Site‐specific N‐glycosylation analysis of human factor XI: Identification of a noncanonical NXC glycosite

Human factor XI (hFXI) is a 160‐kDa disulphide‐linked homodimer zymogen involved in the coagulation cascade. Its deficiency results in bleeding diathesis referred to as hemophilia C. hFXI bears five N‐glycosylation consensus sites per monomer, N₇₂, N₁₀₈, N₃₃₅ on the heavy chain and N₄₃₂, N₄₇₃ on the light chain. This study reports the first in‐depth glycosylation analysis of hFXI based on advanced MS approaches. Hydrophilic interaction LC and MS characterization and quantification of the N‐glycans showed that the two major forms are complex biantennary mono‐α2,6‐sialylated (A₂S₁, 20%) and bis‐α2,6‐sialylated structures (A₂S₂, 66%). Minor triantennary structures (A₃S₃F, ～1.5%; A₃S₃, ～2%) were also identified. MS analyses of intact hFXI revealed full occupation of two of the three heavy‐chain glycosites and almost full‐site occupancy of the light chain. Analysis of hFXI glycopeptides by LC‐MS/MS enabled site‐specific glycan profiling and occupancy. It was evidenced that N₃₃₅ was not glycosylated and that N₇₂ and N₁₀₈ were fully occupied, whereas N₄₃₂ and N₄₇₃ were occupied at about 92 and 95%, respectively. We also identified a new glycosite of the noncanonical format NXC at N₁₄₅, occupied at around 5%. These data provide valuable structural information useful to understand the potential roles of N‐glycosylation on hFXI function and could serve as a structural reference.     

Degradation products analysis of an Fc fusion protein using LC/MS methods

The following analytical methods have been used to identify and quantify degradation products in an E. coli expressed human immunoglobulin G Fc fusion protein in both liquid and lyophilized forms: two-dimensional AEX/RP/MS, limited proteolysis followed by LC/MS, and tryptic digestion followed by LC/MS/MS. After aging in a potassium phosphate pH 7.0 buffer for 3 months at 29 °C, peptide map analysis revealed that asparagine N78 (N297 according to Edelman sequencing) of the CH2 domain was the most rapidly deamidated site in the molecule probably due to the lack of the N-linked glycan on this asparagine, but this deamidation can be prevented under properly formulated conditions. This is the first report on the rate of deamidation on N297 of an IgG molecule without glycosylation. The active protein portion of the Fc fusion protein contains two methionine residues that are potentially susceptible to oxidation. Limited proteolysis was employed to cleave the active protein portion and measure the amount of oxidation. LC/MS analysis identified that the liquid sample aged at 29 °C for 3 months produced 40% oxidation, while the control sample contained only 4% oxidation on the active protein. In contrast to the aged liquid sample, the aged lyophilized sample showed no increase of deamidation or oxidation after storage at 37 °C for 8 months.     

Recombinant human lecithin‐cholesterol acyltransferase Fc fusion: Analysis of N‐ and O‐linked glycans and identification and elimination of a xylose‐based O‐linked tetrasaccharide core in the linker region

