Fast saccharide mapping method for quality consistency evaluation of commercial xylooligosaccharides collected in China

Due to the extensive use of xylooligosaccharides (XOS) as functional food ingredients, many inferior goods and even adulterants are generally found in the market, which may pose a health hazard to certain populations. Chromatography method such as high-performance liquid chromatography (HPLC) and high-performance thin-layer chromatography (HPTLC) is traditionally applied for the quality analysis of XOS. However, it is time consuming due to the prolonged separation and pre- or post- derivatization procedure. In this study, a fast saccharide mapping method based on matrix-assisted laser desorption/time-of-flight mass spectrometry (MALDI-TOF-MS) was developed for the quality consistency analysis of 22 batches of XOS collected from different manufacturers in China. The time needed for saccharides analysis using MALDI-MS was less than 30 min for one plate, at least 6 times faster than that by the traditional HPTLC chromatography method. In addition, MALDI-MS possessed higher resolution for XOS with DP4-DP7 based on the difference of m/z, which is hardly separated using HPTLC. The results showed that XOS were present only in samples XY01-XY11, samples XY12-XY14 only consisted of hex oligosaccharides, and samples XY15-XY22 were free of oligosaccharides. These indicate that the quality consistency of XOS products in the China market was poor, which should be carefully investigated.

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Fast saccharide mapping method was developed based on MADLI-TOF-MS.

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Quality consistency of commercial xylooligosaccharides collected in China was evaluated.

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Glycosidic linkage analysis was also used for identification of xylooligosaccharides.

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Fifty percent of commercial xylooligosaccharides are mislabeled.

Antigen Retrieval and Its Effect on the MALDI-MSI of Lipids in Formalin-Fixed Paraffin-Embedded Tissue

Formalin-fixed paraffin-embedded (FFPE) tissue represents the primary source of clinical tissue and is routinely used in MALDI-MSI studies. However, it is not particularly suitable for lipidomics imaging given that many species are depleted during tissue processing. Irrespective, a number of solvent-resistant lipids remain, but their extraction may be hindered by the cross-link between proteins. Therefore, an antigen retrieval step could enable the extraction of a greater number of lipids and may provide information that is complementary to that which can be obtained from other biomolecules, such as proteins. In this short communication, we aim to address the effect of performing antigen retrieval prior to MALDI-MSI of lipids in FFPE tissue. As a result, an increased number of lipid signals could be detected and may have derived from lipid species that are known to be implicated in the lipid-protein cross-linking that is formed as a result of formalin fixation. Human renal cancer tissue was used as a proof of concept to determine whether using these detected lipid signals were also able to highlight the histopathological regions that were present. These preliminary findings may highlight the potential to enhance the clinical relevance of the lipidomic information obtained from FFPE tissue.

Mass Spectrometric (MS) Analysis of Proteins and Peptides

The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.

A Clean and Tunable Mussel-Inspired Coating Technology by Enzymatic Deposition of Pseudo-Polydopamine (ψ-PDA) Thin Films from Tyramine

The tyrosinase-catalyzed oxidation of tyramine, leading to the deposition of pseudo-polydopamine (ψ-PDA) thin films, is disclosed herein as a superior technology for surface functionalization and coating at a neutral pH and at a low substrate concentration, compared to the standard autoxidative PDA coating protocols. Smooth ψ-PDA thin films of variable thickness up to 87 nm were obtained from 1 mM tyramine by varying tyrosinase concentrations (5-100 U/mL). Compared to the PDA films obtained by the similar enzymatic oxidation of 1 mM dopamine with tyrosinase (T-PDA), ψ-PDA displayed slower deposition kinetics, lower water contact angles in the range of 11°-28°, denoting higher hydrophilicity but similar UV-vis absorption profiles, as well as electrochemical properties and antioxidant activity. MALDI-MS analysis indicated for ψ-PDA a well defined pattern of peaks compatible with dopamine tetrameric structures degraded to a variable extent. The exposure to a tyramine solution of tyrosinase-loaded alginate spheres, or films deposited on glass or polyethylene, resulted in a rapid gel-confined ψ-PDA formation with no leakage or darkening of the solution, allowing the complete recovery and re-utilization of the unreacted tyramine. In contrast, an abundant PDA precipitation outside the gel was observed with dopamine under the same conditions. The ψ-PDA deposition by tyrosinase-catalyzed tyramine oxidation is thus proposed as a controllable and low-waste technology for selective surface functionalization and coating or for clean eumelanin particle production.

