Comparative glycoproteomics of N-linked complex-type glycoforms containing sialic acid in human serum

Precursor carboxy-silica for functionalization with interactive ligands. III. Carbodiimide assisted preparation of immobilized lectin stationary phases for high performance lectin affinity chromatography of sub-glycoproteomics from cancer and disease free human sera

In this study, a precursor carboxy-silica support was demonstrated in the immobilization of two different lectins, namely concanavalin A (Con A) and wheat germ agglutinin (WGA) for use in high performance lectin affinity chromatography (LAC) for the selective capturing and enrichment of glycoproteins from healthy/disease free and cancer human sera. The lectin columns thus obtained (i.e., Con A- and WGA-columns) showed no nonspecific interactions toward some chosen standard glycoproteins and non-glycoproteins. Both columns were shown in sub-glycoproteomics enrichment from human sera including disease free and adenocarcinoma cancer sera. The collected fractions were subjected to LC-MS/MS for identification of the captured glycoproteins, whereby the total number of identified proteins using Con A column from disease-free and cancer sera were 164 and 188, respectively while 133 and 103 proteins were identified in the fractions captured by the WGA column from disease-free and cancer sera samples, respectively. Differentially expressed proteins (DEPs) between the disease free and cancer sera in both the Con A and WGA column fractions were identified via the plot of the abundance vs. the protein ratio whereby the binary logarithm of average intensities of cancer and disease free sera were plotted against the binary logarithm of cancer/disease free sera ratios. The proteins that exhibit log 2 (cancer/healthy) ratio values greater than +2 and less than -2 in both categories are considered as DEPs. Furthermore, for visualization of the data arrangement, Q-Q scatterplot were also used whereby the binary logarithm of cancer serum was plotted against the binary logarithm of disease-free serum for both Con A and WGA. For Con A column, 28 up-regulated and 10 down regulated proteins were identified with a total of 38 DEPs while only two being non-glycoproteins. Furthermore, the up-regulated, and down regulated proteins recorded for WGA column are 14 and 6, respectively, totaling 20 proteins including 3 non-glycoproteins. Some of the non-specific binding to lectin are most likely due to protein-protein interactions.

Protein Glycosylation Investigated by Mass Spectrometry: An Overview

The protein glycosylation is a post-translational modification of crucial importance for its involvement in molecular recognition, protein trafficking, regulation, and inflammation. Indeed, abnormalities in protein glycosylation are correlated with several disease states such as cancer, inflammatory diseases, and congenial disorders. The understanding of cellular mechanisms through the elucidation of glycan composition encourages researchers to find analytical solutions for their detection. Actually, the multiplicity and diversity of glycan structures bond to the proteins, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies make their detection much trickier than other kinds of biopolymers. An overview of the most prominent techniques based on mass spectrometry (MS) for protein glycosylation (glycoproteomics) studies is here presented. The tricks and pre-treatments of samples are discussed as a crucial step prodromal to the MS analysis to improve the glycan ionization efficiency. Therefore, the different instrumental MS mode is also explored for the qualitative and quantitative analysis of glycopeptides and the glycans structural composition, thus contributing to the elucidation of biological mechanisms.

N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping

BACKGROUND

N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. The large-scale characterization of N-linked glycoproteins accomplished by mass spectrometry-based glycoproteomics has provided valuable insights into the interdependence of glycoprotein structure and protein function. However, these studies focused mainly on the analysis of specific sample type, and lack the integration of glycoproteomic data from different tissues, body fluids or cell types.

METHODS

In this study, we collected the human glycosite-containing peptides identified through their de-glycosylated forms by mass spectrometry from over 100 publications and unpublished datasets generated from our laboratory. A database resource termed N-GlycositeAtlas was created and further used for the distribution analyses of glycoproteins among different human cells, tissues and body fluids. Finally, a web interface of N-GlycositeAtlas was created to maximize the utility and value of the database.

RESULTS

The N-GlycositeAtlas database contains more than 30,000 glycosite-containing peptides (representing > 14,000 N-glycosylation sites) from more than 7200 N-glycoproteins from different biological sources including human-derived tissues, body fluids and cell lines from over 100 studies.

CONCLUSIONS

The entire human N-glycoproteome database as well as 22 sub-databases associated with individual tissues or body fluids can be downloaded from the N-GlycositeAtlas website at http://nglycositeatlas.biomarkercenter.org.

