Chip-based reversed-phase liquid chromatography-mass spectrometry of permethylated N-linked glycans: a potential methodology for cancer-biomarker discovery

Resolving Isomeric Glycopeptide Glycoforms with Hydrophilic Interaction Chromatography (HILIC)

The ability to resolve glycans while attached to tryptic peptides would greatly facilitate glycoproteomics, as this would enable site-specific glycan characterization. Peptide/glycopeptide separations are typically performed using reversed-phase liquid chromatography (RPLC), where retention is driven by hydrophobic interaction. As the hydrophilic glycans do not interact significantly with the RPLC stationary phase, it is difficult to resolve glycopeptides that differ only in their glycan structure, even when these differences are large. Alternatively, glycans interact extensively with the stationary phases used in hydrophilic interaction chromatography (HILIC), and consequently, differences in glycan structure have profound chromatographic shifts in this chromatographic mode. Here, we evaluate HILIC for the separation of isomeric glycopeptide mixtures that have the same peptide backbone but isomeric glycans. Hydrophilic functional groups on both the peptide and the glycan interact with the HILIC stationary phase, and thus, changes to either of these moieties can alter the chromatographic behavior of a glycopeptide. The interactive processes permit glycopeptides to be resolved from each other based on differences in their amino acid sequences and/or their attached glycans. The separations of glycans in HILIC are sufficient to permit resolution of isomeric N-glycan structures, such as sialylated N-glycan isomers differing in α2-3 and α2-6 linkages, while these glycans remain attached to peptides.

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.

LC-MS/MS of permethylated N-glycans derived from model and human blood serum glycoproteins

LC-MS/MS is one of the most powerful tools for N-glycan structure elucidation; however, it is still challenging to identify some glycan structures with low abundance. In this study, we investigated the chromatographic behavior of permethylated N-glycans. The relationship between retention times versus molecular weight of dextran, dextrin, and model glycans was investigated. Also, the nonpolar surface area of glycans was calculated and compared to their experimental retention times. Both retention time and nonpolar surface area trends are similar when the intermolecular interaction is included in the calculation. Moreover, retention time corresponds to glycan types and branch types. The N-glycans analysis model, which combines high mass accuracy and retention time, was applied to confirm serum N-glycans. In total, there were 78 N-glycan compositions identified. A linear relationship between retention times and molecular weights were observed for each subgroup of glycan structures, for example, R(2) value for complex N-glycans was determined to be > 0.98. Moreover, the retention time could be further applied to distinguish between structural isomers as well as linkage isomers. MS/MS data were used to confirm the structural isomers.

Integrated Microfluidic Lectin Barcode Platform for High-Performance Focused Glycomic Profiling

Protein glycosylation is one of the key processes that play essential roles in biological functions and dysfunctions. However, progress in glycomics has considerably lagged behind genomics and proteomics, due in part to the enormous challenges in analysis of glycans. Here we present a new integrated and automated microfluidic lectin barcode platform to substantially improve the performance of lectin array for focused glycomic profiling. The chip design and flow control were optimized to promote the lectin-glycan binding kinetics and speed of lectin microarray. Moreover, we established an on-chip lectin assay which employs a very simple blocking method to effectively suppress the undesired background due to lectin binding of antibodies. Using this technology, we demonstrated focused differential profiling of tissue-specific glycosylation changes of a biomarker, CA125 protein purified from ovarian cancer cell line and different tissues from ovarian cancer patients in a fast, reproducible, and high-throughput fashion. Highly sensitive CA125 detection was also demonstrated with a detection limit much lower than the clinical cutoff value for cancer diagnosis. This microfluidic platform holds the potential to integrate with sample preparation functions to construct a fully integrated "sample-to-answer" microsystem for focused differential glycomic analysis. Thus, our technology should present a powerful tool in support of rapid advance in glycobiology and glyco-biomarker development.

Study on Improving Thickness Uniformity of Microfluidic Chip Mold in the Electroforming Process

Electroformed microfluidic chip mold faces the problem of uneven thickness, which decreases the dimensional accuracy of the mold, and increases the production cost. To fabricate a mold with uniform thickness, two methods are investigated. Firstly, experiments are carried out to study how the ultrasonic agitation affects the thickness uniformity of the mold. It is found that the thickness uniformity is maximally improved by about 30% after 2 h electroforming under 200 kHz and 500 W ultrasonic agitation. Secondly, adding a second cathode, a method suitable for long-time electroforming is studied by numerical simulation. The simulation results show that with a 4 mm width second cathode used, the thickness uniformity is improved by about 30% after 2 h of electroforming, and that with electroforming time extended, the thickness uniformity is improved more obviously. After 22 h electroforming, the thickness uniformity is increased by about 45%. Finally, by comparing two methods, the method of adding a second cathode is chosen, and a microfluidic chip mold is made with the help of a specially designed second cathode. The result shows that the thickness uniformity of the mold is increased by about 50%, which is in good agreement with the simulation results.

