Towards a reliable molecular mass determination of intact glycoproteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

6-Aza-2-Thiothymine as an Alternative Matrix for Spatial Proteomics with MALDI-MSI

Matrix Assisted Laser Desorption/Ionisation-Mass Spectrometry Imaging (MALDI-MSI) is a well-established spatial omic technique which enables the untargeted mapping of various classes of biomolecules, including tryptic peptides, directly on tissue. This method relies on the use of matrices for the ionisation and volatilisation of analytes, and α-Cyano-4-hydroxycinnamic acid (CHCA) represents the most widespread matrix for tryptic peptides analysis. However, CHCA also presents certain limitations that foster the quest for novel matrix compounds. 6-aza-2-thiothymine (ATT), traditionally used in MALDI mass spectrometry (MS) for oligonucleotides, small molecules and oxidised phospholipids, has not been thoroughly investigated as a potential matrix for tryptic peptide analysis in MALDI-MS or MALDI-MSI. Therefore, this study addresses this gap by evaluating the capability of ATT to ionise tryptic peptides from Bovine Serum Albumin (BSA) and map in situ-digested peptides from formalin-fixed paraffin-embedded (FFPE) tissue sections in these respective applications. Comparative analysis with CHCA demonstrated the complementary strengths of these matrices for detecting tryptic peptides, establishing ATT as a feasible alternative to CHCA in the MALDI-MSI field and paving the way for future advancements in spatial proteomics.

Glycoform analysis of intact erythropoietin by MALDI FT-ICR mass spectrometry

Recombinant human erythropoietin (EPO) is a complex therapeutic glycoprotein with three N- and one O-glycosylation sites. Glycosylation of EPO influences its safety and efficacy and is defined as a critical quality attribute. Thus, analytical methods for profiling EPO glycosylation are highly demanded. Owing to the complexity of the intact protein, information about EPO glycosylation is commonly derived from released glycan and glycopeptide analysis using mass spectrometry (MS). Alternatively, comprehensive insights into the glycoform heterogeneity of intact EPO are obtained using ESI MS-based methods with or without upfront separation of EPO glycoforms. MALDI MS, typically performed with TOF mass analyzers, has been also used for the analysis of intact EPO but, due to the poor glycoform resolution, has only provided limited glycoform information. Here, we present a MALDI FT-ICR MS method for the glycosylation profiling of intact EPO with improved glycoform resolution and without loss of sialic acid residues commonly observed in MALDI analysis. Three EPO variants were characterized in-depth and up to 199 glycoform compositions were assigned from the evaluation of doubly-charged ions, without any deconvolution of the mass spectra. Key glycosylation features such as sialylation, acetylation, and N-acetyllactosamine repeats were determined and found to agree with previously reported data obtained from orthogonal analyses. The developed method allowed for a fast and straightforward data acquisition and evaluation and can be potentially used for the high-throughput comparison of EPO samples throughout its manufacturing process.

Ionic matrices for matrix-assisted laser desorption/ionization mass spectrometry analysis of microRNA biomarkers

The use of ionic matrices (IMs) was evaluated as an alternative to conventional matrices to analyze microRNAs (miRNAs) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). 2, 4, 6-Trihydroxyacetophenone (THAP), 6-aza-2-thiothymine (ATT) and 3-hydroxypicolinic acid (3-HPA) and their IMs with pyridine (PYR) and butylamine (BA) were studied to analyze a standard mixture of miRNAs: miR-21, let-7g and iso-miR-16. Among all the studied matrices, ATT-PYR at 75 mg/mL in acetonitrile (MeCN):H₂O (50:50, v/v) was selected as the optimal. Furthermore, addition of ammonium citrate dibasic (AC) as signal enhancer was mandatory to obtain an appropriate miRNA detection. ATT-PYR provided the best sensitivity, with limit of detection (LOD) up to 5 nM (equivalent to 1 fmol in the spot) and excellent spot-to-spot repeatability due to the improved homogeneity of the spots compared to the conventional matrices. The applicability of the established method to direct, multiplex and untargeted analysis of miRNAs in serum samples was also investigated.