Mass spectrometry for protein sialoglycosylation

Sialic acids are a family of structurally unique and negatively charged nine-carbon sugars, normally found at the terminal positions of glycan chains on glycoproteins and glycolipids. The glycosylation of proteins is a universal post-translational modification in eukaryotic species and regulates essential biological functions, in which the most common sialic acid is N-acetyl-neuraminic acid (2-keto-5-acetamido-3,5-dideoxy-D-glycero-D-galactononulopyranos-1-onic acid) (Neu5NAc). Because of the properties of sialic acids under general mass spectrometry (MS) conditions, such as instability, ionization discrimination, and mixed adducts, the use of MS in the analysis of protein sialoglycosylation is still challenging. The present review is focused on the application of MS related methodologies to the study of both N- and O-linked sialoglycans. We reviewed MS-based strategies for characterizing sialylation by analyzing intact glycoproteins, proteolytic digested glycopeptides, and released glycans. The review concludes with future perspectives in the field.

Lectin Microarray Combined with Mass Spectrometry Identifies Haptoglobin-Related Protein (HPR) as a Potential Serologic Biomarker for Separating Nonbacterial Pneumonia from Bacterial Pneumonia in Childhood

PURPOSE

Etiological diagnosis of pediatric patients with community-acquired pneumonia is difficult. For therapy, one of the major problems is the difficulty in separating bacterial pneumonia which would benefit from antibiotics from nonbacterial pneumonia. Therefore, to identify potential biomarkers for distinguishing nonbacterial pneumonia from bacterial pneumonia are sought .

EXPERIMENTAL DESIGN

Lectin microarray containing 91 lectins is used to screen serums from pediatric patients with pneumonia. Lectin-based pull-down assay combined with LC-MS/MS is used to identify the potential biomarkers.

RESULTS

SNA-I, a lectin binding preferentially to α2-6 linked sialic acid residues, shows higher binding signals (near 42 kDa) in the mycoplasma pneumonia group, when compared with the other groups. A total of 18 proteins are identified with LC-MS/MS. By western blot analysis, the authors confirm that the expression of haptoglobin-related protein (HPR) is elevated in pediatric patients with pneumonia compared with normal children (p < 0.001). Furthermore, HPR is higher in the mycoplasma pneumonia group (p < 0.01) and the viral pneumonia group (p < 0.05), when compared with the bacterial pneumonia group.

CONCLUSIONS AND CLINICAL RELEVANCE

These results indicate that HPR is a potential serologic biomarker which can differentiate between bacterial pneumonia and nonbacterial pneumonia. Detection of serum HPR might be useful for clinical diagnosis.

Site-Specific Profiling of Serum Glycoproteins Using N-Linked Glycan and Glycosite Analysis Revealing Atypical N-Glycosylation Sites on Albumin and α-1B-Glycoprotein

Most serum proteins are N-linked glycosylated, and therefore the glycoproteomic profiling of serum is essential for characterization of serum proteins. In this study, we profiled serum N-glycoproteome by our recently developed N-glycoproteomic method using solid-phase extraction of N-linked glycans and glycosite-containing peptides (NGAG) coupled with LC-MS/MS and site-specific glycosylation analysis using GPQuest software. Our data indicated that half of identified N-glycosites were modified by at least two glycans, with a majority of them being sialylated. Specifically, 3/4 of glycosites were modified by biantennary N-glycans and 1/3 of glycosites were modified by triantennary sialylated N-glycans. In addition, two novel atypical glycosites (with N-X-V motif) were identified and validated from albumin and α-1B-glycoprotein. The widespread presence of these two glycosites among individuals was further confirmed by individual serum analyses.

High performance affinity chromatography and related separation methods for the analysis of biological and pharmaceutical agents

The last few decades have witnessed the development of many high-performance separation methods that use biologically related binding agents. The combination of HPLC with these binding agents results in a technique known as high performance affinity chromatography (HPAC). This review will discuss the general principles of HPAC and related techniques, with an emphasis on their use for the analysis of biological compounds and pharmaceutical agents. Various types of binding agents for these methods will be considered, including antibodies, immunoglobulin-binding proteins, aptamers, enzymes, lectins, transport proteins, lipids, and carbohydrates. Formats that will be discussed for these methods range from the direct detection of an analyte to indirect detection based on chromatographic immunoassays, as well as schemes based on analyte extraction or depletion, post-column detection, and multi-column systems. The use of biological agents in HPLC for chiral separations will also be considered, along with the use of HPAC as a tool to screen or study biological interactions. Various examples will be presented to illustrate these approaches and their applications in fields such as biochemistry, clinical chemistry, and pharmaceutical research.

