Enhanced Quantitative LC-MS/MS Analysis of N-linked Glycans Derived from Glycoproteins Using Sodium Deoxycholate Detergent

Method for B Cell Receptor Enrichment in Malignant B Cells

B cells are central to the adaptive immune response and provide long-lasting immunity after infection. B cell activation is mediated by the surface membrane-bound B cell receptor (BCR) following recognition of a specific antigen. The BCR has been challenging to analyse using mass spectrometry (MS) due to the difficulty of isolating and enriching this membrane-bound protein complex. There are approximately 120,000 BCRs on the B cell surface; however, depending on the B cell activation state, there may be hundreds-of-millions to billions of proteins in a B cell. Consequently, advanced proteomic techniques such as MS workflows that use purified proteins to yield structural and protein-interaction information have not been published for the BCR complex. This paper describes a method for enriching the BCR complex that is MS-compatible. The method involves a Protein G pull down on agarose beads using an intermediary antibody to each of the BCR complex subcomponents (CD79a, CD79b, and membrane immunoglobulin). The enrichment process is shown to pull down the entire BCR complex and has the advantage of being readily compatible with further proteomic study including MS analysis. Using intermediary antibodies has the potential to enrich all isotypes of the BCR, unlike previous methods described in the literature that use protein G-coated beads to directly pull down the membrane IgG (mIgG) but cannot be used for other mIg isotypes.

Simultaneous capture of hydrophilic and hydrophobic compounds from complex plants by biosurfactant-assisted mechanical amorphous dispersion extraction

A biosurfactant-assisted mechanical amorphous dispersion extraction (BA-MADE) procedure was established for the simultaneous capture of hydrophilic phenolic acids and hydrophobic tanshinones from Salvia miltiorrhiza. Single-factor experiments and the response surface methodology were used to optimize and analyze the crucial parameters for the method, such as the type and amount of amorphous-dispersion extractants, grinding time, extraction time and solid-to-liquid ratio. The optimized parameter values for the BA-MADE process were 407.02 mg of sodium chenodeoxycholate, a grinding time of 4.87 min, an extraction time of 4.92 min, and a solid-to-liquid ratio of 0.5:10 g/mL. The calibration curves of danshensu, rosmarinic acid, lithospermic acid, salvianolic acid B, salvianolic acid A, dihydrotanshinone I, cryptotanshinone, tanshinone I, and tanshinone II A exhibited good linearity in the range of 1-500 μg/mL (R² ≥ 0.9990). The limits of detection of nine analytes ranged from 5.46 to 130 ng/mL, the relative standard deviations (RSDs) of intraday and interday precision were less than 1.95 and 3.56%, respectively, and the recoveries of the real sample were in the range of 85-113%, with RSD% below 3.21%. The BA-MADE method was compared with previously reported methods, such as heating reflux extraction, ultrasonic extraction and microwave-assisted micellar extraction, and the results demonstrated that the developed method has significant advantages in the simultaneous extraction of hydrophilic and hydrophobic active components from Salvia miltiorrhiza.

A novel pneumococcal protein-polysaccharide conjugate vaccine based on biotin-streptavidin

Pneumococcal disease is a serious public health problem worldwide and an important cause of morbidity and mortality among children and adults in developing countries. Although vaccination is among the most effective approaches to prevent and control pneumococcal diseases, approved vaccines have limited protective effects. We developed a pneumococcal protein-polysaccharide conjugate vaccine that is mediated by the non-covalent interaction between biotin and streptavidin. Biotinylated type IV capsular polysaccharide was incubated with a fusion protein containing core streptavidin and Streptococcus pneumoniae virulence protein and relying on the non-covalent interaction between biotin and streptavidin to prepare the protein-polysaccharide conjugate vaccine. Analysis of vaccine efficacy revealed that mice immunized with the protein-polysaccharide conjugate vaccine produced antibodies with high potency against virulence proteins and polysaccharide antigens and were able to induce Th1 and Th17 responses. The antibodies identified using an opsonophagocytic assay were capable of activating the complement system and promoting pathogen elimination by phagocytes. Additionally, mice immunized with the protein-polysaccharide conjugate vaccine and then infected with a lethal dose of Streptococcus pneumoniae demonstrated induced protective immunity. The data indicated that the pneumococcal protein-polysaccharide (biotin-streptavidin) conjugate vaccine demonstrated broad-spectrum activity applicable to a wide range of people and ease of direct coupling between protein and polysaccharide. These findings provide further evidence for the application of biotin-streptavidin in S. pneumoniae vaccines.