Peptide profile and angiotensin-converting enzyme inhibitory activity of Prato cheese with salt reduction and Lactobacillus helveticus as an adjunct culture

Among strategies to improve the health-related aspects of dairy products, great prominence has been given to salt reduction and the use of adjunct cultures that can favor the release of bioactive peptides during cheese ripening. This study aimed to evaluate the effect of the salt reduction, the addition of Lactobacillus helveticus LH-B02 and the ripening time of Prato cheese on the casein hydrolysis profile by capillary electrophoresis, peptide profile by mass spectrometry, and antihypertensive potential evaluated in vitro through the inhibitory activity of the angiotensin-converting enzyme (ACE). Both the salt reduction and the addition of adjunct culture favored the accumulation of the bioactive peptide β-CN (f193-209) (m/z 1881). The adjunct culture led to a higher ACE inhibitory activity during the ripening of Prato cheese, thus proving to be an effective strategy for the development of potentially bioactive cheese.

Eliminating sweet spot in MALDI-MS with hydrophobic ordered structure as target for quantifying biomolecules

In matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), the analyte is usually distributed unevenly throughout the sample spot. The area with aggregated analyte molecules contributing abundant signal, is termed as "sweet spot", which results in poor detection reproducibility and makes it impossible to quantify analytes without internal standards. We proposed a strategy to eliminate sweet spot in MALDI-MS by using a hydrophobic ordered structure as target. The target is fabricated by creating a hydrophobic silicon nanopillar array and subsequently decorating it uniformly with poly(methyl methacrylate) nanodots for capturing analytes. The sweet spot is eliminated by distributing analyte molecules uniformly on this target, and then result in a uniform MS image, which demonstrates an ideal reproducibility. Finally, with the target assisted MALDI-MS as biosensor was suitable to analyze practical sample such as bacitracin A in milk. Horse heart myoglobin and, angiotensin III molecules can be quantified without internal standard using α-cyano-4-hydroxycinnamic acid as matrix. This biosensor presented good linearity, high salts tolerance and high signal-to-noise ratio (up to 271.8), even the 1 mol/L salt concentration. This strategy could provide an alternative for improving the performance of MALDI-MS.

Influence of media composition on recombinant monoclonal IgA1 glycosylation analysed by lectin-based protein microarray and MALDI-MS

Glycosylation of therapeutic glycoproteins significantly affects their physico-chemical properties, bioactivity and immunogenicity. The determination of glycan composition is highly important regarding their development and production. Therefore, there is a demand for analytical techniques enabling rapid and reliable glycoprofiling of therapeutic proteins. For the investigation of changes in glycan structures, we have employed two platforms: lectin-based protein microarray, and MALDI-MS. In lectin-based microarray analysis, the samples of IgA were printed on the microarray slide, incubated with the set of lectins with various specificity and evaluation of changes in glycosylation was based on differences in reactivity of samples with lectins. MALDI-MS was used for N-glycan analysis of IgA1 samples. IgAs are effective as therapeutic agents in defense against viruses that use sialic acid as a receptor. Dimeric IgA1 antibodies were produced by stable cell line IgA1/2G9 on the basal medium at different conditions (different supplementation and feeding) and we also evaluated the effect of different conditions on lactate production, which correlates with IgA productivity. Decrease of lactate levels was observed during supplementation with succinic acid, asparagine, or with mannose feeding. We found by lectin-based microarray analysis that the metabolic shift from glutamine to asparagine or feeding with glucose caused increase of high mannose type glycans what was confirmed also by MALDI-MS. Among other changes in IgA glycosylation determined by lectin-based protein microarray were, for example, reduced galactosylation after supplementation with succinic acid and increase of both sialylation and galactosylation after supplementation with glutamine and feeding with mannose. The elucidation of mechanism of determined changes requires further investigation, but the described analytical approach represent effective platform for determination, screening and evaluation of glycosylation of therapeutic proteins.

A Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Assay for the Relative Quantitation of Antennary Fucosylated N-Glycans in Human Plasma

Changes in the abundance of antennary fucosylated glycans in human total plasma N-glycome (TPNG) have been associated with several diseases ranging from diabetes to various forms of cancer. However, it is challenging to address this important part of the human glycome. Most commonly, time-consuming chromatographic separations are performed to differentially quantify core and antenna fucosylation. Obtaining sufficient resolution for larger, more complex glycans can be challenging. We introduce a matrix-assisted laser desorption/ionization—mass spectrometry (MALDI-MS) assay for the relative quantitation of antennary fucosylation in TPNG. N-linked glycans are released from plasma by PNGase F and further treated with a core fucosidase before performing a linkage-informative sialic acid derivatization. The core fucosylated glycans are thus depleted while the remaining antennary fucosylated glycans are quantitated. Simultaneous quantitation of α2,3-linked sialic acids and antennary fucosylation allows an estimation of the sialyl-Lewis x motif. The approach is feasible using either ultrahigh-resolution Fourier-transform ion cyclotron resonance mass spectrometry or time-of-flight mass spectrometry. The assay was used to investigate changes of antennary fucosylation as clinically relevant marker in 14 colorectal cancer patients. In accordance with a previous report, we found elevated levels of antennary fucosylation pre-surgery which decreased after tumor resection. The assay has the potential for revealing antennary fucosylation signatures in various conditions including diabetes and different types of cancer.

Metabolomic approach for rapid differentiation of Fritillaria bulbs by matrix-assisted laser desorption/ionization mass spectrometry and multivariate statistical analysis

The bulbs of Fritillaria have been used for centuries as food and medicinal products in many Asian countries. Different Fritillaria species have distinct pharmacological effects despite of their similar appearances. Effective differentiation of Fritillaria species can avoid adulteration and is crucial to its clinical uses. In this paper, a hybrid method of matrix assisted laser desorption/ionization mass spectrometry and multivariate statistical analysis was developed for the rapid and reliable differentiation of Fritillaria species for the first time. Significantly different patterns for five Fritillaria species were obtained by MALDI-MS after instant sample extractions. Different groups of Fritillaria were confidently differentiated via an orthogonal partial least square model. In addition, a metabolomic taxonomy of five Fritillaria species was obtained based on MALDI-MS data.

Candida auris infection in the central catheter of a patient without sepsis symptoms

Background

Candida auris is an emerging yeast frequently reported as resistant to multiple antifungal drugs commonly used to treat Candida infections. This specie can colonize the patient's skin and has great ability for producing outbreaks in hospitals. C. auris is phylogenetically related to other Candida species, can be misidentified using conventional biochemical or commercial methods and requires specific technology for its identification.

Case report

We report the first isolate of C. auris in Cali, Colombia, from a central venous catheter in a 37-year-old patient with rheumatoid arthritis and endocarditis who did not have symptoms of sepsis. The yeast was initially misidentified as C. haemulonii using the Phoenix system and subsequently identified as C. auris by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS). The broth microdilution method was used to determine the minimum inhibitory concentration; the isolate was susceptible to fluconazole, itraconazole, voriconazole and amphotericin B.

Conclusions

This report contributes to knowledge of the epidemiology of C. auris infections in individuals with underlying disease and describes an isolate with a behavior different from what is usually reported.

Integrated UPLC-Q/TOF-MS Technique and MALDI-MS to Study of the Efficacy of YiXinshu Capsules Against Heart Failure in a Rat Model

Background: Yixinshu Capsules (YXSC) are widely used in Chinese medicine for the treatment of cardiovascular diseases. However, the therapeutic mechanisms of action are not well understood.

Method: In this study, a metabonomic approach based on integrated UPLC-Q/TOF-MS technique and MALDI-MS was utilized to explore potential metabolic biomarkers that may help increase the understanding of heart failure (HF) and in order to assess the potential mechanisms of YXSC against HF. Plasma metabolic profiles were analyzed by UPLC-Q/TOF-MS with complementary hydrophilic interaction chromatography and reversed-phase liquid chromatography. Moreover, time-course analysis at the 2nd, 4th, and 10th week after permanent occlusion was conducted. In an effort to identify a more reliable potential metabolic marker, common metabolic markers of the 2nd, 4th, and 10th week were selected through multivariate data analysis. Furthermore, MALDI-MS was applied to identify metabolic biomarkers in the blood at apoptotic positions of heart tissues.