Elevation of CA19-9-Related Novel Marker, Core 1 Sialyl Lewis A, in Sera of Adenocarcinoma Patients Verified by a SRM-Based Method

We have attempted to identify a novel glycan tumor marker. Pyridylaminated (PA) O-glycans were prepared from sera, and the corresponding O-glycan profiles were constructed by HPLC separation. By comparing the serum O-glycan profiles from healthy controls with those of cancer patients, we identified a marker candidate, core 1 sialyl Lewis A (NeuAcα2-3Galβ1-3(Fucα1-4)GlcNAcβ1-3Gal) (abbreviated C1SLA), whose concentration appeared to be weakly correlated with CA19-9 values. To quantify this glycan, we developed a selected reaction monitoring (SRM) assay that used a stable isotope, tetradeuterium-labeled pyridylamino (d4-PA) glycan, as an internal standard. The analyte (d0-PA-C1SLA) and the internal standard (d4-PA-C1SLA) were subjected to SRM analyses after two types of HPLC separation. Serum levels of C1SLA, determined as the relative ratio to total O-glycans, were then measured. These analyses revealed that (i) C1SLA is a CA19-9-related glycan, (ii) the mean value of C1SLA in normal controls is 3.41 ppm, (iii) the level of C1SLA was significantly higher in samples of stages II-IV stomach cancers (P = 0.0036) as well as pancreatic cancers (P < 0.0001) compared to that of normal controls, (iv) the relationship between C1SLA and CA19-9 varies from poor to weak depending on the cancer, and (v) C1SLA could be valuable as a diagnostic adjunct for cancer.

Advances in coupling microfluidic chips to mass spectrometry

Microfluidic technology has shown advantages of low sample consumption, reduced analysis time, high throughput, and potential for integration and automation. Coupling microfluidic chips to mass spectrometry (Chip-MS) can greatly improve the overall analytical performance of MS-based approaches and expand their potential applications. In this article, we review the advances of Chip-MS in the past decade, covering innovations in microchip fabrication, microchips coupled to electrospray ionization (ESI)-MS and matrix-assisted laser desorption/ionization (MALDI)-MS. Development of integrated microfluidic systems for automated MS analysis will be further documented, as well as recent applications of Chip-MS in proteomics, metabolomics, cell analysis, and clinical diagnosis.

Sample preparation for mass spectrometric analysis of human serum N-glycans using hydrophilic interaction chromatography-based solid phase extraction

Expression levels of N-linked glycans derived from human serum glycoproteins have been shown to change during the progression of many diseases. Generally, N-glycans released from human serum proteins co-exist with endogenous serum peptides, salts, and other contaminants. Effective removal of these contaminants is essential to obtain the glycan profile of human serum proteins. Here, we developed a sample preparation method for mass spectrometry (MS) analysis of N-linked glycans derived from human serum glycoproteins based on a zwitterionic hydrophilic material named Click TE-Cys. The high hydrophilicity of Click TE-Cys, resulting from its unique surface structure and charge distribution, facilitated removal of co-existing salts and endogenous serum peptides. Furthermore, the present enrichment approach was handled in parallel, thus saving time. Using this method, a total of 47 unique N-glycans released from human serum proteins were identified. The intrabatch and interbatch coefficients of variation for the 47 N-linked glycans were 8.57% ± 0.96% and 9.22% ± 1.03%, respectively. These results demonstrate that the present method is suitable for fast purification of N-linked glycans derived from human serum glycoproteins, and has potential for clinical application.

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.

Protein and site specificity of fucosylation in liver-secreted glycoproteins

Chronic liver diseases are a serious health problem worldwide. One of the frequently reported glycan alterations in liver disease is aberrant fucosylation, which was suggested as a marker for noninvasive serologic monitoring. We present a case study that compares site specific glycoforms of four proteins including haptoglobin, complement factor H, kininogen-1, and hemopexin isolated from the same patient. Our exoglycosidase-assisted LC–MS/MS analysis confirms the high degree of fucosylation of some of the proteins but shows that microheterogeneity is protein- and site-specific. MSn analysis of permethylated detached glycans confirms the presence of LeY glycoforms on haptoglobin, which cannot be detected in hemopexin or complement factor H; all three proteins carry Lewis and H epitopes. Core fucosylation is detectable in only trace amounts in haptoglobin but with confidence on hemopexin and complement factor H, where core fucosylation of the bi-antennary glycans on select glycopeptides reaches 15–20% intensity. These protein-specific differences in fucosylation, observed in proteins isolated from the same patient source, suggest that factors other than up-regulation of enzymatic activity regulate the microheterogeneity of glycoforms. This has implications for selection of candidate proteins for disease monitoring and suggests that site-specific glycoforms have structural determinants, which could lead to functional consequences for specific subsets of proteins or their domains.

Polysialylated N-glycans identified in human serum through combined developments in sample preparation, separations, and electrospray ionization-mass spectrometry