Solid-Phase Chemical Modification for Sialic Acid Linkage Analysis: Application to Glycoproteins of Host Cells Used in Influenza Virus Propagation

Differentiation between the sialyl linkages is often critical to understanding biological consequence. Here we present a facile method for determining these linkages in glycans. Analysis of sialic acids is challenging due to their labile nature during sample preparation and ionization. Derivatization is often required via chemical reaction. Amidation derivatizes all sialic acids regardless of linkage, while esterification enables differentiation between α2,3-linked and α2,6-linked sialic acids. Reactions have been primarily performed on free glycans in solution but have been recently adapted to solid-phase providing unique advantages such as simplified sample preparation, improved yield, and high throughput applications. Here, we immobilized glycoproteins on resin via reductive amination, modified α2,6-linked sialic acids through ethyl esterification, and α2,3-linked sialic acids via amidation. N-glycans and O-glycans were released via enzyme and chemical reactions. The method was applied for analysis of three different MDCK cell lines used for influenza propagation and where distributions of α2,3 and α2,6 sialic acids are critical for cell performance. Linkage specific distribution of these sialic acids was quantitatively determined and unique for each cell line. Our study demonstrates that protein sialylation can be reliably and quantitatively characterized in terms of sialic acid linkage of each glycan using the solid-phase esterification/amidation strategy.

Role of lectin microarrays in cancer diagnosis

The majority of cell differentiation associated tumor markers reported to date are either glycoproteins or glycolipids. Despite there being a large number of glycoproteins reported as candidate markers for various cancers, only a handful are approved by the US Food and Drug Administration. Lectins, which bind to the glycan part of the glycoproteins, can be exploited to identify aberrant glycosylation patterns, which in turn would help in enhancing the specificity of cancer diagnosis. Although conventional techniques such as HPLC and MS have been instrumental in performing the glycomic analyses, these techniques lack multiplexity. Lectin microarrays have proved to be useful in studying multiple lectin-glycan interactions in a single experiment and, with the advances made in the field, hold a promise of enabling glycomic profiling of cancers in a fast and efficient manner.

A rapid and simple approach for glycoform analysis

Fast glycoform analysis is important for quality control of glycoproteins that account for over 40% of the approved biopharmaceuticals. Herein, we realized an Au nanoparticle-based lectin affinity chromatography (LAC) using simple standard laboratory equipment for fast glycoform analysis. Pisum sativum agglutinin (PA), a lectin derived from P. sativum, was covalently conjugated to Au nanoparticles via naturally formed carboxylic groups onto the surface of Au nanoparticles and amino groups of PA. Each model glycoprotein was separated into several fractions including the unbound, weakly bound, modestly bound, and strongly bound glycoforms based on affinity strength of the glycoform toward PA. A single run of Au nanoparticle-based LAC was finished within 18 min, which could be further decreased by centrifuging the mixture of the PA functionalized Au nanoparticles and the glycoproteins at a higher speed. To our knowledge, we are the first to use Au nanoparticles as LAC matrix.

Mutations of rat surfactant protein A have distinct effects on its glycosylation, secretion, aggregation and degradation

AIMS

Surfactant protein A (SP-A) plays critical roles in the innate immune system and surfactant homeostasis of the lung. Mutations in SP-A2 of the carbohydrate recognition domain (CRD) impair its glycosylation and are associated with pulmonary fibrosis in humans. We aim to examine how mutations in SP-A that impair its glycosylation affect its biological properties and lead to disease.

MAIN METHODS

We generated rat SP-A constructs with two types of mutations that impair its glycosylation: N-glycosylation site mutations (N21T, N207S and N21T/N207S) and disease-associated CRD mutations (G231V, F198S). We transfected these constructs into Chinese hamster ovary (CHO)-K1 cells and assessed biochemical differences in cellular and secreted wild-type and mutant SP-As by western blot, immunofluorescence, and sensitivity to enzymatic digestion.