Results: The results showed that HF appeared at the fourth week after permanent occlusion based on echocardiographic assessment. Clear separations were observed between the sham and model group by loading plots of orthogonal projection to latent structure discrimination analysis (OPLS-DA) at different time points after permanent occlusion. Potential markers of interest were extracted from the combining S-plots, variable importance for the projections values (VIP > 1), and t-test (p < 0.05). Twenty-one common metabolic markers over the course of the development and progression of HF after permanent occlusion were identified. These were determined to be mainly related to disturbances in fatty acids, phosphatidylcholine, bile acids, amino acid metabolism, and pyruvate metabolism. Of the metabolic markers, 16 metabolites such as palmitoleic acid, arachidonic acid, and lactic acid showed obvious changes (p < 0.05) and a tendency for returning to baseline values in YXSC-treated HF rats at the 10th week. Moreover, four biomarkers, including palmitoleic acid, palmitic acid, arachidonic, acid and lactic acid, were further validated at the apoptotic position of heart tissue using MALDI-MS, consistent to the variation trends in the plasma.

Conclusions: Taken in concert, our proposed strategy may contribute to the understanding of the complex pathogenesis of ischemia-induced HF and the potential mechanism of YXSC.

Improved MALDI-MS method for the highly sensitive and reproducible detection of biomarker peaks for the proteotyping of Salmonella serotypes

The rapid identification and classification of pathogenic microorganisms, including Salmonella enterica, is important for the surveillance and prevention of foodborne diseases. Matrix-assisted laser desorption\ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been shown to be an effective tool for the rapid identification of microorganisms. In a previous report, a mass database consisting of 12 biomarker proteins, S8, L15, L17, L21, L25, S7, superoxide dismutase (SodA), peptidylprolyl cis-trans isomerase C, Gns, YibT, YaiA, and YciF, was introduced for the serotyping of S. enterica via MALDI-MS (Applied Microbiology and Biotechnology, 2017, 101, 8557-8569). However, the reproducibility of peak detection of biomarkers such as SodA at m\z 23 000 was poor. We report here an optimized MALDI-MS method for detecting these biomarkers with high sensitivity and reproducibility. The issue was solved by controlling the bacterial concentration at 1 × 10 to 1 × 10² MFU (3 × 10⁶ to 3 × 10⁷ CFU\μL, as calculated from the MFU), using the colony suspension supernatant obtained by centrifugation, and using matrix additives such as methylenediphosphonic acid and N-decyl-β-D-maltopyranoside. We propose that the method including the above steps is one of the best for detecting biomarkers with high sensitivity and reproducibility.

A simple MALDI target plate with channel design to improve detection sensitivity and reproducibility for quantitative analysis of biomolecules

Overcoming the detrimental effects of sweet spots during crystallization is an important step to improve the quantitative abilities of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. In this study, we introduce MALDI targets, which exhibit a channel design to reduce sweet spot phenomena and improve reproducibility. The size of the channels was 3.0 mm in length, 0.35 mm in depth, and 0.40 mm in width, adjusted to the width of the implemented laser beam. For sample deposition, the matrix/sample mixture was homogenously deposited into the channels using capillary action. To demonstrate the proof-of-principle, the novel plates were used for the quantification of acetyl-L-carnitine in human blood plasma using a combined standard addition and isotope dilution method. The results showed that the reproducibility of acetyl-L-carnitine detection was highly improved over a conventional MALDI-MS assay, with RSD values of less than 5.9% in comparison with 15.6% using the regular MALDI method. The limits of quantification using the new plates were lowered approximately two-fold in comparison with a standard rastering approach on a smooth stainless-steel plate. Matrix effects were also assessed and shown to be negligible. The new assay was subsequently applied to the quantification of acetyl-L-carnitine in human plasma samples.