The N-glycan diversity of human serum glycoproteins, i.e., the human blood serum N-glycome, is both complex and constrained by the range of glycan structures potentially synthesizable by human glycosylation enzymes. The known glycome, however, has been further limited by methods of sample preparation, available analytical platforms, e.g., based upon electrospray ionization-mass spectrometry (ESI-MS), and software tools for data analysis. In this report several improvements have been implemented in sample preparation and analysis to extend ESI-MS glycan characterization and to include polysialylated N-glycans. Sample preparation improvements included acidified, microwave-accelerated, PNGase F N-glycan release to promote lactonization, and sodium borohydride reduction, that were both optimized to improve quantitative yields and conserve the number of glycoforms detected. Two-stage desalting (during solid phase extraction and on the analytical column) increased sensitivity by reducing analyte signal division between multiple reducing-end-forms or cation adducts. Online separations were improved by using extended length graphitized carbon columns and adding TFA as an acid modifier to a formic acid/reversed phase gradient, providing additional resolving power and significantly improved desorption of both large and heavily sialylated glycans. To improve MS sensitivity and provide gentler ionization conditions at the source-MS interface, subambient pressure ionization with nanoelectrospray (SPIN) was utilized. When these improved methods are combined together with the Glycomics Quintavariate Informed Quantification (GlyQ-IQ) recently described (Kronewitter et al. Anal. Chem. 2014, 86, 6268-6276), we are able to significantly extend glycan detection sensitivity and provide expanded glycan coverage. We demonstrated the application of these advances in the context of the human serum glycome, and for which our initial observations included the detection of a new class of heavily sialylated N-glycans, including polysialylated N-glycans.

Purification of derivatized oligosaccharides by solid phase extraction for glycomic analysis

Profiling of glycans released from proteins is very complex and important. To enhance the detection sensitivity, chemical derivatization is required for the analysis of carbohydrates. Due to the interference of excess reagents, a simple and reliable purification method is usually necessary for the derivatized oligosaccharides. Various SPE based methods have been applied for the clean-up process. To demonstrate the differences among these methods, seven types of self-packed SPE cartridges were systematically compared in this study. The optimized conditions were determined for each type of cartridge and it was found that microcrystalline cellulose was the most appropriate SPE material for the purification of derivatized oligosaccharide. Normal phase HPLC analysis of the derivatized maltoheptaose was realized with a detection limit of 0.12 pmol (S N⁻¹ = 3) and a recovery over 70%. With the optimized SPE method, relative quantification analysis of N-glycans from model glycoproteins were carried out accurately and over 40 N-glycans from human serum samples were determined regardless of the isomers. Due to the high stability and sensitivity, microcrystalline cellulose cartridge showed potential applications in glycomics analysis.

Serum N-glycan profiling predicts prognosis in patients undergoing hemodialysis

Background. The aim of this study is to evaluate the usefulness of serum N-glycan profiling for prognosis in hemodialysis patients. Methods. Serum N-glycan analysis was performed in 100 hemodialysis patients in June 2008 using the glycoblotting method, which allows high-throughput, comprehensive, and quantitative N-glycan analysis. All patients were longitudinally followed up for 5 years. To evaluate the independent predictors for prognosis, patients' background, blood biochemistry, and N-glycans intensity were analyzed using Cox regression multivariate analysis. Selected N-glycans and independent factors were evaluated using the log-rank test with the Kaplan-Meier method to identify the predictive indicators for prognosis. Each patient was categorized according to the number of risk factors to evaluate the predictive potential of the risk criteria for prognosis. Results. In total, 56 N-glycan types were identified in the hemodialysis patients. Cox regression multivariate analysis showed cardiovascular events, body mass index, maximum intima media thickness, and the serum N-glycan intensity of peak number 49 were predictive indicators for overall survival. Risk classification according to the number of independent risk factors revealed significantly poor survival by increasing the number of risk factors. Conclusions. Serum N-glycan profiling may have a potential to predict prognosis in patients undergoing hemodialysis.

Glycomic analysis by glycoprotein immobilization for glycan extraction and liquid chromatography on microfluidic chip

Glycosylation is one of the most common protein modifications and profoundly regulates many biological processes. Aberrant glycosylation is reported to associate with diseases such as cancers, human immunodeficiency virus, and immune disorders. It is considerably important to study protein glycosylation and the associated glycans for diagnostics and disease prognostics. Unlike other protein modifications, glycans attached to proteins are enormously complex. Therefore, the comprehensive analysis of glycans from biological or clinical samples is an unmet technical challenge. Development of the high-throughput method will facilitate the glycomics analysis. In this study, we developed a novel method for the high-throughput analysis of N-glycans from glycoproteins using glycoprotein immobilization for glycan extraction (GIG) coupled with liquid chromatography (LC) in an integrated microfluidic platform (chipLC). The separated glycans were then analyzed by mass spectrometry. Briefly, proteins were first immobilized on a solid support. Glycans on immobilized glycoproteins were modified on solid phase to increase the detection and structure analysis. N-Glycans were then enzymatically released and subsequentially separated by porous graphitized carbon particles packed in the same device. By applying the GIG-chipLC for glycomic analysis of human sera, we identified N-glycans with 148 distinct N-glycan masses. The platform was used to analyze N-glycans from mouse heart tissue and serum. The extracted N-glycans from tissues indicated that unique unsialylated N-glycans were detected in tissues that were missing from the proximal or distal serum, whereas common N-glycans from tissues and serum have mature and sialylated structures. The GIG-chipLC provides a simple and robust platform for glycomic analysis of complex biological and clinical samples.

Serum N-glycan alteration associated with renal cell carcinoma detected by high throughput glycan analysis

PURPOSE

Biomarkers for the early detection and prediction of survival in patients with renal cell carcinoma have not been established. We developed what is to our knowledge a novel glycoblotting method that allows high throughput, comprehensive, quantitative analysis of glycans in human serum. In this study we identified alterations in serum N-glycans associated with renal cell carcinoma.