Recombinant human lecithin‐cholesterol acyltransferase Fc fusion (huLCAT‐Fc) is a chimeric protein produced by fusing human Fc to the C‐terminus of the human enzyme via a linker sequence. The huLCAT‐Fc homodimer contains five N‐linked glycosylation sites per monomer. The heterogeneity and site‐specific distribution of the various glycans were examined using enzymatic digestion and LC‐MS/MS, followed by automatic processing. Almost all of the N‐linked glycans in human LCAT are fucosylated and sialylated. The predominant LCAT N‐linked glycoforms are biantennary glycans, followed by triantennary sugars, whereas the level of tetraantennary glycans is much lower. Glycans at the Fc N‐linked site exclusively contain typical asialobiantennary structures. HuLCAT‐Fc was also confirmed to have mucin‐type glycans attached at T₄₀₇ and S₄₀₉. When LCAT‐Fc fusions were constructed using a G‐S‐G‐G‐G‐G linker, an unexpected +632 Da xylose‐based glycosaminoglycan (GAG) tetrasaccharide core of Xyl‐Gal‐Gal‐GlcA was attached to S₄₁₈. Several minor intermediate species including Xyl, Xyl‐Gal, Xyl‐Gal‐Gal, and a phosphorylated GAG core were also present. The mucin‐type O‐linked glycans can be effectively released by sialidase and O‐glycanase; however, the GAG could only be removed and localized using chemical alkaline β‐elimination and targeted LC‐MS/MS. E₄₁₆ (the C‐terminus of LCAT) combined with the linker sequence is likely serving as a substrate for peptide O‐xylosyltransferase. HuLCAT‐Fc shares some homology with the proposed consensus site near the linker sequence, in particular, the residues underlined PPP E₄₁₆GS₄₁₈G G G GDK. GAG incorporation can be eliminated through engineering by shifting the linker Ser residue downstream in the linker sequence.     

Over 4100 protein identifications from a Xenopus laevis fertilized egg digest using reversed‐phase chromatographic prefractionation followed by capillary zone electrophoresis–electrospray ionization–tandem mass spectrometry analysis

A tryptic digest generated from Xenopus laevis fertilized embryos was fractionated by RPLC. One set of 30 fractions was analyzed by 100‐min CZE‐ESI‐MS/MS separations (50 h total instrument time), and a second set of 15 fractions was analyzed by 3‐h UPLC‐ESI‐MS/MS separations (45 h total instrument time). CZE‐MS/MS produced 70% as many protein IDs (4134 versus 5787) and 60% as many peptide IDs (22 535 versus 36 848) as UPLC‐MS/MS with similar instrument time (50 h versus 45 h) but with 50 times smaller total consumed sample amount (1.5 μg versus 75 μg). Surprisingly, CZE generated peaks that were 25% more intense than UPLC for peptides that were identified by both techniques, despite the 50‐fold lower loading amount; this high sensitivity reflects the efficient ionization produced by the electrokinetically pumped nanospray interface used in CZE. This report is the first comparison of CZE‐MS/MS and UPLC‐MS/MS for large‐scale eukaryotic proteomic analysis. The numbers of protein and peptide identifications produced by CZE‐ESI‐MS/MS approach those produced by UPLC‐MS/MS, but with nearly two orders of magnitude lower sample amounts.     

Conventional and microwave‐assisted SPPS approach: a comparative synthesis of PTHrP(1–34)NH2

Attracted by the possibility to optimize time and yield of the synthesis of difficult peptide sequences by MW irradiation, we compared Fmoc/tBu MW‐assisted SPPS of 1–34 N‐terminal fragment of parathyroid hormone‐related peptide (PTHrP) with its conventional SPPS carried out at RT. MWs were applied in both coupling and deprotection steps of SPPS protocol. During the stepwise elongation of the resin‐bound peptide, monitoring was conducted by performing MW‐assisted mini‐cleavages and analyzing them by UPLC‐ESI‐MS. Identification of some deletion sequences was helpful to recognize critical couplings and as such helped to guide the introduction of MW irradiations to these stages. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Characteristics of mass spectrometric analyses coupled to gas chromatography and liquid chromatography for 22-oxacalcitriol, a vitamin D3 analog, and related compounds

The characteristics of the mass spectra of vitamin D₃ related compounds were investigated by GC–MS and LC–MS using 22-oxacalcitriol (OCT), an analog of 1,25-dihydroxyvitamin D₃, and related compounds. Fragmentation during GC–MS (electron impact ionization) of TMS-derivatives of OCT and the postulated metabolites gave useful structural information concerning the vitamin D₃-skeleton and its side-chain, especially with respect to the oxidation positions of metabolites. In contrast, few fragment ions were observed in LC–MS (atmospheric pressure chemical ionization), showing that LC–MS gave poor structural information, except for molecular mass. However, when comparing the signal-to-noise ratio (S/N) observed during GC–MS and LC–MS analysis for OCT in plasma extracts, the S/N in LC–MS was over ten-times greater than in GC–MS, possibly due to the low recovery on derivatization and thermal-isomerization in GC–MS. Furthermore, both the GC–MS and the LC–MS allowed the analysis of many postulated metabolites in a single injection without any prior isolation of target metabolites from biological fluids by LC. These results suggest that GC–MS and LC–MS analysis for vitamin D₃ related compounds such as OCT each have unique and distinct advantages. Therefore, the complementary use of both techniques enables the rapid and detailed characterization of vitamin D₃ related compounds.     