Advances in MS Based Strategies for Probing Ligand-Target Interactions: Focus on Soft Ionization Mass Spectrometric Techniques

The non-covalent interactions between small drug molecules and disease-related proteins (ligand-target interactions) mediate various pharmacological processes in the treatment of different diseases. The development of the analytical methods to assess those interactions, including binding sites, binding energies, stoichiometry and association-dissociation constants, could assist in clarifying the mechanisms of action, precise treatment of targeted diseases as well as the targeted drug discovery. For the last decades, mass spectrometry (MS) has been recognized as a powerful tool to study the non-covalent interactions of the ligand-target complexes with the characteristics of high sensitivity, high-resolution, and high-throughput. Soft ionization mass spectrometry, especially the electrospray mass spectrometry (ESI-MS) and matrix assisted laser desorption ionization mass spectrometry (MALDI-MS), could achieve the complete transformation of the target analytes into the gas phase, and subsequent detection of the small drug molecules and disease-related protein complexes, and has exerted great advantages for studying the drug ligands-protein targets interactions, even in case of identifying active components as drug ligands from crude extracts of medicinal plants. Despite of other analytical techniques for this purpose, such as the NMR and X-ray crystallography, this review highlights the principles, research hotspots and recent applications of the soft ionization mass spectrometry and its hyphenated techniques, including hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (CX-MS), and ion mobility spectrometry mass spectrometry (IMS-MS), in the study of the non-covalent interactions between small drug molecules and disease-related proteins.

Enzymatic Cascades for Tailored 13C6 and 15N Enriched Human Milk Oligosaccharides

Several health benefits, associated with human milk oligosaccharides (HMOS), have been revealed in the last decades. Further progress, however, requires not only the establishment of a simple “routine” method for absolute quantification of complex HMOS mixtures but also the development of novel synthesis strategies to improve access to tailored HMOS. Here, we introduce a combination of salvage-like nucleotide sugar-producing enzyme cascades with Leloir-glycosyltransferases in a sequential pattern for the convenient tailoring of stable isotope-labeled HMOS. We demonstrate the assembly of [¹³C₆]galactose into lacto-N- and lacto-N-neo-type HMOS structures up to octaoses. Further, we present the enzymatic production of UDP-[¹⁵N]GlcNAc and its application for the enzymatic synthesis of [¹³C₆/¹⁵N]lacto-N-neo-tetraose for the first time. An exemplary application was selected—analysis of tetraose in complex biological mixtures—to show the potential of tailored stable isotope reference standards for the mass spectrometry-based quantification, using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) as a fast and straightforward method for absolute quantification of HMOS. Together with the newly available well-defined tailored isotopic HMOS, this can make a crucial contribution to prospective research aiming for a more profound understanding of HMOS structure-function relations.

Absorption and Metabolic Behavior of Hesperidin (Rutinosylated Hesperetin) after Single Oral Administration to Sprague-Dawley Rats

We investigated the absorption and metabolic behavior of hesperidin (hesperetin-7-O-rutinoside) in the blood system of Sprague-Dawley rats by liquid chromatography- and matrix-assisted laser desorption ionization mass spectrometries (LC-MS and MALDI-MS). After a single oral administration of hesperidin (10 mg/kg), which was expected to be absorbed in its degraded hesperetin form, we detected intact hesperidin in the portal vein blood (t_max, 2 h) for the first time. We successfully detected glucuronized hesperidin in the circulating bloodstream, while intact hesperidin had disappeared. Further MS analyses revealed that homoeriodictyol and eriodictyol conjugates were detected in both portal and circulating blood systems. This indicated that hesperidin and/or hesperetin are susceptible to methylation and demethylation during the intestinal membrane transport process. Sulfated and glucuronized metabolites were also detected in both blood systems. In conclusion, hesperidin can enter into the circulating bloodstream in its conjugated forms, together with the conjugated forms of hesperetin, homoeriodictyol, and/or eriodictyol.