KEY FINDINGS

Mutations of the CRD completely impaired SP-A secretion, whereas mutations of N-glycosylation sites had little effect. Both types of mutations formed nonidet p-40 (NP-40) insoluble aggregates, but the aggregates only from CRD mutations could be partially rescued by a chemical chaperone, 4-phenylbutyrate acid (4-PBA). The majority of CRD mutant SP-A was retained in the endoplasmic reticulum. Moreover, both types of mutations reduced SP-A stability, with CRD mutant SP-A being more sensitive to chymotrypsin digestion. Both types of soluble mutant SP-A could be degraded by the proteasome pathway, while insoluble aggregates could be additionally degraded by the lysosomal pathway.

SIGNIFICANCE

Our data provide evidence that the differential glycosylation of SP-A may play distinct roles in SP-A secretion, aggregation and degradation which may contribute to familial pulmonary fibrosis caused by SP-A2 mutations.

Targeting human serum fucome by an integrated liquid-phase multicolumn platform operating in "cascade" to facilitate comparative mass spectrometric analysis of disease-free and breast cancer sera

A fully integrated platform was developed for capturing/fractionating human fucome from disease-free and breast cancer sera. It comprised a multicolumn operated by HPLC pumps and switching valves for the simultaneous depletion of high abundance proteins via affinity-based subtraction and the capturing of fucosylated glycoproteins via lectin affinity chromatography followed by the fractionation of the captured glycoproteins by reversed phase chromatography (RPC). Two lectin columns specific to fucose, namely Aleuria aurantia lectin (AAL) and Lotus tetragonolobus agglutinin (LTA) were utilized. The platform allowed the "cascading" of the serum sample from column-to-column in the liquid phase with no sample manipulation between the various steps. This guaranteed no sample loss and no propagation of experimental biases between the various columns. Finally, the fucome was fractionated by RPC yielding desalted fractions in volatile acetonitrile-rich mobile phase, which after vacuum evaporation were subjected to trypsinolysis for LC-MS/MS analysis. This permitted the identification of the differentially expressed proteins (DEP) in breast cancer serum yielding a broad panel of 35 DEP from the combined LTA and AAL captured proteins and a narrower panel of eight DEP that were commonly differentially expressed in both LTA and AAL fractions, which are considered as more representative of cancer altered fucome.

Glycopeptide analysis, recent developments and applications

Glycopeptide-based analysis is used to inform researchers about the glycans on one or more proteins. The method's key attractive feature is its ability to link glycosylation information to exact locations (glycosylation sites) on proteins. Numerous applications for glycopeptide analysis are known, and several examples are described herein. The techniques used to characterize glycopeptides are still emerging, and recently, research focused on facilitating aspects of glycopeptide analysis has advanced significantly in the areas of sample preparation, MS fragmentation, and automation of data analysis. These recent developments, described herein, provide the foundation for the growth of glycopeptide analysis as a blossoming field.

Mass Spectrometry Investigation of Glycosylation Aberration via De-N-Glycopeptide Analysis

Proteomics research on glycan alterations has received great attention owing to their implications in disease initiation and progression. Determination of the glycoprotein expression remains one of the most challenging tasks as the glycan residues in a given glycoprotein exist in complex branched structures and differ in linkage. In view of the vital role of glycan changes in cellular processes and disease progression, there has been an increased interest in developing methodologies for the detection of these changes. A subset of proteomics methods are discussed here that demonstrate the utility of the glycan-free de-N-glycopeptide analysis for the screening of complex glycoproteome as well as discovery of glycopeptide/glycoprotein biomarkers.

Large-scale quantitative glycoproteomics analysis of site-specific glycosylation occupancy

Disease-associated aberrant glycosylation may be protein specific and glycosylation site specific. Quantitative assessment of glycosylation changes at a site-specific molecular level may represent one of the initial steps for systematically revealing the glycosylation abnormalities associated with a disease or biological state. Comparative quantitative profiling of glycoproteome to provide accurate quantification of site-specific glycosylation occupancy has been a challenging task, requiring a concerted approach drawing from a variety of techniques. In this report, we present a quantitative glycoproteomics method that allows global scale identification and comparative quantification of glycosylation site occupancy using mass spectrometry. We further demonstrated this approach by quantitatively characterizing the N-glycoproteome of human pancreas.

