CSF N-Glycomics Using MALDI MS Techniques

In this chapter, we will present the methodology currently applied in our laboratory for the structural elucidation of the cerebrospinal fluid (CSF) N-glycome. N-glycans are released from denatured carboxymethylated glycoproteins by digestion with peptide-N-glycosidase F (PNGase F) and purified using both C18 Sep-Pak® and porous graphitized carbon (PGC) HyperSep™ Hypercarb™ solid phase extraction (SPE) cartridges. The glycan pool is subsequently permethylated to increase mass spectrometry sensitivity. Molecular assignments are performed through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) analysis considering either the protein N-linked glycosylation pathway or MALDI TOF MS/MS data. Each stage has been optimized to obtain high-quality mass spectra in reflector mode with an optimal signal-to-noise ratio up to m/z 4800. This method has been successfully adopted to associate specific N-glycome profiles to the early and the advanced phases of Alzheimer's disease (AD).

Integration of fluorescence and MALDI imaging for microfluidic chip-based screening of potential thrombin inhibitors from natural products

The microfluidic technology provides an ideal platform for in situ screening of enzyme inhibitors and activators from natural products. This work described a surface-modified ITO glass-PDMS hybrid microfluidic chip for evaluating thrombin interaction with its potential inhibitors by fluorescence imaging and matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI). The fluorescence-labeled substrate was immobilized on a conductive ITO glass slide coated with gold nanoparticles/thiol-β-cyclodextrin modified TiO2 nanowires (Au-β-CD@TiO2 NWs) via Au-S bonds. A PDMS microchannel plate was placed on top of the modified ITO slide. The premixed solutions of thrombin and candidate thrombin inhibitors were infused into the microchannels to form a microreactor environment. The enzymatic reaction was rapidly monitored by fluorescence microscopy, and MALDI MS was used to validate and quantify the enzymatic hydrolysate of thrombin to determine the enzyme kinetic process and inhibitory activities of selected flavonoids. The fluorescence and MALDI MS results showed that luteolin, cynaroside, and baicalin have good thrombin inhibitory activity and their half-maximal inhibitory concentrations (IC50) were below 30 μM. The integration of fluorescence imaging and MALDI MSI for in situ monitoring and quantifying the enzymatic reaction in a microfluidic chip is capable of rapid and accurate screening of thrombin inhibitors from natural products.

Prospective on Imaging Mass Spectrometry in Clinical Diagnostics

Imaging mass spectrometry (IMS) is a molecular technology utilized for spatially driven research, providing molecular maps from tissue sections. This article reviews matrix-assisted laser desorption ionization (MALDI) IMS and its progress as a primary tool in the clinical laboratory. MALDI mass spectrometry has been used to classify bacteria and perform other bulk analyses for plate-based assays for many years. However, the clinical application of spatial data within a tissue biopsy for diagnoses and prognoses is still an emerging opportunity in molecular diagnostics. This work considers spatially driven mass spectrometry approaches for clinical diagnostics and addresses aspects of new imaging-based assays that include analyte selection, quality control/assurance metrics, data reproducibility, data classification, and data scoring. It is necessary to implement these tasks for the rigorous translation of IMS to the clinical laboratory; however, this requires detailed standardized protocols for introducing IMS into the clinical laboratory to deliver reliable and reproducible results that inform and guide patient care.

Affi-BAMS™: A Robust Targeted Proteomics Microarray Platform to Measure Histone Post-Translational Modifications

For targeted protein panels, the ability to specifically assay post-translational modifications (PTMs) in a quantitative, sensitive, and straightforward manner would substantially advance biological and pharmacological studies. The present study highlights the effectiveness of the Affi-BAMS™ epitope-directed affinity bead capture/MALDI MS platform for quantitatively defining complex PTM marks of H3 and H4 histones. Using H3 and H4 histone peptides and isotopically labelled derivatives, this affinity bead and MALDI MS platform achieves a range of >3 orders of magnitude with a technical precision CV of <5%. Using nuclear cellular lysates, Affi-BAMS PTM-peptide capture resolves heterogeneous histone N-terminal PTMs with as little as 100 µg of starting material. In an HDAC inhibitor and MCF7 cell line model, the ability to monitor dynamic histone H3 acetylation and methylation events is further demonstrated (including SILAC quantification). Affi-BAMS (and its capacity for the multiplexing of samples and target PTM-proteins) thus provides a uniquely efficient and effective approach for analyzing dynamic epigenetic histone marks, which is critical for the regulation of chromatin structure and gene expression.