The Reliable, Automatic Classification of Neonates in First-Tier MALDI-MS Screening for Sickle Cell Disease

Previous research has shown that a MALDI-MS technique can be used to screen for sickle cell disease (SCD), and that a system combining automated sample preparation, MALDI-MS analysis and classification software is a relevant approach for first-line, high-throughput SCD screening. In order to achieve a high-throughput "plug and play" approach while detecting "non-standard" profiles that might prompt the misclassification of a sample, we have incorporated various sets of alerts into the decision support software. These included "biological alert" indicators of a newborn's clinical status (e. g., detecting samples with no or low HbA), and "technical alerts" indicators for the most common non-standard profiles, i.e., those which might otherwise lead to sample misclassification. We evaluated these alerts by applying them to two datasets (produced by different laboratories). Despite the random generation of abnormal spectra by one-off technical faults or due to the nature and quality of the samples, the use of alerts fully secured the process of automatic sample classification. Firstly, cases of β-thalassemia were detected. Secondly, after a visual check on the tagged profiles and reanalysis of the corresponding biological samples, all the samples were correctly reclassified without prompting further alerts. All of the samples for which the results were not tagged were well classified (i.e., sensitivity and specificity = 1). The alerts were mainly designed for detecting false-negative classifications; all the FAS samples misclassified by the software as FA (a false negative) were marked with an alert. The implementation of alerts in the NeoScreening^® Laboratory Information Management System's decision support software opens up perspectives for the safe, reliable, automated classification of samples, with a visual check solely on abnormal results or samples. It should now be possible to evaluate the combination of the NeoSickle^® analytical solution and the NeoScreening^® Laboratory Information Management System in a real-life, prospective study of first-line SCD screening.

Immuno-MALDI MS dataset for improved detection of HCVcoreAg in sera

Complicated and large-scale challenge the contemporary biomedical community faces are development of highly-sensitive analytical methods for detection of protein markers associated with development of pathogenic mechanisms [2]. The atomic force microscopy (AFM) method in combination with specific fishing is unique among other analytical protein detection approaches; it allows visualization and counting of single protein molecules [3–6]. The present dataset focus on mass spectrometry method for detection of human hepatitis C virus core antigen (HCV core Ag) taking into account the potential modification with cations in blood serum samples, using mica chips for the atomic force microscopy (AFM-chips). To conduct specific protein fishing, we used flat AFM-chips preliminary sensibilized with molecular probes – aptamers, which are single-stranded DNA sequences. In our study we used four types of aptamers up to 85 nucleotides specific against the target protein – HCVcoreAg [3,4]. Working (n = 19) and control (n = 11) AFM-chips with aptamers were preliminarily immobilized on the surface in four zones and incubated in blood serum samples (See Supplementary fig. 1). Analysis of MS data regarding modification of marker protein peptides with Na+, K+, K2Cl+, and Na2Cl + ions enables to enhance the reliability of target proteins detection in the serum thereby demonstrating a high diagnostic potential.

norHarmane containing ionic liquid matrices for low molecular weight MALDI-MS carbohydrate analysis: The perfect couple with α-cyano-4-hydroxycinnamic acid

Cinnamic acid derivatives, particularly α-cyano-4-hydroxycinnamic acid (E-α-cyano-4-hydroxycinnamic acid or (E)-2-cyano-3-(4-hydroxyphenyl)prop-2-enoate; CHCA), have been extensively used especially for protein and peptide analysis. Together with the introduction of ionic liquid MALDI matrix (ILM) started the study of applications of IL prepared with CHCA and a counter organic base (ie, aliphatic amines) in which CHCA moiety is the chromophore responsible of UV-laser absorption. Despite the extensive studies of norharmane (9H-pyrido[3,4-b]indole; nHo) applications as matrix and its peculiar basic properties in the ground and electronic excited state, nHo containing ILM was never tested in MALDI-MS experiments. This pyrido-indole compound was introduced as MALDI matrix 22 years ago for different applications including low molecular weight (LMW) carbohydrates (neutral, acidic, and basic carbohydrates). These facts encouraged us to use it as a base, for the first time, for ILM preparation. As a rational design of new IL MALDI matrices, E-α-cyanocinnamic acid.nHo and E-cinnamic acid.nHo were prepared and their properties as matrices studied. Their performance was compared with that of (a) the corresponding IL prepared with butylamine as basic component, (b) the corresponding crystalline E-α-cyanocinnamic and E-cinnamic acid, and (c) the classical crystalline matrices (2,5-dihydroxybenzoic acid, DHB; nHo) used in the analysis of neutral/sulfated carbohydrates. The IL DHB.nHo was tested, too. Herein, we demonstrate the outstanding performance for the IL CHCA.nHo for LMW carbohydrate in positive and negative ion mode (linear and reflectron modes). Sulfated oligosaccharides were detected in negative ion mode, and although the dissociation of sulfate groups was not completely suppressed the relative intensity (RI) of [M - Na]^- peak was quite high. Additionally, to better understand the quite different performance of each IL tested as matrix, the physical and morphological properties in solid state were studied (optical image; MS image).