Glycoproteomics enabled by tagging sialic acid- or galactose-terminated glycans

In this paper, we present two complementary strategies for enrichment of glycoproteins on living cells that combine the desirable attributes of "robust enrichment" afforded by covalent-labeling techniques and "specificity for glycoproteins" typically provided by lectin or antibody affinity reagents. Our strategy involves the selective introduction of aldehydes either into sialic acids by periodate oxidation (periodate oxidation and aniline-catalyzed oxime ligation (PAL)) or into terminal galactose and N-acetylgalactosamine residues by galactose oxidase (galactose oxidase and aniline-catalyzed oxime ligation (GAL)), followed by aniline-catalyzed oxime ligation with aminooxy-biotin to biotinylate the glycans of glycoprotein subpopulations with high efficiency and cell viability. As expected, the two methods exhibit reciprocal tagging efficiencies when applied to fully sialylated cells compared with sialic acid-deficient cells. To assess the utility of these labeling methods for glycoproteomics, we enriched the PAL- and GAL-labeled (biotinylated) glycoproteome by adsorption onto immobilized streptavidin. Glycoprotein identities (IDs) and N-glycosylation site information were then obtained by liquid chromatography-tandem mass spectrometry on total tryptic peptides and on peptides subsequently released from N-glycans still bound to the beads using peptide N-glycosidase F. A total of 175 unique N-glycosylation sites were identified, belonging to 108 nonredundant glycoproteins. Of the 108 glycoproteins, 48 were identified by both methods of labeling and the remainder was identified using PAL on sialylated cells (40) or GAL on sialic acid-deficient cells (20). Our results demonstrate that PAL and GAL can be employed as complementary methods of chemical tagging for targeted proteomics of glycoprotein subpopulations and identification of glycosylation sites of proteins on cells with an altered sialylation status.

Cancer proteomics

Cancer presents high mortality and morbidity globally, largely due to its complex and heterogenous nature, and lack of biomarkers for early diagnosis. A proteomics study of cancer aims to identify and characterize functional proteins that drive the transformation of malignancy, and to discover biomarkers to detect early-stage cancer, predict prognosis, determine therapy efficacy, identify novel drug targets, and ultimately develop personalized medicine. The various sources of human samples such as cell lines, tissues, and plasma/serum are probed by a plethora of proteomics tools to discover novel biomarkers and elucidate mechanisms of tumorigenesis. Innovative proteomics technologies and strategies have been designed for protein identification, quantitation, fractionation, and enrichment to delve deeper into the oncoproteome. In addition, there is the need for high-throughput methods for biomarker validation, and integration of the various platforms of oncoproteome data to fully comprehend cancer biology.

Identification and accurate quantitation of biological oligosaccharide mixtures

Structure-specific characterization and quantitation is often required for effective functional studies of oligosaccharides. Inside the gut, HMOs are preferentially bound and catabolized by the beneficial bacteria. HMO utility by these bacteria employs structure-specific catabolism based on a number of glycosidases. Determining the activity of these enzymes requires accurate quantitation of a large number of structures. In this study, we describe a method for the quantitation of human milk oligosaccharide (HMO) structures employing LC/MS and isotopically labeled internal standards. Data analysis was accomplished with a newly developed software tool, LC/MS Searcher, that employs a reference structure library to process LC/MS data yielding structural identification with accurate quantitation. The method was used to obtain a meta-enzyme analysis of bacteria, the simultaneous characterization of all glycosidases employed by bacteria for the catabolism of milk oligosaccharides. Analysis of consumed HMO structures confirmed the utility of a β-1,3-galactosidase in Bifidobacterium longum subsp. infantis ATCC 15697 (B. infantis). In comparison, Bifidobacterium breve ATCC 15700 showed significantly less HMO catabolic activity compared to B. infantis.

Investigation of ovarian cancer associated sialylation changes in N-linked glycopeptides by quantitative proteomics

Background

In approximately 80% of patients, ovarian cancer is diagnosed when the patient is already in the advanced stages of the disease. CA125 is currently used as the marker for ovarian cancer; however, it lacks specificity and sensitivity for detecting early stage disease. There is a critical unmet need for sensitive and specific routine screening tests for early diagnosis that can reduce ovarian cancer lethality by reliably detecting the disease at its earliest and treatable stages.

Results

In this study, we investigated the N-linked sialylated glycopeptides in serum samples from healthy and ovarian cancer patients using Lectin-directed Tandem Labeling (LTL) and iTRAQ quantitative proteomics methods. We identified 45 N-linked sialylated glycopeptides containing 46 glycosylation sites. Among those, ten sialylated glycopeptides were significantly up-regulated in ovarian cancer patients’ serum samples. LC-MS/MS analysis of the non-glycosylated peptides from the same samples, western blot data using lectin enriched glycoproteins of various ovarian cancer type samples, and PNGase F (+/−) treatment confirmed the sialylation changes in the ovarian cancer samples.