Low-molecular-mass iron in healthy blood plasma is not predominately ferric citrate

Blood contains a poorly characterized pool of labile iron called non-transferrin-bound iron (NTBI). In patients with iron-overload diseases such as hemochromatosis, NTBI accumulates in the liver, heart, and other organs. This material is probably nonproteinaceous and low molecular mass (LMM). However, the number, concentration, mass, and chemical composition of NTBI species remain unknown despite decades of effort. Here, solutions of plasma from humans, pigs, horses, and mice were passed through a 10 kDa cutoff membrane, affording flow-through solutions (FTSs) containing ∼1 μM iron. The FTSs were subjected to size-exclusion liquid chromatography at pH 8.5, 6.5, and 4.5. Iron was detected by an online inductively-coupled-plasma mass spectrometer. LC-ICP-MS chromatograms of the FTSs exhibited 2-6 iron-containing species with apparent masses between 400 and 2500 Da. Their approximate concentrations in plasma were 10-8-10-7 M. Not every FTS sample contained every LMM iron species, indicating individual variations. The most reproducible iron species had apparent masses of 400 and 500 Da. Chromatograms of the FTSs from established hemochromatosis patients exhibited no significant differences relative to controls. The peak positions and intensities depended on column pH. Some FTS iron adsorbed onto the column, especially at higher pH. Column-adsorbing-iron coordinated apo-transferrin whereas the more tightly coordinated iron species did not. Ferric citrate standards exhibited LMM iron peaks that were similar to but not the same as those obtained in FTSs. The results indicate that the LMM iron species in healthy blood plasma is not primarily ferric citrate; however, this may be one of many contributing complexes.

Cracking the Sugar Code by Mass Spectrometry : An Invited Perspective in Honor of Dr. Catherine E. Costello, Recipient of the 2017 ASMS Distinguished Contribution Award

The structural study of glycans and glycoconjugates is essential to assign their roles in homeostasis, health, and disease. Once dominated by nuclear magnetic resonance spectroscopy, mass spectrometric methods have become the preferred toolbox for the determination of glycan structures at high sensitivity. The patterns of such structures in different cellular states now allow us to interpret the sugar codes in health and disease, based on structure-function relationships. Dr. Catherine E. Costello was the 2017 recipient of the American Society for Mass Spectrometry's Distinguished Contribution Award. In this Perspective article, we describe her seminal work in a historical and geographical context and review the impact of her research accomplishments in the field.8 ᅟ Graphical abstract.

Human disease glycomics: technology advances enabling protein glycosylation analysis - part 1

INTRODUCTION

Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics). The technologies currently available for glycomics are becoming streamlined and standardized and many features of protein glycosylation can now be determined using instruments available in most protein analytical laboratories. Areas covered: This review focuses on the current glycomics technologies being commonly used for the analysis of the microheterogeneity of monosaccharide composition, sequence, branching and linkage of released N- and O-linked glycans that enable the determination of precise glycan structural determinants presented on secreted proteins and on the surface of all cells. Expert commentary: Several emerging advances in these technologies enabling glycomics analysis are discussed. The technological and bioinformatics requirements to be able to accurately assign these precise glycan features at biological levels in a disease context are assessed.

Microchip capillary gel electrophoresis combined with lectin affinity enrichment employing magnetic beads for glycoprotein analysis

Due to the constant search for reliable methods to investigate glycoproteins in complex biological samples, an alternative approach combining affinity enrichment with rapid and sensitive analysis on-a-chip is presented. Glycoproteins were specifically captured by lectin-coated magnetic beads, eluted by competitive sugars, and investigated with microchip capillary gel electrophoresis (MCGE), i.e., CGE-on-a-chip. We compared our results to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) data, which turned out to be in very good agreement. While SDS-PAGE offers the possibility of subsequent mass spectrometric analysis of captured and separated analytes, MCGE scores with time savings, higher throughput, and lower sample consumption as well as quality control (QC) and process analytical technology (PAT) applicability. Due to these advantages, a lectin-based glycoprotein capture protocol can easily be optimized. In our case, two different types of magnetic beads were tested and compared regarding lectin binding. The selectivity of our strategy was demonstrated with a set of model glycoproteins, as well as with human serum and serum depleted from high-abundance proteins. The specificity of the capturing method was investigated revealing to a certain degree an unspecific binding between each sample and the beads themselves, which has to be considered for any specific enrichment and data interpretation. In addition, two glycoproteins from Trichoderma atroviride, a fungus with mycoparasitic activity and only barely studied glycoproteome, were enriched by means of a lectin and so identified for the first time.