Monitoring of antibody glycosylation pattern based on microarray MALDI-TOF mass spectrometry

Biologically manufactured monoclonal antibodies (mAb) can strongly vary in their efficacy and affinity. Therefore, engineering and production of the mAb is highly regulated and requires product monitoring, especially in terms of N-glycosylation patterns. In this work, we present a high-throughput matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) method based on a microarray technology to monitor N-glycopeptides of IgG1 produced in a perfusion cell culture. A bottom-up approach combined with zwitterionic-hydrophilic interaction liquid chromatography for sample purification was used to determine the day-by-day variation of the terminal galactose within two major N-glycoforms. Our results show that microarrays for mass spectrometry (MAMS) are a robust platform for the rapid determination of the carbohydrate distribution. The spectral repeatability is characterized by a low coefficient of variations (1.7% and 7.1% for the FA2 and FA2G1 structures, respectively) and allows to detect the N-glycosylation variability resulting from operating conditions during the bioreactor process. The observed trend of released N-glycans was confirmed using capillary gel electrophoresis with laser-induced fluorescence detection. Therefore, the microarray technology is a promising analytical tool for glycosylation control during the production process of recombinant proteins.

Mass spectrometric characterization of the zein protein composition in maize flour extracts upon protein separation by SDS-PAGE and 2D gel electrophoresis

Highly homogenous α zein protein was isolated from maize kernels in an environment-friendly process using 95% ethanol as solvent. Due to the polyploidy and genetic polymorphism of the plant source, the application of high resolution separation methods in conjunction with precise analytical methods, such as MALDI-TOF-MS, is required to accurately estimate homogeneity of products that contain natural zein protein. The α zein protein product revealed two main bands in SDS-PAGE analysis, one at 25 kDa and other at 20 kDa apparent molecular mass. Yet, high resolution 2DE revealed approximately five protein spot groups in each row, the first at ca. 25 kDa and the second at ca. 20 kDa. Peptide mass fingerprinting data of the proteins in the two dominant SDS-PAGE bands matched to 30 amino acid sequence entries out of 102 non-redundant data base entries. MALDI-TOF-MS peptide mapping of the proteins from all spots indicated the presence of only α zein proteins. The most prominent ion signals in the MALDI mass spectra of the protein mixture of the 25 kDa SDS gel band after in-gel digestion were found at m/z 1272.6 and m/z 2009.1, and the most prominent ion signals of the protein mixture of the 20 kDa band after in-gel digestion were recorded at m/z 1083.5 and m/z 1691.8. These ion signals have been found typical for α zein proteins and may serve as marker ion signals which upon chymotryptic digestion reliably indicate the presence of α zein protein in two hybrid corn products.

Counterion Dye Staining of Proteins in One- and Two-Dimensional Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis and Tryptic Gel Digestion of Stained Protein for Mass Spectrometry

A fast and matrix-assisted laser desorption/ionization-mass spectrometry compatible protein staining method in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis is described. It is based on the counterion dye staining method that employs oppositely charged two dyes, zincon and ethyl violet to form an ion-pair complex. The protocol including fixing, staining, and quick washing steps can be completed in 1-1.5 h depending upon gel thickness. It has the sensitivity comparable to the colloidal Coomassie Brilliant Blue G stain using phosphoric acid as a component of staining solution (4-8 ng). The counterion dye stain does not induce protein modifications that complicate interpretation of peptide mapping data from mass spectrometry. Considering the speed, sensitivity, and compatibility with mass spectrometry, the counterion dye stain may be more practical than any other dye-based protein stains for routine proteomic researches.