Quantitative analysis of bisphenol A eluted into canned tomato and mackerel by matrix-assisted laser desorption ionization mass spectrometry using anthracene as matrix

Quantitative analysis of bisphenol A (BPA) was performed by matrix-assisted laser desorption ionization mass spectrometry. It was found that BPA was ionized as deprotonated species when anthracene was used as the matrix. A peak of deprotonated BPA and a peak assignable to epoxy resin were observed on analysis of liquids in canned tomato and mackerel samples. In addition, many identical peaks were observed from the liquids in both cans, indicating that epoxy resin was degraded and BPA was eluted into the canned tomato and mackerel during the storage period. It was suggested that the mackerel heat-treatment process and the acidity of tomato were responsible for the elution of BPA. Using bisphenol B (BPB) as the internal standard, the concentrations of BPA were determined to be 0.55 ± 0.05 and 1.72 ± 0.13 ng/µL (µg/mL) for the canned tomato and mackerel samples, respectively. These canned products were imported goods, and their BPA levels exceeded the safe concentration recommended by The Can Manufacturers Institute of Japan. The results indicate that consumers should exercise caution when consuming canned products particularly those manufactured overseas, which have different safety standards.

Analysis of tri-benzeneboronic esters of monosaccharides formed in aqueous solution by MALDI-TOF MS and DFT calculations

The affinity interactions between boronic acids and sugars have been successfully exploited in many fields, such as the sensing of saccharides, selective enrichment of glycoconjugates, and drug delivery. However, despite multiple techniques having been adopted to investigate the reaction of boronate affinity, the pathway of boronate esters formation under aqueous conditions remains controversial. We report a MALDI-MS approach to investigate the interactions between phenylboronic acid and monosaccharides in neutral aqueous solution by using polylevodopa as an innovative substrate instead of conventional matrix. A series of unusual tri-benzeneboronic esters were then revealed. The mass spectrometry data indicate that they bear a dibenzenepyroboronate cyclic ester moiety with seven-membered ring or eight-membered ring. With the aid of theoretical computations, their most likely geometrical structures are elucidated, and these tri-benzeneboronic esters are proposed to be formed via a boroxine binding monosaccharide pathway. This work provides more insight into the mechanism of boronate affinity interaction between boronic acid and sugars and proves the developed MALDI-MS approach is promising for studying interactions between small molecules.

Mass Spectrometry of Esterified Cyclodextrins

Cyclodextrins are cyclic oligosaccharides that have received special attention due to their cavity-based structural architecture that imbues them with outstanding properties, primarily related to their capacity to host various guest molecules, from low-molecular-mass compounds to polymers. Cyclodextrin derivatization has been always accompanied by the development of characterization methods, able to unfold complicated structures with increasing precision. One of the important leaps forward is represented by mass spectrometry techniques with soft ionization, mainly matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). In this context, esterified cyclodextrins (ECDs) benefited also from the formidable input of structural knowledge, thus allowing the understanding of the structural impact of reaction parameters on the obtained products, especially for the ring-opening oligomerization of cyclic esters. The current review envisages the common mass spectrometry approaches such as direct MALDI MS or ESI MS analysis, hyphenated liquid chromatography-mass spectrometry, and tandem mass spectrometry, employed for unraveling the structural features and particular processes associated with ECDs. Thus, the accurate description of complex architectures, advances in the gas phase fragmentation processes, assessment of secondary reactions, and reaction kinetics are discussed in addition to typical molecular mass measurements.

Polyethylene Glycol-Isophorone Diisocyanate Polyurethane Prepolymers Tailored Using MALDI MS

The reaction of diols with isocyanates, leading to mono-functional and di-functional prepolymers may be investigated using various characterization methods which show the overall conversion of isocyanate monomers. On the other hand, matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) polymer characterization can be employed to identify the monomer units, the end-group functionalities, molecular weight averages, and to determine the copolymer sequence. Herein, we focus on prepolymer synthesis using isophorone diisocyanate (IPDI), a widely used diisocyanate for prepolymers preparation, especially in waterborne polyurethane materials. Thus, the reaction between polyethylene glycol diol and IPDI was in-depth investigated by mass spectrometry to determine the influence of the reaction parameters on the prepolymer's structure. The relative content of the different functional oligomer species at given reaction times was determined in the reaction mixture. More specifically, the offline analysis revealed the influence of reaction parameters such as reaction temperature, the concentration of reactants, and the amount of dibutyltin dilaurate catalyst. The established MALDI MS analysis involved measurements of samples, first, directly collected from the reaction mixture and secondly, following derivatization with methanol. The obtained results revealed the effects of reaction parameters on the functionalization reaction with isocyanates, allowing to achieve a better reaction control.

MALDI MS Imaging of Cucumbers

There are many different methodologies in the literature for the preparation of plant material for subsequent MALDI MSI analysis. This chapter overviews preparation of cucumbers (Cucumis sativus L.), with emphasis on sample freezing, cryosectioning, and matrix deposition. This should act as a representative example of sample preparation for plant tissue, and due to wide sample variation (e.g., leaves, seeds, and fruit) and analytes of interest, method optimization will be required for different samples.