Advances in mass spectrometry-based glycoproteomics: An update covering the period 2017-2021

Protein glycosylation is one of the most common posttranslational modifications, and plays an essential role in a wide range of biological processes such as immune response, intercellular signaling, inflammation, host-pathogen interaction, and protein stability. Glycoproteomics is a proteomics subfield dedicated to identifying and characterizing the glycans and glycoproteins in a given cell or tissue. Aberrant glycosylation has been associated with various diseases such as Alzheimer's disease, viral infections, inflammation, immune deficiencies, congenital disorders, and cancers. However, glycoproteomic analysis remains challenging because of the low abundance, site-specific heterogeneity, and poor ionization efficiency of glycopeptides during LC-MS analyses. Therefore, the development of sensitive and accurate approaches to efficiently characterize protein glycosylation is crucial. Methods such as metabolic labeling, enrichment, and derivatization of glycopeptides, coupled with different mass spectrometry techniques and bioinformatics tools, have been developed to achieve sophisticated levels of quantitative and qualitative analyses of glycoproteins. This review attempts to update the recent developments in the field of glycoproteomics reported between 2017 and 2021.

A rapid method for relative quantification of N-glycans from a therapeutic monoclonal antibody during trastuzumab biosimilar development

Glycosylation is a common post-translational modification and critical quality attribute that can modulate the efficacy of therapeutic proteins. In the production of monoclonal antibodies (mAbs), quantifying the glycoform profile is a vital characterization step. Traditional glycan analysis is time consuming and involves steps at extreme temperature or pH, which may alter glycans. Here, we describe a rapid method for glycan analysis in which glycans are released from mAb samples that are bound to protein A columns. Since host cell proteins, which may also contain glycans, were already removed, this step enables analysis of cell culture products. Glycans released from the mAb samples are then derivatized with InstantPC™ labeling agent and analyzed by HILIC-FLD-MS. To illustrate the method, the glycan profiles of six trastuzumab (Herceptin®) antibody lots and four biosimilar developmental lots were analyzed. The results derived from our novel method, which takes less than 90 min, are compared with those from a typical glycan preparation approach.

Determination of Isomeric Glycan Structures by Permethylation and Liquid Chromatography-Mass Spectrometry (LC-MS)

The existence of glycans in isomeric forms is responsible for the multifariousness of their properties and biological functions. Their altered expression has been associated with various diseases and cancers. Analysis of native glycans is not very sensitive due to the low ionization efficiency of glycans. These facts necessitate their comprehensive structural studies and establishes a high demand for sensitive and reliable techniques. In this chapter, we discuss the strategies for effective separation and identification of permethylated isomeric glycans. The sample preparation for permethylated glycans derived from model glycoproteins and complex biological samples, analyzed using LC-MS/MS, is delineated. We introduce protein extraction and release of glycans, followed by strategies to purify the released glycans, which are reduced and permethylated to improve ionization efficiency and stabilize sialic acid residues. High-temperature LC-based separation on PGC (porous graphitized carbon) column is conducive to isomeric separation of glycans and allows their sensitive identification and quantification using MS/MS.

N-Glycomics of Cerebrospinal Fluid: Method Comparison

Cerebrospinal fluid (CSF) contains valuable biological and neurological information. However, its glycomics analysis is hampered due to the low amount of protein in the biofluid, as has been demonstrated by other glycomics studies using a substantial amount of CSF. In this work, we investigated different N-glycan sample preparation approaches to develop a more sensitive method. These methods, one with an increased amount of buffer solution during the N-glycan release step with a lower amount of sample volume and the other with Filter-Aided N-Glycan Separation (FANGS), were compared with recent work to demonstrate their effectiveness. It was demonstrated that an increased amount of buffer solution showed higher intensity in comparison to the previously published method and FANGS. This suggested that digestion efficiency during the N-glycan release step was not in an optimal condition from the previously published method, and that there is a substantial loss of sample with FANGS when preparing N-glycans from CSF.