Graphical abstract

nES GEMMA Analysis of Lectins and Their Interactions with Glycoproteins - Separation, Detection, and Sampling of Noncovalent Biospecific Complexes

In order to better understand biological events, lectin-glycoprotein interactions are of interest. The possibility to gather more information than the mere positive or negative response for interactions brought mass spectrometry into the center of many research fields. The presented work shows the potential of a nano-electrospray gas-phase electrophoretic mobility molecular analyzer (nES GEMMA) to detect weak, noncovalent, biospecific interactions besides still unbound glycoproteins and unreacted lectins without prior liquid phase separation. First results for Sambucus nigra agglutinin, concanavalin A, and wheat germ agglutinin and their retained noncovalent interactions with glycoproteins in the gas phase are presented. Electrophoretic mobility diameters (EMDs) were obtained by nES GEMMA for all interaction partners correlating very well with molecular masses determined by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) of the individual molecules. Moreover, EMDs measured for the lectin-glycoprotein complexes were in good accordance with theoretically calculated mass values. Special focus was laid on complex formation for different lectin concentrations and binding specificities to evaluate the method with respect to results obtained in the liquid phase. The latter was addressed by capillary electrophoresis on-a-chip (CE-on-a-chip). Of exceptional interest was the fact that the formed complexes could be sampled according to their size onto nitrocellulose membranes after gas-phase separation. Subsequent immunological investigation further proved that the collected complex actually retained its native structure throughout nES GEMMA analysis and sampling. Graphical Abstract ᅟ.

Current landscape of protein glycosylation analysis and recent progress toward a novel paradigm of glycoscience research

This review covers the basics and some applications of methodologies for the analysis of glycoprotein glycans. Analytical techniques used for glycoprotein glycans, including liquid chromatography (LC), capillary electrophoresis (CE), mass spectrometry (MS), and high-throughput analytical methods based on microfluidics, were described to supply the essentials about biopharmaceutical and biomarker glycoproteins. We will also describe the MS analysis of glycoproteins and glycopeptides as well as the chemical and enzymatic releasing methods of glycans from glycoproteins and the chemical reactions used for the derivatization of glycans. We hope the techniques have accommodated most of the requests from glycoproteomics researchers.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010

This review is the sixth update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis.

Mapping the glycation sites in the neoglycoconjugate from hexasaccharide antigen of Vibrio cholerae, serotype Ogawa and the recombinant tetanus toxin C-fragment carrier

We report herein the glycation sites in a vaccine candidate for cholera formed by conjugation of the synthetic hexasaccharide fragment of the O-specific polysaccharide of Vibrio cholerae, serotype Ogawa, to the recombinant tetanus toxin C-fragment (rTT-Hc) carrier. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of the vaccine revealed that it is composed of a mixture of neoglycoconjugates with carbohydrate : protein ratios of 1.9 : 1, 3.0 : 1, 4.0 : 1, 4.9 : 1, 5.9 : 1, 6.9 : 1, 7.9 : 1 and 9.1 : 1. Liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of the tryptic and GluC V8 digests allowed identification of 12 glycation sites in the carbohydrate-protein neoglycoconjugate vaccine. The glycation sites are located exclusively on lysine (Lys) residues and are listed as follows: Lys 22, Lys 61, Lys 145, Lys 239, Lys 278, Lys 318, Lys 331, Lys 353, Lys 378, Lys 389, Lys 396 and Lys 437. Based on the 3-D representation of the rTT-Hc protein, all the glycation sites correspond to lysines located at the outer surface of the protein.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2007-2008

This review is the fifth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2008. The first section of the review covers fundamental studies, fragmentation of carbohydrate ions, use of derivatives and new software developments for analysis of carbohydrate spectra. Among newer areas of method development are glycan arrays, MALDI imaging and the use of ion mobility spectrometry. The second section of the review discusses applications of MALDI MS to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, biopharmaceuticals, glycated proteins, glycolipids, glycosides and various other natural products. There is a short section on the use of MALDI mass spectrometry for the study of enzymes involved in glycan processing and a section on the use of MALDI MS to monitor products of the chemical synthesis of carbohydrates with emphasis on carbohydrate-protein complexes and glycodendrimers. Corresponding analyses by electrospray ionization now appear to outnumber those performed by MALDI and the amount of literature makes a comprehensive review on this technique impractical. However, most of the work relating to sample preparation and glycan synthesis is equally relevant to electrospray and, consequently, those proposing analyses by electrospray should also find material in this review of interest.