MATERIALS AND METHODS

We performed a comprehensive N-glycan structural analysis of serum from 64 patients with renal cell carcinoma and 34 age matched, healthy volunteers using glycoblotting methods and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. The peak intensity of N-glycan was analyzed using logistic regression analysis and ROCs were used to select candidate N-glycans. Candidate N-glycans with a statistically significant relationship to renal cell carcinoma or overall survival were independently evaluated using a Cox regression model to determine superiority compared to other conventional renal cell carcinoma biomarkers.

RESULTS

We identified 56 types of N-glycans in serum from healthy volunteers and patients with renal cell carcinoma. Peaks 40 and 43 were significantly more intense in patients than in volunteers. Peak 19 intensity was significantly higher and peak 49 intensity was significantly lower in patients with renal cell carcinoma who survived for a longer period. Multivariate analysis revealed that peaks 19 and 49 were independent predictors of overall survival.

CONCLUSIONS

Serum N-glycan analysis is a promising approach to discovering new biomarkers for renal cell carcinoma. Further study is warranted to validate our results.

Microfluidic chip-based technologies: emerging platforms for cancer diagnosis

The development of early and personalized diagnostic protocols is considered the most promising avenue to decrease mortality from cancer and improve outcome. The emerging microfluidic-based analyzing platforms hold high promises to fulfill high-throughput and high-precision screening with reduced equipment cost and low analysis time, as compared to traditional bulky counterparts in bench-top laboratories. This article overviewed the potential applications of microfluidic technologies for detection and monitoring of cancer through nucleic acid and protein biomarker analysis. The implications of the technologies in cancer cytology that can provide functional personalized diagnosis were highlighted. Finally, the future niches for using microfluidic-based systems in tumor screening were briefly discussed.

The usefulness of hydrazine derivatives for mass spectrometric analysis of carbohydrates

Over the last years, extensive studies have evaluated glycans from different biological samples and validated the importance of glycosylation as one of the most important post-translational modifications of proteins. Although a number of new methods for carbohydrate analysis have been published and there has been significant progress in their identification, the development of new approaches to study these biomolecules and understand their role in living systems are still vivid challenges that intrigue glycobiologists. In the last decade, the success in analyses of oligosaccharides has been driven mainly by the development of innovative, highly sensitive mass spectrometry techniques. For enhanced mass spectrometry detection, carbohydrate molecules are often derivatized. Besides, the type of labeling can influence the fragmentation pattern and make the structural analysis less complicated. In this regard, in 2003 we introduced the low scale, simple non-reductive tagging of glycans employing phenylhydrazine (PHN) as the derivatizing reagent. PHN-labeled glycans showed increased detection and as reported previously they can be analyzed by HPLC, ESI, or MALDI immediately after derivatization. Under tandem mass spectrometry conditions, PHN-derivatives produced useful data for the structural elucidation of oligosaccharides. This approach of analysis has helped to reveal new isomeric structures for glycans of known/unknown composition and has been successfully applied for the profiling of N-glycans obtained from serum samples and cancer cells. The efficacy of this labeling has also been evaluated for different substituted hydrazine reagents. This review summarizes all types of reducing-end labeling based on hydrazone-linkage that have been used for mass spectrometric analyses of oligosaccharides. This review is also aimed at correcting some past misconceptions or interpretations reported in the literature.

Recent trends in analytical and structural glycobiology

The great complexity of glycosylated biomolecules necessitates a set of powerful analytical methodologies to reveal functionally important structural features. Mass spectrometry (MS), with its different ionization techniques, mass analyzers, and detection strategies, has become the most important analytical method in glycomic and glycoproteomic investigations. In combination with MS, microscale separations (based on capillary chromatography and electrophoresis) and carbohydrate microchemistry, we feature here conceptually important applications of the recent years. This review focuses on methodological advances pertaining to disease biomarker research, immunology, developmental biology, and measurements of importance to biopharmaceuticals. High-sensitivity determinations and sample enrichment/preconcentration are particularly emphasized in glycomic and glycoproteomic profiling.

GlycoPep Detector: a tool for assigning mass spectrometry data of N-linked glycopeptides on the basis of their electron transfer dissociation spectra

Electron transfer dissociation (ETD) is commonly used in fragmenting N-linked glycopeptides in their mass spectral analyses to complement collision-induced dissociation (CID) experiments. The glycan remains intact through ETD, while the peptide backbone is cleaved, providing the sequence of amino acids for a glycopeptide. Nonetheless, data analysis is a major bottleneck to high-throughput glycopeptide identification based on ETD data, due to the complexity and diversity of ETD mass spectra compared to CID counterparts. GlycoPep Detector (GPD) is a web-based tool to address this challenge. It filters out noise peaks that interfere with glycopeptide sequencing, correlates input glycopeptide compositions with the ETD spectra, and assigns a score for each candidate. By considering multiple ion series (c-, z-, and y-ions) and scoring them separately, the software gives more weighting to the ion series that matches peaks of high intensity in the spectra. This feature enables the correct glycopeptide to receive a high score while keeping scores of incorrect compositions low. GPD has been utilized to interpret data collected on six model glycoproteins (RNase B, avidin, fetuin, asialofetuin, transferrin, and AGP) as well as a clade C HIV envelope glycoprotein, C.97ZA012 gp140ΔCFI. In every assignment made by GPD, the correct glycopeptide composition earns a score that is about 2-fold higher than other incorrect glycopeptide candidates (decoys). The software can be accessed at http://glycopro.chem.ku.edu/ZZKHome.php .