Glucose unit index (GUI) of permethylated glycans for effective identification of glycans and glycan isomers

Retention time is the most common and widely used criterion to report the separation of glycans using Liquid Chromatography (LC), but it varies widely across different columns, instruments and laboratories. This variation is problematic when inter-laboratory data is compared. Furthermore, it influences reproducibility and hampers efficient data interpretation. In our endeavor to overcome this variance, we propose the use of the Glucose Unit Index (GUI) on C18 and PGC column-based separation of reduced and permethylated glycans. GUI has previously been utilized for retention time normalization of native and labeled glycans. We evaluated this method with reduced and permethylated glycans derived from model glycoproteins fetuin and ribonuclease B (RNase B), and then implemented it to human blood serum to generate C18 and PGC column-based isomeric glycan libraries. GUI values for glycan compositions were calculated with respect to the glucose units derived from dextrin, which was employed as an elution standard. The GUI values were validated on three different LC systems (UltiMate 3000 Nano UHPLC systems) in two laboratories to ensure the reliability and reproducibility of the method. Applicability on real samples was demonstrated using human breast cancer cell lines. A total of 116 permethylated N-glycans separated on a C18 column and 134 glycans separated on a PGC column were compiled in a library. Overall, the established GUI method and the demonstration of reproducible inter- and intra-laboratory GUI values would aid the future development of automated glycan and isomeric glycan identification methods.

N-Linked Surface Glycan Biosynthesis, Composition, Inhibition, and Function in Cnidarian-Dinoflagellate Symbiosis

The success of symbioses between cnidarian hosts (e.g., corals and sea anemones) and micro-algal symbionts hinges on the molecular interactions that govern the establishment and maintenance of intracellular mutualisms. As a fundamental component of innate immunity, glycan-lectin interactions impact the onset of marine endosymbioses, but our understanding of the effects of cell surface glycome composition on symbiosis establishment remains limited. In this study, we examined the canonical N-glycan biosynthesis pathway in the genome of the dinoflagellate symbiont Breviolum minutum (family Symbiodiniaceae) and found it to be conserved with the exception of the transferase GlcNAc-TII (MGAT2). Using coupled liquid chromatography-mass spectrometry (LC-MS/MS), we characterized the cell surface N-glycan content of B. minutum, providing the first insight into the molecular composition of surface glycans in dinoflagellates. We then used the biosynthesis inhibitors kifunensine and swainsonine to alter the glycan composition of B. minutum. Successful high-mannose enrichment via kifunensine treatment resulted in a significant decrease in colonization of the model sea anemone Aiptasia (Exaiptasia pallida) by B. minutum. Hybrid glycan enrichment via swainsonine treatment, however, could not be confirmed and did not impact colonization. We conclude that functional Golgi processing of N-glycans is critical for maintaining appropriate cell surface glycan composition and for ensuring colonization success by B. minutum.

Improved in-solution trypsin digestion method for methanol-chloroform precipitated cellular proteomics sample

Methanol-chloroform based protein precipitation is an essential step in many liquid chromatography-tandem mass spectrometry-based cellular proteomics applications. However, re-solubilization of the total protein precipitate is difficult using regular in-solution digestion protocol. Sodium deoxycholate is reported as an efficient surfactant for re-solubilization of membrane fractions. In this study, we demonstrated an application combining methanol-chloroform based protein precipitations and deoxycholic acid assisted re-solubilization of pellets to evaluate the improvement of protein identifications in mass spectrometry-based bottom-up proteomics. We evaluated the modified method using an equal amount of Raw 264.7 mouse macrophage cell lysate. Detailed in-solution trypsin digestion studies were presented on methanol-chloroform precipitated samples with or without deoxycholic acid treatments and compared with popular sample digestion methods. A mass spectrometric analysis confirmed an 82% increase in protein identification in deoxycholic acid-treated samples compared to other established methods. Furthermore, liquid chromatography-tandem mass spectrometry analysis of an equal amount of proteins from methanol-chloroform precipitated, and methanol-chloroform/deoxycholic acid-treated macrophage cell lysate showed a 14% increase and 27% unique protein identifications. We believe this improved digestion method could be a complementary or alternative method for mammalian cell sample preparations where sodium dodecyl sulfate based lysis buffer is frequently used.