Conclusion

Herein, we demonstrated that several proteins are aberrantly sialylated in N-linked glycopeptides in ovarian cancer and detection of glycopeptides with abnormal sialylation changes may have the potential to serve as biomarkers for ovarian cancer.

Recent progress in quantitative glycoproteomics

Protein glycosylation is acknowledged as one of the major posttranslational modifications that elicit significant effects on protein folding, conformation, distribution, stability, and activity. The changes in glycoprotein abundance, glycosylation degree, and glycan structure are associated with a variety of diseases. Therefore, the quantitative study of glycoproteomics has become a new and popular research topic, and is quickly emerging as an important technique for biomarker discovery. Mass spectrometry-based protein quantification technologies provide a powerful tool for the systematic and quantitative assessment of the quantitative differences in the protein profiles of different samples. Combined with various glycoprotein/glycopeptide enrichment strategies and other glycoprotein analysis methods, these techniques have been further developed for application in quantitative glycoproteomics. A comprehensive quantitative analysis of the glycoproteome in a complex biological sample remains challenging because of the enormous complexity of biological samples, intrinsic characteristics of glycoproteins, and lack of universal quantitative technology. In this review, recently developed technologies in quantitative glycoproteome, especially those focused on two of the most common types of glycosylation (N-linked and O-linked glycoproteome), were summarized. The strengths and weaknesses of the various approaches were also discussed.

Equal ratio of graphite carbon to activated charcoal for enrichment of N-glycopeptides prior to matrix-assisted laser desorption/ionization time-of-flight mass spectrometric identification

Site-specific glycoprofiling of N-glycoproteins is based on the enrichment of glycopeptides. In this study, we develop a simple and economical ZipTip microcolumn packed with a 1:1 ratio of graphite carbon to activated charcoal (w/w) (termed as GA-ZipTip microcolumn) to efficiently isolate and enrich N-glycopeptides from digested mixtures of individual glycoproteins and also investigate the ratio effect on the isolation and enrichment of glycopeptides. The experimental data showed that the microcolumn could efficiently and reproducibly isolate N-glycopeptides from enzymatic mixtures of ovalbumin, fetuin, haptoglobin and human plasma. The results obtained here demonstrate that the GA-ZipTip microcolumn is a powerful tool to enrich unbiasedly N-glycopeptides, which will be benefit for glycoproteomics and complex biological samples.

Technologies and strategies for glycoproteomics and glycomics and their application to clinical biomarker research

Several approaches and technologies are currently available to study the glycosylated proteome (glycoproteomics) or the entire repertoire of glycans in a biological system (glycomics). The biological importance of glycosylation has driven the development of novel, sensitive separation and detection methods. New and improved methodologies, such as high throughput array systems and liquid chromatography-mass spectrometry for glycan profiling and sequencing, are emerging and are being applied in clinical research. A major thrust of glycoproteomics and glycomic clinical research is the application of these analytical tools to cancer research and is aimed at the discovery of glycan-based biomarkers for diagnosis of early stage human cancers, monitoring disease progression, measuring response to therapy, and detecting recurrence. The identification of cancer biomarkers requires a multidisciplinary approach and therefore this review discusses the strategies, technologies and methods currently used for N-glycoprotein/glycanbiomarker research.

Investigation of sialylation aberration in N-linked glycopeptides by lectin and tandem labeling (LTL) quantitative proteomics

The accuracy in quantitative analysis of N-linked glycopeptides and glycosylation site mapping in cancer is critical to the fundamental question of whether the aberration is due to changes in the total concentration of glycoproteins or variations in the type of glycosylation of proteins. Toward this goal, we developed a lectin-directed tandem labeling (LTL) quantitative proteomics strategy in which we enriched sialylated glycopeptides by SNA, labeled them at the N-terminus by acetic anhydride ((1)H(6)/(2)D(6)) reagents, enzymatically deglycosylated the differentially labeled peptides in the presence of heavy water (H(2)(18)O), and performed LC/MS/MS analysis to identify glycopeptides. We successfully used fetuin as a model protein to test the feasibility of this LTL strategy not only to find true positive glycosylation sites but also to obtain accurate quantitative results on the glycosylation changes. Further, we implemented this method to investigate the sialylation changes in prostate cancer serum samples as compared to healthy controls. Herein, we report a total of 45 sialylated glycopeptides and an increase of sialylation in most of the glycoproteins identified in prostate cancer serum samples. Further quantitation of nonglycosylated peptides revealed that sialylation is increased in most of the glycoproteins, whereas the protein concentrations remain unchanged. Thus, LTL quantitative technique is potentially an useful method for obtaining simultaneous unambiguous identification and reliable quantification of N-linked glycopeptides.