Glycomic profiling of tissue sections by LC-MS

Because routine preparation of glycan samples involves multiple reaction and cleaning steps at which sample loss occurs, glycan analysis is typically performed using large tissue samples. This type of analysis yields no detailed molecular spatial information and requires special care to maintain proper storage and shipping conditions. We describe here a new glycan sample preparation protocol using minimized sample preparation steps and optimized procedures. Tissue sections and spotted samples first undergo on-surface enzymatic digestion to release N-glycans. The released glycans are then reduced and permethylated prior to online purification and LC-electrospray ionization (ESI)-MS analysis. The efficiency of this protocol was initially evaluated using model glycoproteins and human blood serum (HBS) spotted on glass or Teflon slides. The new protocol permitted the detection of permethylated N-glycans derived from 10 ng RNase B. On the other hand, 66 N-glycans were identified when injecting the equivalent of permethylated glycans derived from a 0.1-μL aliquot of HBS. On-tissue enzymatic digestion of nude mouse brain tissue permitted the detection of 43 N-glycans. The relative peak areas of these 43 glycans were comparable to those from a C57BL/6 mouse reported by the Consortium for Functional Glycomics (CFG). However, the sample size analyzed in the protocol described here was substantially smaller than for the routine method (submicrogram vs mg). The on-tissue N-glycan profiling method permits high sensitivity and reproducibility and can be widely applied to assess the spatial distribution of glycans associated with tissue sections, and may be correlated with immunoflourescence imaging when adjacent tissue sections are analyzed.

Microfluidic chip-based nano-liquid chromatography tandem mass spectrometry for quantification of aflatoxins in peanut products

Aflatoxins (AFs), a group of mycotoxins, are generally produced by fungi Aspergillus species. The naturally occurring AFs including AFB1, AFB2, AFG1, and AFG2 have been clarified as group 1 human carcinogen by International Agency for Research on Cancer. Developing a sensitive analytical method has become an important issue to accurately quantify trace amount of AFs in foodstuffs. In this study, we employed a microfluidic chip-based nano LC (chip-nanoLC) coupled to triple quadrupole mass spectrometer (QqQ-MS) system for the quantitative determination of AFs in peanuts and related products. Gradient elution and multiple reaction monitoring were utilized for chromatographic separation and MS measurements. Solvent extraction followed by immunoaffinity solid-phase extraction was employed to isolate analytes and reduce matrix effect from sample prior to chip-nanoLC/QqQ-MS analysis. Good recoveries were found to be in the range of 90.8%-100.4%. The linear range was 0.048-16 ng g(-1) for AFB1, AFB2, AFG1, AFG2 and AFM1. Limits of detection were estimated as 0.004-0.008 ng g(-1). Good intra-day/inter-day precision (2.3%-9.5%/2.3%-6.6%) and accuracy (96.1%-105.7%/95.5%-104.9%) were obtained. The applicability of this newly developed chip-nanoLC/QqQ-MS method was demonstrated by determining the AFs in various peanut products purchased from local markets.

Chip-based nLC-TOF-MS is a highly stable technology for large-scale high-throughput analyses

Many studies focused on the discovery of novel biomarkers for the diagnosis and treatment of disease states are facilitated by mass spectrometry-based technology. HPLC coupled to mass spectrometry is widely used; miniaturization of this technique using nano-liquid chromatography (LC)-mass spectrometry (MS) usually results in better sensitivity, but is associated with limited repeatability. The recent introduction of chip-based technology has significantly improved the stability of nano-LC-MS, but no substantial studies to verify this have been performed. To evaluate the temporal repeatability of chip-based nano-LC-MS analyses, N-glycans released from a serum sample were repeatedly analyzed using nLC-PGC-chip-TOF-MS on three non-consecutive days. With an average inter-day coefficient of variation of 4 %, determined on log10-transformed integrals, the repeatability of the system is very high. Overall, chip-based nano-LC-MS appears to be a highly stable technology, which is suitable for the profiling of large numbers of clinical samples for biomarker discovery.

Isomer-specific chromatographic profiling yields highly sensitive and specific potential N-glycan biomarkers for epithelial ovarian cancer

Aberrant glycosylation has been observed for decades in essentially all types of cancer, and is now well established as an indicator of carcinogenesis. Mining the glycome for biomarkers, however, requires analytical methods that can rapidly separate, identify, and quantify isomeric glycans. We have developed a rapid-throughput method for chromatographic glycan profiling using microfluidic chip-based nanoflow liquid chromatography (nano-LC)/mass spectrometry. To demonstrate the utility of this method, we analyzed and compared serum samples from epithelial ovarian cancer cases (n=46) and healthy control individuals (n=48). Over 250 N-linked glycan compound peaks with over 100 distinct N-linked glycan compositions were identified. Statistical testing identified 26 potential glycan biomarkers based on both compositional and structure-specific analyses. Using these results, an optimized model was created incorporating the combined abundances of seven potential glycan biomarkers. The receiver operating characteristic (ROC) curve of this optimized model had an area under the curve (AUC) of 0.96, indicating robust discrimination between cancer cases and healthy controls. Rapid-throughput chromatographic glycan profiling was found to be an effective platform for structure-specific biomarker discovery.