Hyperglucosylated adhesin‐derived peptides as antigenic probes in multiple sclerosis: Structure optimization and immunological evaluation

Peptides mimicking antigenic epitopes targeted by antibodies can be powerful tools to be used as antigen surrogates for the specific diagnosis and treatment of autoimmune diseases. Obtaining structural insights about the nature of peptide–antibody interaction in complex mixtures such as sera is a critical goal. In multiple sclerosis (MS), we previously demonstrated that the N‐linked β‐d ‐glucopyranosyl moieties (N‐Glc) containing epitopes in nontypeable Haemophilus influenzae adhesin C‐terminal portion HMW1(1205–1526) were essential for high‐affinity antibody binding in a subpopulation of MS patients. With the aim of developing peptide probes and assessing their binding properties to antibodies from sera of representative patients, we performed the systematic analysis of synthetic peptides based on HMW1(1347–1354) fragment bearing one or two N‐Glc respectively on Asn‐1349 and/or Asn‐1352. The N‐glucosylated nonapeptides efficiently bind to IgG antibodies, displaying IC₅₀ in the range 10^?8–10^?10 M by competitive indirect enzyme‐linked immunosorbent assay (ELISA) in three representative MS patient sera. We selected the di‐N‐glucosylated adhesin peptide Ac‐KAN (Glc)VTLN (Glc)TT‐NH₂ as the shortest sequence able to inhibit high‐avidity interaction with N‐Glc targeting IgM antibodies. Nuclear magnetic resonance (NMR)‐ and circular dichroism (CD)‐based characterization showed that the binding properties of these antigens could not be ascribed to structural differences induced by the presence of up to two N‐glucosyl moieties. Therefore, the antibody binding is not easily correlated to the position of the sugar or to a determined conformation in water.     

Mass spectrometric analysis of innovator,counterfeit, and follow‐on recombinant human growth hormone

We have performed a detailed characterization of recombinant human growth hormone that included the identification of the entire sequence with disulfide linkages as well as subtle modifications by a sensitive liquid chromatography coupled online with tandem mass spectrometry (LC‐MS) approach using the accurate peptide mass (FTICR MS) and sequence assignment (MS/MS measurement). The extent of oxidation, deamidation, and chain cleavages were measured by the ratio of peak areas of the nonmodified peptide vs. the sum of peak area of the nonmodified and modified peptides in the same LC‐MS analysis. The subtle but distinct differences were found in the recombinant human growth from the three manufacturers (the follow‐on, counterfeit, and the original innovator products). In relative comparison, the follow‐on product had the highest degree of oxidation at methionine residues, followed by the counterfeit product, and the original innovator product had the least amount of oxidation at all three sites with the similar oxidation order. In cases, the oxidation order was Met14 > Met125 > Met170. In contrast, the follow‐on had the least amount of deamidation at aspargine (Asn149), and the counterfeit had the highest degree of deamidation at this site. For the chain cleavage, the follow‐on product had the highest cleavage occurring at T 10 peptide (between Asn99 and Ser100), the counterfeit had the highest cleavage on T4 peptide, (between Glu30 and Phe31), and the original innovator product with the least amount of cleavages on both sites. These subtle but distinct differences are likely because of nonidentical manufacturing, formulation procedures, and storage conditions. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Epitope motif of an anti‐nitrotyrosine antibody specific for tyrosine‐nitrated peptides revealed by a combination of affinity approaches and mass spectrometry