Glycoproteomic markers of hepatocellular carcinoma-mass spectrometry based approaches

Hepatocellular carcinoma (HCC) is the third most-common cause of cancer-related death worldwide. Most cases of HCC develop in patients that already have liver cirrhosis and have been recommended for surveillance for an early onset of HCC. Cirrhosis is the final common pathway for several etiologies of liver disease, including hepatitis B and C, alcohol, and increasingly non-alcoholic fatty liver disease. Only 20-30% of patients with HCC are eligible for curative therapy due primarily to inadequate early-detection strategies. Reliable, accurate biomarkers for HCC early detection provide the highest likelihood of curative therapy and survival; however, current early-detection methods that use abdominal ultrasound and serum alpha fetoprotein are inadequate due to poor adherence and limited sensitivity and specificity. There is an urgent need for convenient and highly accurate validated biomarkers for HCC early detection. The theme of this review is the development of new methods to discover glycoprotein-based markers for detection of HCC with mass spectrometry approaches. We outline the non-mass spectrometry based methods that have been used to discover HCC markers including immunoassays, capillary electrophoresis, 2-D gel electrophoresis, and lectin-FLISA assays. We describe the development and results of mass spectrometry-based assays for glycan screening based on either MALDI-MS or ESI analysis. These analyses might be based on the glycan content of serum or on glycan screening for target molecules from serum. We describe some of the specific markers that have been developed as a result, including for proteins such as Haptoglobin, Hemopexin, Kininogen, and others. We discuss the potential role for other technologies, including PGC chromatography and ion mobility, to separate isoforms of glycan markers. Analyses of glycopeptides based on new technologies and innovative softwares are described and also their potential role in discovery of markers of HCC. These technologies include new fragmentation methods such as EThcD and stepped HCD, which can identify large numbers of glycopeptide structures from serum. The key role of lectin extraction in various assays for intact glycopeptides or their truncated versions is also described, where various core-fucosylated and hyperfucosylated glycopeptides have been identified as potential markers of HCC. Finally, we describe the role of LC-MRMs or lectin-FLISA MRMs as a means to validate these glycoprotein markers from patient samples. These technological advancements in mass spectrometry have the potential to lead to novel biomarkers to improve the early detection of HCC.

Identification of fungal isolates by MALDI-TOF mass spectrometry in veterinary practice: validation of a web application

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a reliable method to identify fungal isolates. The success of this approach relies on the availability of exhaustive databases, but the latter were built with a focus on human pathogens. We assessed a large in-house database of reference spectra and a dedicated web application for their suitability for use in veterinary laboratories. A panel of 290 mold and yeast isolates representing 69 different fungal species was isolated from various animals (including pets, cattle, and zoo animals) and identified using both MALDI-TOF MS and conventional techniques. The performance of the 2 methods was compared, and identifications were confirmed by DNA sequencing. MALDI-TOF MS allowed distinction between some closely related species and achieved 89% correct identification at the species level. In comparison, only 60% of the isolates were correctly identified with conventional approaches. Using this online application, MALDI-TOF MS thus appears to be a relevant alternative for the identification of fungal isolates encountered by animal health professionals.

Effects of incubation temperature and acetonitrile amount on microwave-assisted tryptic digestion of proteins

The effects of incubation temperature and acetonitrile (ACN) amount on microwave-assisted tryptic digestion of horse skeletal muscle myoglobin (MYG) and bovine serum albumin (BSA) were investigated. Microwave-assisted tryptic digestion was performed on BSA or MYG solutions containing different amounts (0, 10, and 20%) of ACN for different times (10, 20, 30, 40, and 50 min) at different temperatures (25, 37, and 55 °C). Conventional overnight tryptic digestion was also conducted with gentle mixing at 37 °C for 16 h. Digested samples were analyzed using matrix-assisted laser desorption/ionization mass spectrometry. Similar sequence coverage (SC) values were obtained under most conditions except when the protein sample solutions were digested with 20% ACN at 55 °C, which provided the lowest SC for both MYG and BSA for all investigated digestion times. Considering the missed cleavage (MC) ratios for 50-min microwave-assisted digestion, the highest MC ratio, (i.e., lowest trypsin activity) was observed for the digestion condition of 20% ACN at 55 °C for both proteins, while the lowest MC ratio was observed with 0% ACN at 25 °C for MYG and with 0% ACN at 55 °C for BSA. Conventional overnight tryptic digestion at 37 °C provided more completely cleaved peptides than 50-min microwave-assisted tryptic digestion at the same temperature.