Capillary electrophoresis time-of-flight mass spectrometry for a confident elucidation of a glycopeptide map of recombinant human erythropoietin

Capillary electrophoresis coupled to orthogonal accelerated time-of-flight mass spectrometry (CE/TOFMS) was used for the analysis of O- and N-glycopeptides of recombinant human erythropoietin (rhEPO). O(126) and N(83) with a tetraantennary complex type glycan (N(83)-4Ant) were selected as glycopeptide models to develop an optimum CE/TOFMS methodology capable of detecting and characterizing the wide variety of glycopeptides present in the glycoprotein digest. Glycopeptide adsorption in the inner surface of the fused-silica capillary was prevented after using a capillary conditioning of 1 M HAc between runs. On the other hand, different acidic conditions in the sheath liquid (SL) and in the background electrolyte (BGE) were tested with the aim of studying their influence in glycopeptide fragmentation. Finally, the fragmentor voltage value of the TOF-MS instrument was optimized to avoid the involuntary fragmentation of the native glycopeptides. Hence, the established method may be regarded as an excellent starting point to obtain reliable glycopeptide maps of complex glycoproteins such as rhEPO by CE/TOFMS.

Capillary electrophoresis/mass spectrometry for the separation and characterization of bovine Cu,Zn-superoxide dismutase

The native form of Cu,Zn-superoxide dismutase (SOD-1) is a homodimer that coordinates one Cu(2+) and one Zn(2+) per monomer. Cu(2+) and Zn(2+) ions play crucial roles in enzyme activity and structural stability, respectively. In addition, dimer formation is essential for SOD-1 functionality, and in humans several SOD-1 mutant isoforms have been associated with certain types of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disorder. In this paper we used capillary electrophoresis and mass spectrometry to study the different structures of bovine SOD-1. The metal ions of the native enzyme (Cu(2),Zn(2)-dimer SOD-1) were released in acidic medium in order to obtain apo-SOD-1, which is a monomer. Both substances were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and capillary electrophoresis with ultraviolet and electrospray ionization mass spectrometry detection (CE/UV and CE/ESI-MS, respectively). With MALDI-TOF-MS, using matrices of sinapinic acid (SA) or 2,5-dihydroxybenzoic acid (DHB) with or without trifluoroacetic acid (TFA), similar mass spectra were obtained for the metalated and non-metalated samples. In both cases, an average molecular mass corresponding to the apo-monomer SOD-1 was calculated. This finding indicated that the metals were released from the Cu(2),Zn(2)-dimer SOD-1 during sample preparation or ionization. For CE/UV and CE/ESI-MS, two background electrolytes (BGEs) potentially compatible with ESI-MS detection were used, namely 1 M of acetic acid (pH 2.3) and 10 mM of ammonium acetate (pH 7.3). Using a sheath liquid of 2-propanol/water (60:40 v/v), with or without 0.1% v/v of formic acid, CE/ESI-MS sensitivity was enhanced when the acidic BGE and the acidic sheath liquid were used. However, the electrophoretic profiles and the mass spectra obtained suggested that the metals of Cu(2),Zn(2)-dimer SOD-1 were released, which generated the apo-monomer during the electrophoretic separation. The neutral BGE provided enhanced conditions for the detection of the native enzyme. The differences between the mass spectra obtained for the Cu(2),Zn(2)-dimer and the apo-monomer forms were significant and the presence of formic acid in the sheath liquid affected only sensitivity. Our results highlight the importance of selecting appropriate non-denaturing separation and detection conditions to obtain reliable structural information about non-covalent protein complexes by CE/ESI-MS.

Erythropoietin and analogs

Erythropoietin (EPO), a glycoprotein hormone, stimulates the growth of red blood cells and as a consequence it increases tissue oxygenation. This performance enhancing effect is responsible for the ban of erythropioetin in sports since 1990. Especially its recombinant synthesis led to the abuse of this hormone, predominatly in endurance sports. The analytical differentiation of endogenously produced erythropoietin from its recombinant counterpart by using isoelectric focusing and double blotting is a milestone in the detection of doping with recombinant erythropoietin. However, various analogous of the initial recombinant products, not always easily detectable by the standard IEF-method, necessitate the development of analytical alternatives for the detection of EPO doping. The following chapter summarizes its mode of action, the various forms of recombinant erythropoietin, the main analytical procedures and strategies for the detection of EPO doping as well as a typical case report.