Nitration of tyrosine residues has been shown to be an important oxidative modification in proteins and has been suggested to play a role in several diseases such as atherosclerosis, asthma, lung and neurodegenerative diseases. Detection of nitrated proteins has been mainly based on the use of nitrotyrosine‐specific antibodies. In contrast, only a small number of nitration sites in proteins have been unequivocally identified by MS. We have used a monoclonal 3‐NT‐specific antibody, and have synthesized a series of tyrosine‐nitrated peptides of prostacyclin synthase (PCS) in which a single specific nitration site at Tyr‐430 had been previously identified upon reaction with peroxynitrite 17 . The determination of antibody‐binding affinity and specificity of PCS peptides nitrated at different tyrosine residues (Tyr‐430, Tyr‐421, Tyr‐83) and sequence mutations around the nitration sites provided the identification of an epitope motif containing positively charged amino acids (Lys and/or Arg) N‐terminal to the nitration site. The highest affinity to the anti‐3NT‐antibody was found for the PCS peptide comprising the Tyr‐430 nitration site with a K_D of 60 nM determined for the peptide, PCS(424‐436‐Tyr‐430NO₂); in contrast, PCS peptides nitrated at Tyr‐421 and Tyr‐83 had substantially lower affinity. ELISA, SAW bioaffinity, proteolytic digestion of antibody‐bound peptides and affinity‐MS analysis revealed highest affinity to the antibody for tyrosine‐nitrated peptides that contained positively charged amino acids in the N‐terminal sequence to the nitration site. Remarkably, similar N‐terminal sequences of tyrosine‐nitration sites have been recently identified in nitrated physiological proteins, such as eosinophil peroxidase and eosinophil‐cationic protein. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Some Peculiarities of the Dynamics of the Immunoglobulin M Structure

Abstract

The isotropic mobility of separate regions of the intact molecule of immunoglobulin M (IgM) and its Fab and (Fc)₅ fragments was studied using spin-labeling of carbohydrate (2,2,6,6-tetramethyl-4-aminopiperidine-l-oxyl) and peptide (2,2,5,5-tetramethyl-3-dichloro-triazinylaminopyrrolidine-l-oxyl) moieties.

The spin-labeled oligosaccharide groups (OGs) in the Fab region are shown to have much more amplitude of anisotropic motion than those in the (Fc)₅ region. The spin label in the latter is evidently attached in the Cμ3 domain to one of its OGs which is probably stabilized by ionic contacts between terminal N-acetylneuraminic acid residue and the peptide moiety of the IgM molecule.

When the amount of the glycosidase-cleaved carbohydrate does not exceed 10–15%, most OGs affected are of the Fab region. Upon profound splitting (≥50%) the OGs of the (Fc)₅region are also affected; that results evidently in loosening the ionic contacts between the shortened OGs and the peptide moiety of IgM, and consequently in increasing mobility of the former.

The structure of the (Fc)₅ region of IgM is labile; after detaching this moiety from the intact IgM molecule, its structure is stabilized, but one of its domains (Cμ3) becomes more mobile than it is in the intact IgM molecule; at the same time the amplitude of anisotropic motion of OG bound here is decreased. In the latter case, this decrease depends on the sequence of spin-labeling and fragmentation.

The most probable cause of stabilization of the (Fc)₅ fragment is the heating of IgM solution to 56°C during fragmentation with trypsin. At this temperature the τ value for the (Fc)₅ fragment is unusually low, equaling 23 ns.

The spin-labeling in the peptide part of IgM occurs mostly in the Fab region which is a rather rigid moiety as expected.     