Mass spectrometry based glycoproteomics--from a proteomics perspective

Glycosylation is one of the most important and common forms of protein post-translational modification that is involved in many physiological functions and biological pathways. Altered glycosylation has been associated with a variety of diseases, including cancer, inflammatory and degenerative diseases. Glycoproteins are becoming important targets for the development of biomarkers for disease diagnosis, prognosis, and therapeutic response to drugs. The emerging technology of glycoproteomics, which focuses on glycoproteome analysis, is increasingly becoming an important tool for biomarker discovery. An in-depth, comprehensive identification of aberrant glycoproteins, and further, quantitative detection of specific glycosylation abnormalities in a complex environment require a concerted approach drawing from a variety of techniques. This report provides an overview of the recent advances in mass spectrometry based glycoproteomic methods and technology, in the context of biomarker discovery and clinical application.

Mass spectrometry and glycomics

Glycosylation defines the adhesive properties of animal cell surfaces and the surrounding extracellular environments. Because cells respond to stimuli by altering glycan expression, glycan structures vary according to spatial location in tissue and temporal factors. These dynamic structural expression patterns, combined with the essential roles glycans play in physiology, drive the need for analytical methods for glycoconjugates. In addition, recombinant glycoprotein drug products represent a multibillion dollar market. Effective analytical methods are needed to speed the identification of new targets and the development of industrial glycoprotein products, both new and biosimilar. Mass spectrometry is an enabling technology in glycomics. This review summarizes mass spectrometry of glycoconjugate glycans. The intent is to summarize appropriate methods for glycans given their chemical properties as distinct from those of proteins, lipids, and small molecule metabolites. Special attention is given to the uses of mass spectral profiling for glycomics with respect to the N-linked, O-linked, ganglioside, and glycosaminoglycan compound classes. Next, the uses of tandem mass spectrometry of glycans are summarized. The review finishes with an update on mass spectral glycoproteomics.

Multi-dimensional liquid chromatography in proteomics--a review

Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. This still-emerging combination of technologies aims to describe and characterize all expressed proteins in a biological system. Because of upper limits on mass detection of mass spectrometers, proteins are usually digested into peptides and the peptides are then separated, identified and quantified from this complex enzymatic digest. The problem in digesting proteins first and then analyzing the peptide cleavage fragments by mass spectrometry is that huge numbers of peptides are generated that overwhelm direct mass spectral analyses. The objective in the liquid chromatography approach to proteomics is to fractionate peptide mixtures to enable and maximize identification and quantification of the component peptides by mass spectrometry. This review will focus on existing multidimensional liquid chromatographic (MDLC) platforms developed for proteomics and their application in combination with other techniques such as stable isotope labeling. We also provide some perspectives on likely future developments.

Automated platform for fractionation of human plasma glycoproteome in clinical proteomics

This publication describes the development of an automated platform for the study of the plasma glycoproteome. The method consists of targeted depletion in-line with glycoprotein fractionation. A key element of this platform is the enabling of high throughput sample processing in a manner that minimizes analytical bias in a clinical sample set. The system, named High Performance Multi-Lectin Affinity Chromatography (HP-MLAC), is composed of a serial configuration of depletion columns containing anti-albumin antibody and protein A with in-line multilectin affinity chromatography (M-LAC) which consists of three mixtures of lectins concanavalin A (ConA), jacalin (JAC), and wheat germ agglutinin (WGA). We have demonstrated that this platform gives high recoveries for the fractionation of the plasma proteome (> or = 95%) and excellent stability (over 200 runs). In addition, glycoproteomes isolated using the HP-MLAC platform were shown to be highly reproducible and glycan specific as demonstrated by rechromatography of selected fractions and proteomic analysis of the unbound (glycoproteome 1) and bound (glycoproteome 2) fractions.