The sweet and sour of serological glycoprotein tumor biomarker quantification

Aberrant and dysregulated protein glycosylation is a well-established event in the process of oncogenesis and cancer progression. Years of study on the glycobiology of cancer have been focused on the development of clinically viable diagnostic applications of this knowledge. However, for a number of reasons, there has been only sparse and varied success. The causes of this range from technical to biological issues that arise when studying protein glycosylation and attempting to apply it to practical applications. This review focuses on the pitfalls, advances, and future directions to be taken in the development of clinically applicable quantitative assays using glycan moieties from serum-based proteins as analytes. Topics covered include the development and progress of applications of lectins, mass spectrometry, and other technologies towards this purpose. Slowly but surely, novel applications of established and development of new technologies will eventually provide us with the tools to reach the ultimate goal of quantification of the full scope of heterogeneity associated with the glycosylation of biomarker candidate glycoproteins in a clinically applicable fashion.

Site-specific glycoforms of haptoglobin in liver cirrhosis and hepatocellular carcinoma

Haptoglobin is a liver-secreted glycoprotein with four N-glycosylation sites. Its glycosylation was reported to change in several cancer diseases, which prompted us to examine site-specific glycoforms of haptoglobin in liver cirrhosis and hepatocellular carcinoma. To this end, we have used two-dimensional separation composed of hydrophilic interaction and nano-reverse phase chromatography coupled to QTOF mass spectrometry of the enriched glycopeptides. Our results show increased fucosylation of haptoglobin in liver disease with up to six fucoses associated with specific glycoforms of one glycopeptide. Structural analysis using exoglycosidase treatment and MALDI-MS/MS of detached permethylated glycans led to the identification of Lewis Y-type structures observed particularly in the pooled hepatocellular carcinoma sample. To confirm the increase of the Lewis Y structures observed by LC-MS, we have used immunoaffinity detection with Lewis Y-specific antibodies. The presence of multiply fucosylated Lewis Y glycoforms of haptoglobin in the disease context could have important functional implications.

Analytical glycobiology at high sensitivity: current approaches and directions

This review summarizes the analytical advances made during the last several years in the structural and quantitative determinations of glycoproteins in complex biological mixtures. The main analytical techniques used in the fields of glycomics and glycoproteomics involve different modes of mass spectrometry and their combinations with capillary separation methods such as microcolumn liquid chromatography and capillary electrophoresis. The need for high-sensitivity measurements have been emphasized in the oligosaccharide profiling used in the field of biomarker discovery through MALDI mass spectrometry. High-sensitivity profiling of both glycans and glycopeptides from biological fluids and tissue extracts has been aided significantly through lectin preconcentration and the uses of affinity chromatography.

Developments in the identification of glycan biomarkers for the detection of cancer

Changes in glycosylation readily occur in cancer and other disease states. Thanks to recent advances in the development of analytical techniques and instrumentation, especially in mass spectrometry, it is now possible to identify blood-derived glycan-based biomarkers using glycomics strategies. This review is an overview of the developments made in the search for glycan-based cancer biomarkers and the technologies currently in use. It is anticipated that the progressing instrumental and bioinformatics developments will allow the identification of relevant glycan biomarkers for the diagnosis, early detection, and monitoring of cancer treatment with sufficient sensitivity and specificity for clinical use.

Sub 2-μm macroporous silica particles derivatized for enhanced lectin affinity enrichment of glycoproteins

A new, mechanically stable silica microparticle with macrosized internal pores (1.6 μm particles with 100 nm pores) has been developed for chromatography. The particles are characterized by an extensive network of interconnected macropores with a high intraparticle void volume, as observed by transmission electron microscopy (TEM). They are synthesized by an aerosol assembly technique called ultrasonic spray pyrolysis (USP). The particles have a high surface area for a macroporous material, ∼200 m(2)/g, making them suitable for large biomolecular separations. To demonstrate their potential for bioseparations, they have been functionalized with lectins for affinity enrichment of glycoproteins. The material was derivatized with two lectins, Concanavalin A (Con A) and Aleuria aurantia lectin (AAL), and binding properties were tested with standard glycoproteins. The columns exhibited excellent binding capacities for microaffinity enrichment: Con A was able to bind 75 μg of a standard glycoprotein in a 50 × 1 mm column. Following initial tests, the lectin microcolumns were utilized for enrichment of glycoproteins from 1 μL volumes of blood serum samples, performed in triplicate for each lectin. The enriched serum fractions were subjected to side-by-side glycomic and glycoproteomic profiling analyses with mass spectrometry to show that the new particles offer excellent sensitivity for microscale analyses of precious biological sample materials. The unique combination of the macroporous architecture and small particle diameter suggests the material may have advantages for conventional modes of chromatographic separation of macromolecules in an ultra-high-pressure liquid chromatography (UHPLC) format.