Formation of truncated peptide by‐products via sequence‐specific formyl group transfer from Trp(For) residues to Nα in the course of Boc‐SPPS

(N^In)‐Formyl protective group of tryptophan has been introduced as a base/nucleophile‐labile protective group. It has long been known that a free Nα‐amino group of the peptide can serve as a nucleophile: an irreversible formyl N^In → NH₂ transfer is consistently observed when deformylation is performed last on an otherwise deprotected peptide that possesses free Nα‐amino group. Obviously, this particular side reaction should be expected any time free amino group is exposed to Trp(For), but, at the best of our knowledge, has never been reported in the course of Boc‐SPPS. In the present communication, we describe a set of appropriately designed model experiments that permitted to detect the title side reaction both in solution and in solid‐phase reactions. We observed intermolecular formyl group transfer with a model compound, Trp(For)‐NH₂. Importantly, we also observed this migration on solid support with the rate roughly estimated to be up to 1% of residues per minute. We also observed that the formyl‐group transfer reaction occurred in a sequence‐dependent manner and was suppressed to a non‐detectable level using ‘in situ neutralization’ technique. Because this side reaction is sequence dependent, there might be situations when the rate of the formation of N_α‐formyl termination by‐products is significant. In other cases, the N_α‐For truncated by‐products would not contaminate the final peptide significantly but still could be a source of microheterogeneity. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Synergistic capture of Clostridium botulinum type A neurotoxin by scFv antibodies to novel epitopes

A non‐immune library of human single chain fragment variable (scFv) antibodies displayed on Saccharomyces cerevisiae was screened for binding to the Clostridium botulinum neurotoxin serotype A binding domain [BoNT/A (H_c)] with the goal of identifying scFv to novel epitopes. To do this, an antibody‐mediated labeling strategy was used in which antigen‐binding yeast clones were selected after labeling with previously characterized monoclonal antibodies (MAbs) specific to the H_c. Twenty unique scFv clones were isolated that bound H_c. Of these, 3 also bound to full‐length BoNT/A toxin complex with affinities ranging from 5 to 48 nM. Epitope binning showed that the three unique clones recognized at least two epitopes distinct from one another as well as from the detection MAbs. After production in E. coli, scFv were coupled to magnetic particles and tested for their ability to capture BoNT/A holotoxin using an Endopep‐MS assay. In this assay, toxin captured by scFv coated magnetic particles was detected by incubation of the complex with a peptide containing a BoNT/A‐specific cleavage sequence. Mass spectrometry was used to detect the ratio of intact peptide to cleavage products as evidence for toxin capture. When tested individually, each of the scFv showed a weak positive Endopep‐MS result. However, when the particles were coated with all three scFv simultaneously, they exhibited significantly higher Endopep‐MS activity, consistent with synergistic binding. These results demonstrate novel approaches toward the isolation and characterization of scFv antibodies specific to unlabeled antigens. They also provide evidence that distinct scFv antibodies can work synergistically to increase the efficiency of antigen capture onto a solid support. Biotechnol. Bioeng. 2011;108: 2456–2467. © 2011 Wiley Periodicals, Inc.     

Structural changes induced by the deamidation and isomerization of asparagine revealed by the crystal structure of Ustilago sphaerogena ribonuclease U2B

Under physiological conditions, the deamidation and isomerization of asparagine to isoaspartate (isoAsp) proceeds nonenzymatically via succinimide. Although a large number of proteins have been reported to contain isoAsp, information concerning the three‐dimensional structure of proteins containing isoaspartate is still limited. We have crystallized isoAsp containing Ustilago sphaerogena ribonuclease U2B, and determined the crystal structure at 1.32 Å resolution. The structure revealed that the formation of isoAsp32 induces a single turn unfolding of the α‐helix from Asp29 to Asp34, and the region from Asp29 to Arg35 forms a U‐shaped loop structure. The electron density map shows that isoAsp32 retained the L‐configuration at the C_α atom. IsoAsp32 is in gauche conformation about a C_α? C_β bond, and the polypeptide chain bends by ～90° at isoAsp32. IsoAsp32 protrudes from the surface of the protein, and the abnormal β‐peptide bond in the main‐chain and α‐carboxylate in the side‐chain is fully exposed. The structure suggests that the deamidation of the Asn and the isoAsp formation in proteins could confer immunogenicity. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 1003–1010, 2010.     

