 using machine learning and deep neural approaches, which improve the predictive power of current biomarkers. The topmost identified regulator, ESRRA, is activated in immunotherapy-resistant tumors. Its inhibition killed tumors by suppressing energy metabolism and activating two immune mechanisms: (i) cytokine induction, causing proinflammatory macrophage polarization, and (ii) antigen-presentation stimulation, recruiting CD8+ T cells into tumors. We also demonstrate a wide utility of BipotentR by applying it to angiogenesis and growth suppressor evasion pathways. BipotentR (http://bipotentr.dfci.harvard.edu/) provides a resource for evaluating patient response and discovering drug targets that act simultaneously through multiple mechanisms. SIGNIFICANCE: BipotentR presents resources for evaluating patient response and identifying targets for drugs that can kill tumors through multiple mechanisms concurrently. Inhibition of the topmost candidate target killed tumors by suppressing energy metabolism and effects on two immune mechanisms. This article is highlighted in the In This Issue feature, p. 517.

Can Wearable Inertial Measurement Units Be Used to Measure Sleep Biomechanics? Establishing Initial Feasibility and Validity.

Wearable motion sensors, specifically, Inertial Measurement Units, are useful tools for the assessment of orientation and movement during sleep. The DOTs platform (Xsens, Enschede, The Netherlands) has shown promise for this purpose. This pilot study aimed to assess its feasibility and validity for recording sleep biomechanics. Feasibility was assessed using four metrics: Drift, Battery Life, Reliability of Recording, and Participant Comfort. Each metric was rated as Stop (least successful), Continue But Modify Protocol, Continue But Monitor Closely, or Continue Without Modifications (most successful). A convenience sample of ten adults slept for one night with a DOT unit attached to their sternum, abdomen, and left and right legs. A survey was administered the following day to assess participant comfort wearing the DOTs. A subset of five participants underwent a single evaluation in a Vicon (Oxford Metrics, Oxford, UK) motion analysis lab to assess XSENS DOTs' validity. With the two systems recording simultaneously, participants were prompted through a series of movements intended to mimic typical sleep biomechanics (rolling over in lying), and the outputs of both systems were compared to assess the level of agreement. The DOT platform performed well on all metrics, with Drift, Battery Life, and Recording Reliability being rated as Continue Without Modifications. Participant Comfort was rated as Continue But Monitor Closely. The DOT Platform demonstrated an extremely high level of agreement with the Vicon motion analysis lab (difference of <0.025°). Using the Xsens DOT platform to assess sleep biomechanics is feasible and valid in adult populations. Future studies should further investigate the feasibility of using this data capture method for extended periods (e.g., multiple days) and in other groups (e.g., paediatric populations).

Large-Scale Analysis of Apolipoprotein CIII Glycosylation by Ultrahigh Resolution Mass Spectrometry.

Apolipoprotein-CIII (apo-CIII) is a glycoprotein involved in lipid metabolism and its levels are associated with cardiovascular disease risk. Apo-CIII sialylation is associated with improved plasma triglyceride levels and its glycosylation may have an effect on the clearance of triglyceride-rich lipoproteins by directing these particles to different metabolic pathways. Large-scale sample cohort studies are required to fully elucidate the role of apo-CIII glycosylation in lipid metabolism and associated cardiovascular disease. In this study, we revisited a high-throughput workflow for the analysis of intact apo-CIII by ultrahigh-resolution MALDI FT-ICR MS. The workflow includes a chemical oxidation step to reduce methionine oxidation heterogeneity and spectrum complexity. Sinapinic acid matrix was used to minimize the loss of sialic acids upon MALDI. MassyTools software was used to standardize and automate MS data processing and quality control. This method was applied on 771 plasma samples from individuals without diabetes allowing for an evaluation of the expression levels of apo-CIII glycoforms against a panel of lipid biomarkers demonstrating the validity of the method. Our study supports the hypothesis that triglyceride clearance may be regulated, or at least strongly influenced by apo-CIII sialylation. Interestingly, the association of apo-CIII glycoforms with triglyceride levels was found to be largely independent of body mass index. Due to its precision and throughput, the new workflow will allow studying the role of apo-CIII in the regulation of lipid metabolism in various disease settings.

The Value of Radio Frequency Identification in Quality Management of the Blood Transfusion Chain in an Academic Hospital Setting.