Mucin-type O-glycosylation--putting the pieces together

The O-glycosylation of Ser and Thr by N-acetylgalactosamine-linked (mucin-type) oligosaccharides is often overlooked in protein analysis. Three characteristics make O-linked glycosylation more difficult to analyse than N-linked glycosylation, namely: (a) no amino acid consensus sequence is known; (b) there is no universal enzyme for the release of O-glycans from the protein backbone; and (c) the density and number of occupied sites may be very high. For significant biological conclusions to be drawn, the complete picture of O-linked glycosylation on a protein needs to be determined. This review specifically addresses the analytical approaches that have been used, and the challenges remaining, in the characterization of both the composition and structure of mucin-type O-glycans, and the determination of the occupancy and heterogeneity at each amino acid attachment site.

Mass spectrometry in the characterization of human genetic N-glycosylation defects

Human genetic diseases that affect N-glycosylation result from the defective synthesis of the N-linked sugar moiety (glycan) of glycoproteins. The role of glycans for proper protein folding and biological functions is illustrated in the variety and severity of clinical manifestations shared by congenital disorders of glycosylation (CDG). This family of inherited metabolic disorders includes defects in the assembly of the oligosaccharide precursor that lead to an under-occupancy of N-glycosylation sites (CDG-I), and defects of glycan remodeling (CDG-II). Mass spectrometry constitutes a key tool for characterization of CDG-I defects by mass resolution of native protein glycoforms that differ for glycosylation-site occupancy. Glycan MS analyses in CDG-II is mandatory to detect whenever possible a repertoire of structures to pinpoint candidate enzymes and genes responsible for the abnormal N-glycan synthesis. In this manuscript, we review the MS applications in the area of CDG and related disorders with a special emphasis on those techniques that have been already applied or might become functional for diagnosis, characterization, and treatment monitoring in some specific conditions.

The effects of culture conditions on the glycosylation of secreted human placental alkaline phosphatase produced in Chinese hamster ovary cells

The effects of different culture conditions, suspension and microcarrier culture and temperature reduction on the structures of N-linked glycans attached to secreted human placental alkaline phosphatase (SEAP) were investigated for CHO cells grown in a controlled bioreactor. Both mass spectrometry and anion-exchange chromatography were used to probe the N-linked glycan structures and distribution. Complex-type glycans were the dominant structures with small amounts of high mannose glycans observed in suspension and reduced temperature cultures. Biantennary glycans were the most common structures detected by mass spectrometry, but triantennary and tetraantennary forms were also detected. The amount of sialic acid present was relatively low, approximately 0.4 mol sialic acid/mol SEAP for suspension cultures. Microcarrier cultures exhibited a decrease in productivity compared with suspension culture due to a decrease in both maximum viable cell density (15-20%) and specific productivity (30-50%). In contrast, a biphasic suspension culture in which the temperature was reduced at the beginning of the stationary phase from 37 to 33 degrees C, showed a 7% increase in maximum viable cell density, a 62% increase in integrated viable cell density, and a 133% increase in specific productivity, leading to greater than threefold increase in total productivity. Both microcarrier and reduced temperature cultures showed increased sialylation and decreased fucosylation when compared to suspension culture. Our results highlight the importance of glycoform analysis after process modification as even subtle changes (e.g., changing from one microcarrier to another) may affect glycan distributions.

Integrated analytical strategies for the study of phosphorylation and glycosylation in proteins

The post-translational modification (PTM) of proteins is a common biological mechanism for regulating protein localization, function, and turnover. The direct analysis of modifications is required because they are not coded by genes, and thus are not predictable. Different MS-based proteomic strategies are used for the analysis of PTMs, such as phosphorylation and glycosylation, and are composed of a structural simplification step of the protein followed by specific isolation step to extract the classes of modified peptides (also called "sub-proteomes") before mass spectrometry. This specific isolation step is necessary because PTMs occur at a sub-stoichiometric level and signal suppression of the modified fractions in the mass spectrometer occurs in the presence of the more-abundant non-modified counterpart. The request of innovative analytical strategies in PTM studies is the capability to localize the modification sites, give detailed structural information on the modification, and determine the isoform composition with increased selectivity, sensitivity, and throughput. This review focuses on the description of recent integrated analytical systems proposed for the analysis of PTMs in proteins, and their application to profile the glycoproteome and the phosphoproteome in biological samples. Comments on the difficulties and usefulness of the analytical strategies are given.