Nanoscale reversed-phase liquid chromatography-mass spectrometry of permethylated N-glycans

Reversed-phase liquid chromatography on the nanoscale coupled to electrospray tandem mass spectrometry was used to analyse a mixture of four commercial glycan standards, and the method was further adapted to N-glycans enzymatically released from alpha-1-acid glycoprotein and immunoglobulin gamma. Glycans were permethylated to enable their separation by reversed-phase chromatography and to facilitate interpretation of fragmentation data. Prior to derivatization of glycans by permethylation, they were reduced to cancel anomerism because, although feasible, it was not desired to separate α- and β-anomers. The effect of supplementing chromatographic solvent with sodium hydroxide to guide adduct formation was investigated. Raising the temperature in which the separation was performed improved chromatographic resolution and affected retention times as expected. It was shown by using the tetrasaccharides sialyl Lewis X and sialyl Lewis A that reversed-phase chromatography could achieve the separation of methylated isobaric glycan analytes. Isobaric glycans were detected among the N-glycans of immunoglobulin gamma and further analysed by tandem mass spectrometry.

Structural glycomic analyses at high sensitivity: a decade of progress

The field of glycomics has recently advanced in response to the urgent need for structural characterization and quantification of complex carbohydrates in biologically and medically important applications. The recent success of analytical glycobiology at high sensitivity reflects numerous advances in biomolecular mass spectrometry and its instrumentation, capillary and microchip separation techniques, and microchemical manipulations of carbohydrate reactivity. The multimethodological approach appears to be necessary to gain an in-depth understanding of very complex glycomes in different biological systems.

The glycolyzer: automated glycan annotation software for high performance mass spectrometry and its application to ovarian cancer glycan biomarker discovery

Human serum glycomics is a promising method for finding cancer biomarkers but often lacks the tools for streamlined data analysis. The Glycolyzer software incorporates a suite of analytic tools capable of identifying informative glycan peaks out of raw mass spectrometry data. As a demonstration of its utility, the program was used to identify putative biomarkers for epithelial ovarian cancer from a human serum sample set. A randomized, blocked, and blinded experimental design was used on a discovery set consisting of 46 cases and 48 controls. Retrosynthetic glycan libraries were used for data analysis and several significant candidate glycan biomarkers were discovered via hypothesis testing. The significant glycans were attributed to a glycan family based on glycan composition relationships and incorporated into a linear classifier motif test. The motif test was then applied to the discovery set to evaluate the disease state discrimination performance. The test provided strongly predictive results based on receiver operator characteristic curve analysis. The area under the receiver operator characteristic curve was 0.93. Using the Glycolyzer software, we were able to identify a set of glycan biomarkers that highly discriminate between cases and controls, and are ready to be formally validated in subsequent studies.

Profiling and comparative analysis of glycoproteins in Hs578BST and Hs578T and investigation of prolyl 4-hydroxylase alpha polypeptide II expression and influence in breast cancer cells

To identify potential cancer related glycoproteins in breast cancer cells, we enriched N-linked glycoproteins by lentil lectin from the human breast cancer cell line Hs578T and the normal breast cell line Hs578BST for proteomic comparison. Glycoproteins were separated and compared by two-dimensional electrophoresis. Twenty-four glycoproteins were identified that expressed remarkably differently, among which nine were involved in the progress of collagen synthesis. Prolyl 4-hydroxylase alpha polypeptide II (P4HA2) expression and influence in breast cancer was further investigated. Immunohistochemistry revealed that P4HA2 was upregulated in breast tumor cells compared with its adjacent normal tissues. Moreover, overexpression and RNA interference of P4HA2 showed that P4HA2 expression suppressed cell proliferation and migration in Hs578T in vitro.

Improving N-glycan coverage using HPLC-MS with electrospray ionization at subambient pressure

Human serum glycan profiling with mass spectrometry (MS) has been employed to study several disease conditions and is demonstrating promise in, for example, clinical biomarker discovery. However, the low glycan ionization efficiency and the large dynamic range of glycan concentrations in human sera can hinder comprehensive profiling. In particular, large glycans are problematic because they are present at low concentrations and are prone to fragmentation. Here we show that, following liquid chromatographic separation on graphite columns, subambient pressure ionization with nanoelectrospray (SPIN)-MS can expand the serum glycome profile in comparison with the conventional atmospheric pressure electrospray ionization (ESI)-MS with a heated capillary inlet. Notably, the ions generated by the SPIN interface were observed at higher charge states for approximately half of the annotated glycans. Out of a total of 130 detected glycans, 34 were only detected with the SPIN-MS, resulting in improved coverage of glycan families as well as of glycans with larger numbers of labile monosaccharides.

Comparing MALDI-MS, RP-LC-MALDI-MS and RP-LC-ESI-MS glycomic profiles of permethylated N-glycans derived from model glycoproteins and human blood serum

The glycomic profiling of purified glycoproteins and biological specimen is routinely achieved through different analytical methods, but mainly through MS and LC-MS. The enhanced ionization efficiency and improved tandem MS interpretation of permethylated glycans have prompted the popularity of this approach. This study focuses on comparing the glycomic profiling of permethylated N-glycans derived from model glycoproteins and human blood serum using MALDI-MS as well as RP-LC-MALDI-MS and RP-LC-ESI-MS. In the case of model glycoproteins, the glycomic profiles acquired using the three methods were very comparable. However, this was not completely true in the case of glycans derived from blood serum. RP-LC-ESI-MS analysis of reduced and permethylated N-glycans derived from 250 nl of blood serum allowed the confident detection of 73 glycans (the structures of which were confirmed by mass accuracy and tandem MS), while 53 and 43 structures were identified in the case of RP-LC-MALDI-MS and MALDI-MS analyses of the same sample, respectively. RP-LC-ESI-MS analysis facilitates automated and sensitive tandem MS acquisitions. The glycan structures that were detected only in the RP-LC-ESI-MS analysis were glycans existing at low abundances. This is suggesting the higher detection sensitivity of RP-LC-ESI-MS analysis, originating from both reduced competitive ionization and saturation of detectors, facilitated by the chromatographic separation. The latter also permitted the separation of several structural isomers; however, isomeric separations pertaining to linkages were not detected.