BACKGROUND: A complex process like the blood transfusion chain could benefit from modern technologies such as radio frequency identification (RFID). RFID could, for example, play an important role in generating logistic and temperature data of blood products, which are important in assessing the quality of the logistic process of blood transfusions and the product itself. OBJECTIVE: This study aimed to evaluate whether location, time stamp, and temperature data generated in real time by an active RFID system containing temperature sensors attached to red blood cell (RBC) products can be used to assess the compliance of the management of RBCs to 4 intrahospital European and Dutch guidelines prescribing logistic and temperature constraints in an academic hospital setting. METHODS: An RFID infrastructure supported the tracking and tracing of 243 tagged RBCs in a clinical setting inside the hospital at the blood transfusion laboratory, the operating room complex, and the intensive care unit within the Academic Medical Center, a large academic hospital in Amsterdam, the Netherlands. The compliance of the management of 182 out of the 243 tagged RBCs could be assessed on their adherence to the following guidelines on intrahospital storage, transport, and distribution: (1) RBCs must be preserved within an environment with a temperature between 2°C and 6°C; (2) RBCs have to be transfused within 1 hour after they have left a validated cooling system; (3) RBCs that have reached a temperature above 10°C must not be restored or must be transfused within 24 hours or else be destroyed; (4) unused RBCs are to be returned to the BTL within 24 hours after they left the transfusion laboratory. RESULTS: In total, 4 blood products (4/182 compliant; 2.2%) complied to all applicable guidelines. Moreover, 15 blood products (15/182 not compliant to 1 out of several guidelines; 8.2%) were not compliant to one of the guidelines of either 2 or 3 relevant guidelines. Finally, 148 blood products (148/182 not compliant to 2 guidelines; 81.3%) were not compliant to 2 out of the 3 relevant guidelines. CONCLUSIONS: The results point out the possibilities of using RFID technology to assess the quality of the blood transfusion chain itself inside a hospital setting in reference to intrahospital guidelines concerning the storage, transport, and distribution conditions of RBCs. This study shows the potentials of RFID in identifying potential bottlenecks in hospital organizations' processes by use of objective data, which are to be tackled in process redesign efforts. The effect of these efforts can subsequently be evaluated by the use of RFID again. As such, RFID can play a significant role in optimization of the quality of the blood transfusion chain.

N-Linked Glycans in the Variable Domain of IgG Anti-Citrullinated Protein Antibodies Predict the Development of Rheumatoid Arthritis.

OBJECTIVE: Anti-citrullinated protein antibodies (ACPAs) are disease-specific biomarkers in rheumatoid arthritis (RA). More than 90% of IgG ACPAs harbor N-linked glycans in the antibody variable (V) domain. The corresponding N-glycosylation sites in ACPA V-region sequences result from somatic hypermutation, a T cell-dependent process. As ample evidence indicates that T cells drive the maturation of the ACPA response prior to arthritis onset, we undertook this study to investigate whether the presence of glycans in IgG ACPA V domains predicts the transition from predisease autoimmunity to overt RA. METHODS: We analyzed 2 independent sets of serum samples obtained from 126 ACPA-positive first-degree relatives (FDRs) of RA patients. Both sets originated from an Indigenous North American population and comprised cross-sectional and longitudinal samples of individuals who did or did not develop inflammatory arthritis. Serum IgG ACPAs were affinity-purified and subjected to ultra high-performance liquid chromatography-based glycan analysis. RESULTS: In both data sets, FDR-derived IgG ACPA displayed markedly lower levels of V domain glycans (<50%) compared to IgG ACPA from RA patients. Notably, FDRs who later developed RA showed extensive V-domain glycosylation before the onset of arthritis. Moreover, IgG ACPA V-domain glycosylation was strongly associated with future development of RA (hazard ratio 6.07 [95% confidence interval 1.46-25.2]; P = 0.013). CONCLUSION: Extensive glycosylation of the IgG ACPA V domain is present in a subset of predisposed FDRs of Indigenous North American RA patients. The presence of this feature substantially increases the risk of RA development. Based on these findings, we propose that glycosylation of the IgG ACPA V domain represents a predictive marker for RA development in ACPA-positive individuals and may serve to better target prevention measures.

HappyTools: A software for high-throughput HPLC data processing and quantitation.

High-performance liquid chromatography (HPLC) is widely used for absolute quantitation. The advent of new columns and HPLC technology has enabled higher sample throughput, and hence, larger scale studies that perform quantitation on different sample types (e.g. healthy controls vs. patients with rheumatoid arthritis) using HPLC are becoming feasible. However, there remains a lack of methods that can analyse the increased number of HPLC samples. To address this in part, the modular toolkit HappyTools has been developed for the high-throughput targeted quantitation of HPLC measurements. HappyTools enables the user to create an automated workflow that includes retention time (tr) calibration, data extraction and the calculation of several quality criteria for data curation. HappyTools has been tested on a biopharmaceutical standard and previously published clinical samples. The results show comparable accuracy between HappyTools, Waters Empower and ThermoFisher Chromeleon. However, HappyTools offered superior precision and throughput when compared with Waters Empower and ThermoFisher Chromeleon. HappyTools is released under the Apache 2.0 license, both the source code and a Windows binary can be freely downloaded from https://github.com/Tarskin/HappyTools.

MIgGGly (mouse IgG glycosylation analysis) - a high-throughput method for studying Fc-linked IgG N-glycosylation in mice with nanoUPLC-ESI-MS.

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.

High-Throughput Analysis of IgG Fc Glycopeptides by LC-MS.

This chapter contains a nanoscale liquid chromatography-mass spectrometry method for the glycoform profiling of the conserved Fc N-glycosylation site of monoclonal and polyclonal immunoglobulin G (IgG). It describes in detail LaCyTools, a program for automated data (pre-)processing of the obtained LC-MS data. The minimal sample preparation necessary is explained as well as an optional method for affinity purification of (polyclonal) antibodies from serum or plasma.After (optional) affinity purification, the pure IgG is cleaved with trypsin. The tryptic glycopeptides are separated almost exclusively on their peptide backbone. This ensures similar response factors for all glycoforms in the MS detection and allows the collection of separate glycoform profiles for different IgG isoforms or allotypes. LaCyTools automatically performs label-free (relative) quantitation of the obtained data after minimal manual input and additionally calculates several quality criteria which can be used for data curation at the level of both individual analytes and entire LC-MS runs.