Comparative Membrane N-Glycomics of Different Breast Cancer Cell Lines To Understand Breast Cancer Brain Metastasis

The mechanism of brain metastatic breast cancer has gained attention because of its increased incidence rate and its low survival rate. Aberrant protein glycosylation is thought to be a contributing factor in this metastatic mechanism, in which metastatic cancer cells can pass through the blood-brain barrier (BBB). The cell membrane is the outermost layer of a cell and in direct contact with the environment and with other cells, making membrane glycans especially important in many biological processes that include mediating cell-cell adhesion, cell signaling, and interactions. Thus, membrane glycomics has attracted more interest for a variety of disease studies in recent years. To reveal the role that membrane N-glycans play in breast cancer brain metastasis, in this study, membrane enrichment was achieved by ultracentrifugation. Liquid chromatography-tandem mass spectrometry was employed to analyze enriched membrane N-glycomes from five breast cancer cell lines and one brain cancer cell line. Relative quantitative glycomic data from each cell line were compared to MDA-MB-231BR, which is the brain-seeking cell line. The higher sialylation level observed in MDA-MB-231BR suggested the importance of sialylation as it might assist with cell invasion and the penetration of the BBB. Some highly sialylated N-glycans, such as HexNAc₅Hex₆DeoxyHex₁NeuAc₃ and HexNAc₆Hex₇DeoxyHex₁NeuAc₃, exhibited higher abundances in 231BR, indicating their possible contributions to breast cancer brain metastasis as well as their potential to be indicators for the breast cancer brain metastasis.

Novel methods in glycomics: a 2019 update

Introduction: Glycomics, which aims to define the glycome of a biological system to better assess the biological attributes of the glycans, has attracted increasing interest. However, the complexity and diversity of glycans present challenging barriers to glycome definition. Technological advances are major drivers in glycomics.Areas covered: This review summarizes the main methods and emphasizes the most recent advances in mass spectrometry-based methods regarding glycomics following the general workflow in glycomic analysis.Expert opinion: Recent mass spectrometry-based technological advances have significantly lowered the barriers in glycomics. The field of glycomics is moving toward both generic and precise analysis.

Mass spectrometry-based qualitative and quantitative N-glycomics: An update of 2017-2018

N-glycosylation is one of the most frequently occurring protein post-translational modifications (PTMs) with broad cellular, physiological and pathological relevance. Mass spectrometry-based N-glycomics has become the state-of-the-art instrumental analytical pipeline for sensitive, high-throughput and comprehensive characterization of N-glycans and N-glycomes. Improvement and new development of methods in N-glycan release, enrichment, derivatization, isotopic labeling, separation, ionization, MS, tandem MS and informatics accompany side-by-side wider and deeper application. This review provides a comprehensive update of mass spectrometry-based qualitative and quantitative N-glycomics in the years of 2017-2018.

Revealing the Biological Attributes of N-Glycan Isomers in Breast Cancer Brain Metastasis Using Porous Graphitic Carbon (PGC) Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)

Breast cancer is a leading cancer in women and is considered to be the second-most common metastatic cancer following lung cancer. An estimated 10-16% of breast cancer patients are suffering from brain metastasis, and the diagnostic cases of breast cancer brain metastasis are increasing. Nevertheless, the mechanisms behind this process are still unclear. Aberrant glycosylation has been proved to be related to many diseases and cancer metastasis. However, studies of N-glycan isomer function in breast cancer brain metastasis are limited. In this study, the expressions of N-glycan isomers derived from five breast cancer cell lines and one brain cancer cell line were investigated and compared to a brain-seeking cell line, 231BR, to acquire a better understanding of the role glycan isomers play in breast cancer brain metastasis. The high temperature nanoPGC-LC-MS/MS achieved an efficient isomeric separation and permitted the identification and quantitation of 144 isomers from 50 N-glycan compositions. There were significant expression alterations of these glycan isomers among the different breast cancer cell lines. The increase of total glycan abundance and sialylation level were observed to be associated with breast cancer invasion. With regard to individual isomers, the greatest number of sialylated isomers was observed along with significant expression alterations in 231BR, suggesting a relationship between glycan sialylation and breast cancer brain metastasis. Furthermore, the increase of the α2,6-sialylation level in 231BR likely contributes to the passage of breast cancer cells through the blood-brain barrier, thus facilitating breast cancer brain metastasis. Meanwhile, the upregulation of highly sialylated glycan isomers with α2,6-linked sialic acids were found to be associated with breast cancer metastasis. This investigation of glycan isomer expressions, especially the unique isomeric expression in brain-seeking cell line 231BR, provides new information toward understanding the potential roles glycan isomers play during breast cancer metastasis and more clues for a deeper insight of this bioprocess.