Glycoscience aids in biomarker discovery

The glycome consists of all glycans (or carbohydrates) within a biological system, and modulates a wide range of important biological activities, from protein folding to cellular communications. The mining of the glycome for disease markers represents a new paradigm for biomarker discovery; however, this effort is severely complicated by the vast complexity and structural diversity of glycans. This review summarizes recent developments in analytical technology and methodology as applied to the fields of glycomics and glycoproteomics. Mass spectrometric strategies for glycan compositional profiling are described, as are potential refinements which allow structure-specific profiling. Analytical methods that can discern protein glycosylation at a specific site of modification are also discussed in detail. Biomarker discovery applications are shown at each level of analysis, highlighting the key role that glycoscience can play in helping scientists understand disease biology.

Systematic comparison of reverse phase and hydrophilic interaction liquid chromatography platforms for the analysis of N-linked glycans

Due to the hydrophilic nature of glycans, reverse phase chromatography has not been widely used as a glycomic separation technique coupled to mass spectrometry. Other approaches such as hydrophilic interaction chromatography and porous graphitized carbon chromatography are often employed, though these strategies frequently suffer from decreased chromatographic resolution, long equilibration times, indefinite retention, and column bleed. Herein, it is shown that, through an efficient hydrazone formation derivatization of N-linked glycans (~4 h of additional sample preparation time which is carried out in parallel), numerous experimental and practical advantages are gained when analyzing the glycans by online reverse phase chromatography. These benefits include an increased number of glycans detected, increased peak capacity of the separation, and the ability to analyze glycans on the identical liquid chromatography-mass spectrometry platform commonly used for proteomic analyses. The data presented show that separation of derivatized N-linked glycans by reverse phase chromatography significantly out-performs traditional separation of native or derivatized glycans by hydrophilic interaction chromatography. Furthermore, the movement to a more ubiquitous separation technique will afford numerous research groups the opportunity to analyze both proteomic and glycomic samples on the same platform with minimal time and physical change between experiments, increasing the efficiency of "multiomic" biological approaches.

Defining putative glycan cancer biomarkers by MS

For decades, the association between aberrant glycosylation and many types of cancers has been shown. However, defining the changes of glycan structures has not been demonstrated until recently. This has been facilitated by the major advances in MS and separation science, which allows the detailed characterization of glycan changes associated with cancer. MS glycomics methods have been successfully employed to compare the glycomic profiles of different human specimens collected from disease-free individuals and patients with cancer. Additionally, comparing the glycomic profiles of glycoproteins purified from specimen collected from disease-free individuals and patients with cancer has also been performed. These types of glycan analyses employing MS or LC-MS allow the characterization of native, labeled and permethylated glycans. This review discusses the different glycomic and glycoproteomic methods employed for defining glycans as cancer biomarkers of different organs, including breast, colon, esophagus, liver, lung, ovarian, pancreas and prostate.

Uptake and incorporation of sialic acid by the tick Ixodes ricinus

We describe the detection of sialylated N-linked glycans in partially fed Ixodes ricinus tick females using matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. Sialylated glycans were detected in salivary glands as well as in tick guts and we propose the host origin of these structures. In addition, we mapped the transport of sialylated structures from the blood meal through the gut to the salivary glands using electron microscopy. Specific localization of sialylated glycans to basement membranes of salivary glands was observed. Finally, the influence of the sample preparation methods for electron microscopy on ultrastructure and immunogold labeling was evaluated.

Multiple precursor ion scanning of gangliosides and sulfatides with a reversed-phase microfluidic chip and quadrupole time-of-flight mass spectrometry

Precise profiling of polar lipids including gangliosides and sulfatides is a necessary step in understanding the diverse physiological role of these lipids. We have established an efficient method for the profiling of polar lipids using reversed-phase nano high-performance liquid chromatography microfluidic chip quadrupole time-of-flight mass spectrometry (nano-HPLC-chip Q-TOF/MS). A microfluidic chip design provides improved chromatographic performance, efficient separation, and stable nanospray while the advanced high-resolution mass spectrometer allowed for the identification of complex isobaric polar lipids such as NeuAc- and NeuGc-containing gangliosides. Lipid classes were identified based on the characteristic fragmentation product ions generated during data-dependent tandem mass spectrometry (MS/MS) experiments. Each class was monitored by a postprocessing precursor ion scan. Relatively simple quantitation and identification of intact ions was possible due to the reproducible retention times provided by the nano-HPLC chip. The method described in this paper was used to profile polar lipids from mouse brain, which was found to contain 17 gangliosides and 13 sulfatides. Types and linkages of the monosaccharides and their acetyl modifications were identified by low-energy collision-induced dissociation (CID) (40 V), and the type of sphingosine base was identified by higher energy CID (80 V). Accurate mass measurements and chromatography unveiled the degree of unsaturation and hydroxylation in the ceramide lipid tails.