Label‐free determination of protein–ligand binding constants using mass spectrometry and validation using surface plasmon resonance and isothermal titration calorimetry

We performed a systematic comparison of three label‐free methods for quantitative assessment of binding strengths of proteins interacting with small molecule ligands. The performance of (1) nanoelectrospray ionization mass spectrometry (nESI‐MS), (2) surface plasmon resonance (SPR), and (3) isothermal titration calorimetry (ITC) was compared for the determination of dissociation constants (K_D). The model system studied for this purpose was the human carbonic anhydrase I (hCAI) with eight known and well characterized sulfonamide inhibitors (Krishnamurthy et al., Chem. Rev. 2008, 108: 946–1051). The binding affinities of the inhibitors chosen vary by more than four orders of magnitude e.g., the K_D value determined for ethoxzolamide by nESI‐MS was 5 ± 1 nM and the K_D value for sulfanilamide was 145.7 ± 10.0 µM. The agreement of the determined K_D values by the three methods investigated was excellent for ethoxzolamide and benzenesulfonamide (variation with experimental error), good for acetazolamide and 4‐carboxybenzenesulfonamide (variation by ～ one order of magnitude), but poor for others e.g., sulpiride. The accuracies of the K_D values are determined, and advantages and drawbacks of the individual methods are discussed. Moreover, we critically evaluate the three examined methods in terms of ease of the measurement, sample consumption, time requirement, and discuss their limitations. Copyright © 2009 John Wiley & Sons, Ltd.     

Chemical composition of cornicle secretion of the brown citrus aphid Toxoptera citricida

Brown citrus aphid Toxoptera citricida Kirkadly is considered as an important pest of citrus because it vectors citrus tristeza closterovirus. Aphids secrete a fluid from their cornicles as a defensive mechanism against natural enemies. Earlier studies on cornicle secretions of aphids focus only on triglycerides and fatty acids. In the present study, three different methods are used to investigate the chemical composition of the cornicle fluid of T. citricida. Gas chromatography with flame ionization detection is used to detect and quantify the triglycerides after trimethylsilyl derivatization, and gas chromatography‐mass spectrometry (GC‐MS) is used to determine the fatty acid composition after derivatization with boron trifluoride–methanol. Other compounds are detected using GC‐MS after methoxyamine hydrochloride and N‐methyl‐N‐(trimethylsilyl)trifluoroacetamide derivatization. The major fatty acid in the cornicle secretion of T. citricida is palmitic acid. Oleic, stearic, myristic, myristoleic and sorbic acids are also detected, although in low amounts. Sorboyl, dipalmitoyl (C_6‐2, C₁₆, C₁₆) and disorboyl, stearoyl (C_6‐2, C_6‐2, C₁₈) are the main triglycerides detected in cornicle secretion. Trehalose is the most predominant sugar (558.2 mm ), followed by glucose (92.0 mm ) and inositol (48.8 mm ). Many amino acids, including proline, glycine, alanine and serine, are also detected. In addition, the cornicle secretion is rich in many organic acids, including malic, citric, succinic and lactic acid. Information obtained from the present study improves our understanding of the chemical composition of the cornicle secretion of the brown citrus aphid.     

Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine–lysine distances

Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL‐MS), in which protein complexes are crosslinked and characterized using liquid chromatography‐mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine‐reactive N‐hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS³) have a linker arm that is 11.4 Å long when fully extended, allowing C_α (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ～24 Å apart. However, XL‐MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ～3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high‐quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine–lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS³, a distance constraint of 26–30 Å between C_α atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL‐MS results to structures or in modeling. We also discuss the comparison of XL‐MS results to MD simulations and known structures as a means to test and validate experimental XL‐MS methods.     

Electrospray ionization mass spectroscopic analysis of peptides modified with N-ethylmaleimide or iodoacetanilide

The cysteine-specific modifiers we reported previously, N-ethylmaleimide (NEM) and iodoacetanilide (IAA), have been applied to label cysteine residues of peptides in combination with electrospray ionization mass spectrometry (ESI-MS/MS), and their scope in proteomic studies was examined. Peptides modified with N-ethylmaleimide (NEM) or iodoacetanilide (IAA) showed significant enhancement in ionization efficiencies. These modifiers were also found to remain intact in tandem mass spectrometry. Both combinations of N-ethylmaleimide (NEM) and d₅-N-ethylmaleimide (d₅-NEM), and iodoacetanilide (IAA) and ¹³C₆-iodoacetanilide (¹³C₆-IAA) were also shown to be applicable to quantitative analysis of a peptide.     