Characterization of glycan isomers using magnetic carbon nanoparticles as a MALDI co-matrix

Matrix-assisted laser desorption ionization-in source decay (MALDI-ISD) analysis is a useful technique in the structural analysis of glycans. Our recent publication demonstrated that magnetic carbon nanoparticles (MCNPs), used as a MALDI co-matrix, significantly enhanced ISD efficiency for glycomic analysis by MALDI-TOF. In this study, MCNPs were used for the structural study of isomeric glycans. Results from the standard glycans confirmed easy distinction of positional and linkage isomers without the need for further derivatization of glycan molecules. Extensive glycosidic and cross-ring fragmented ions provided different fragment patterns for various glycan isomers. Core- and branch-fucosylated isomers were distinguished by several unique ions, and pseudo-MS3 data were used to recognize the fucosylated branch. Although no diagnostic fragment ion was observed for 2,3- and 2,6-linked sialic acid isomers, their MALDI-ISD patterns were found to be significantly different (P < 0.05). Furthermore, the method introduced in this study could not only be used for the identification of glycan isomers but has also proved effective for the isomeric structural confirmation of gangliosides. GD1a and GD1b gangliosides were easily distinguished by the diagnostic ion originated from GD1a, produced by Z4αZ2β cleavages. Moreover, liquid chromatography coupled with MALDI-TOF was applied to analyze N-glycan isomers derived from a pooled human blood serum sample, providing an alternative method of isomeric glycomic analysis of biological specimens.

Advances in mass spectrometry-based glycoproteomics

Protein glycosylation, an important PTM, plays an essential role in a wide range of biological processes such as immune response, intercellular signaling, inflammation, and host-pathogen interaction. Aberrant glycosylation has been correlated with various diseases. However, studying protein glycosylation remains challenging because of low abundance, microheterogeneities of glycosylation sites, and poor ionization efficiency of glycopeptides. Therefore, the development of sensitive and accurate approaches to characterize protein glycosylation is crucial. The identification and characterization of protein glycosylation by MS is referred to as the field of glycoproteomics. Methods such as enrichment, metabolic labeling, and derivatization of glycopeptides in conjunction with different MS techniques and bioinformatics tools, have been developed to achieve an unequivocal quantitative and qualitative characterization of glycoproteins. This review summarizes the recent developments in the field of glycoproteomics over the past 6 years (2012 to 2018).

Clinical application of quantitative glycomics

Aberrant glycosylation has been associated with many diseases. Decades of research activities have reported many reliable glycan biomarkers of different diseases which enable effective disease diagnostics and prognostics. However, none of the glycan markers have been approved for clinical diagnosis. Thus, a review of these studies is needed to guide the successful clinical translation. Area covered: In this review, we describe and discuss advances in analytical methods enabling clinical glycan biomarker discovery, focusing only on studies of released glycans. This review also summarizes the different glycobiomarkers identified for cancers, Alzheimer's disease, diabetes, hepatitis B and C, and other diseases. Expert commentary: Along with the development of techniques in quantitative glycomics, more glycans or glycan patterns have been reported as better potential biomarkers of different diseases and proved to have greater diagnostic/diagnostic sensitivity and specificity than existing markers. However, to successfully apply glycan markers in clinical diagnosis, more studies and verifications on large biological cohorts need to be performed. In addition, faster and more efficient glycomic strategies need to be developed to shorten the turnaround time. Thus, glycan biomarkers have an immense chance to be used in clinical prognosis and diagnosis of many diseases in the near future.