Gas Exchange of In Vitro and Ex Vitro Grown Grapevine Plants

Net photosynthetic rate (P _N) and dark respiration rate (R _D) were measured in Vitis vinifera L. cvs. Dimiat 4/24 (23^rd subculture), Dimiat 4/38 (22^nd subculture), and Italian Riesling 3/47 (22^nd subculture) on days 3, 2, and 1 (1^st series) before transfer from the in vitro culture and on days 14, 15, 16 (2^nd series) and 28, 29, 30 (3^rd series) after the transfer. P _N of in vitro and ex vitro plants was strongly affected by irradiance. P _N and R _D of in vitro plantlets were lower and transpiration rate (E) was higher compared to those of ex vitro plantlets. P _N, R _D, and E changed in the course of acclimation.     

An automated robotic platform for rapid profiling oligosaccharide analysis of monoclonal antibodies directly from cell culture

Oligosaccharides attached to Asn297 in each of the C_H2 domains of monoclonal antibodies play an important role in antibody effector functions by modulating the affinity of interaction with Fc receptors displayed on cells of the innate immune system. Rapid, detailed, and quantitative N-glycan analysis is required at all stages of bioprocess development to ensure the safety and efficacy of the therapeutic. The high sample numbers generated during quality by design (QbD) and process analytical technology (PAT) create a demand for high-performance, high-throughput analytical technologies for comprehensive oligosaccharide analysis. We have developed an automated 96-well plate-based sample preparation platform for high-throughput N-glycan analysis using a liquid handling robotic system. Complete process automation includes monoclonal antibody (mAb) purification directly from bioreactor media, glycan release, fluorescent labeling, purification, and subsequent ultra-performance liquid chromatography (UPLC) analysis. The entire sample preparation and commencement of analysis is achieved within a 5-h timeframe. The automated sample preparation platform can easily be interfaced with other downstream analytical technologies, including mass spectrometry (MS) and capillary electrophoresis (CE), for rapid characterization of oligosaccharides present on therapeutic antibodies.     

A new tool for monoclonal antibody analysis: Application of IdeS proteolysis in IgG domain-specific characterization

Monoclonal antibody (mAb) products are extraordinarily heterogeneous due to the presence of a variety of enzymatic and chemical modifications, such as deamidation, isomerization, oxidation, glycosylation, glycation, and terminal cyclization. The modifications in different domains of the antibody molecule can result in different biological consequences. Therefore, characterization and routine monitoring of domain-specific modifications are essential to ensure the quality of the therapeutic antibody products. For this purpose, a rapid and informative methodology was developed to examine the heterogeneity of individual domains in mAb products. A recently discovered endopeptidase, IdeS, cleaves heavy chains below the hinge region, producing F(ab')₂ and Fc fragments. Following reduction of disulfide bonds, three antibody domains (LC, Fd, and Fc/2) can be released for further characterization. Subsequent analyses by liquid chromatography/mass spectrometry, capillary isoelectric focusing, and glycan mapping enable domain-specific profiling of oxidation, charge heterogeneity, and glycoform distribution. When coupled with reversed phase chromatography, the unique chromatographic profile of each molecule offers a simple strategy for an identity test, which is an important formal test for biopharmaceutical quality control purposes. This methodology is demonstrated for a number of IgGs of different subclasses (IgG1, IgG2, IgG4), as well as an Fc fusion protein. The presented technique provides a convenient platform approach for scientific and formal therapeutic mAb product characterization. It can also be applied in regulated drug substance batch release and stability testing of antibody and Fc fusion protein products, in particular for identity and routine monitoring of domain-specific modifications.