Dissolve-spin: Desalting oligonucleotides for MALDI MS analysis

Desalting oligonucleotides (ONs) for matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) analysis was achieved using a simple dissolve-spin approach. The ON is dissolved in an organic solvent. Insoluble salts are removed by centrifugation. ONs are highly polar molecules and are generally believed insoluble in organic solvents with moderate polarity such as acetonitrile (ACN), 1,4-dioxane, ethyl acetate, and THF. However, we found that in the presence of a suitable proton source such as pyridinium chloride, a quantity of ON that is sufficient for MALDI MS analysis could be dissolved. Because inorganic salts are insoluble in such relatively non-polar solvents, the finding can be utilized for desalting ONs for MALDI MS analysis. Comparisons of MS spectra of intentionally salted ONs that underwent the new desalting procedure with those that did not undergo the procedure provided unambiguous evidence that the desalting method is highly effective.

Unraveling metabolic alterations in transgenic mouse model of Alzheimer's disease using MALDI MS imaging with 4-aminocinnoline-3-carboxamide matrix

Revealing the metabolic abnormalities of central and peripheral systems in Alzheimer's disease (AD) mouse model is of paramount importance for understanding AD disease. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a powerful label-free technique that has been extensively utilized for the interrogation of spatial changes of various metabolites in neurodegenerative disease. However, technical limitations still exist in MALDI MS, and there is a need to improve the performance of traditional MALDI for a deeper investigation of metabolic alterations in the AD mouse model. In this work, 4-aminocinnoline-3-carboxamide (4-AC) was developed into a novel dual-polarity MALDI matrix. Compared with traditionally used MALDI matrices such as 2,5-dihydroxybenzoic acid (DHB) and 9-aminoacridine (9-AA), 4-AC exhibited superior performance in UV absorption at 355 nm, ion yields, background interference, and vacuum stability, making it an ideal MALDI matrix for comprehensive evaluation of metabolic alteration in the brain and serum of APP/PS1 transgenic mouse model of AD. In total, 93 metabolites exhibited different levels of regional changes in the brain of AD mice as compared to the age-matched controls. Moreover, in the serum of AD mice, 81 altered metabolites distinguishing the AD group from the control were observed by using multivariate statistical analysis. It is expected that the application of the MALDI MSI method developed in this work to visualize the spatio-chemical change of various metabolites may improve our understanding of the etiopathogenesis of AD.

A novel method for multiplex protein biomarker analysis of human serum using quantitative MALDI mass spectrometry

In this work, we have extended our previously proposed approach for determining protein concentrations in human serum (using MALDI-TOF mass spectrometry) to include simultaneous analysis of several proteins associated with acute inflammation (alpha-2-macroglobulin, fetuin-A, serum amyloid A1). This technique can be used to diagnose systemic inflammation and provides results in 4-5 h. The developed approach was verified using standard immunological methods (ELISA). Samples from 87 individuals, in specific groups, were used for testing and validation: control; inflammatory soft tissue disease accompanied by sepsis; influenza A infection; or COVID-19. The feasibility of differentiating patient groups with the aforementioned conditions was analyzed using a combination of the inflammatory markers described. For fetuin-A and serum amyloid A1, diagnostically significant concentration ranges were established.

High-throughput screening and spatial profiling of low-mass pesticides using a novel Ti3C2 MXene nanowire (TMN) as MALDI MS matrix

Pesticides play critical roles in agricultural fields; however, pesticide residues can cause serious damage to human health and the ecological environment; therefore, developing a rapid and sensitive method for pesticide detection is urgently needed. Nanostructure-assisted matrix laser desorption/ionization (MALDI) mass spectrometry (MS) has great potential for the detection of low-mass pesticides. In this study, a novel Ti₃C₂ MXene nanowire (TMN) was prepared by a facile sol-gel method and served as a matrix to enhance MALDI MS performance in the analysis of pesticides in positive ion mode. The TMN showed superior performance in the high-throughput detection of six kinds of pesticides (organophosphorus, organochlorine, carbamate, neonicotinoids, triazole, and oxadiazines), with ultrahigh sensitivity (detection limits at sub-ppt levels), remarkable repeatability, excellent salt tolerance, and extremely low background compared to traditional organic matrices due to the specific polyaromatic structure and the doping of nitrogen. Furthermore, this matrix was successfully employed for the analysis of residual pesticides in traditional Chinese herbs, and the level of diniconazole was quantified with a linear range of 0-50 ng/mL (R² > 0.99). More importantly, the spatial distribution of various endogenous compounds (e.g., amino acids and saccharides, fatty acids, alkaloids, and plant hormones) and xenobiotic pesticides from the intact root of the medicinal plant P. quinquefolium was clearly visualized using the TMN self-assembly film as a matrix for MALDI imaging mass spectrometry (IMS). With superior advantages such as sensitivity, simplicity, rapidness, and minimal sample requirement, TMN as a matrix-assisted MALDI MS shows great promise for various applications.

MALDI Matrices for the Analysis of Low Molecular Weight Compounds: Rational Design, Challenges and Perspectives

The analysis of low molecular weight (LMW) compounds is of great interest to detect small pharmaceutical drugs rapidly and sensitively, or to trace and understand metabolic pathways. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) plays a central role in the analysis of high molecular weight (bio)molecules. However, its application for LMW compounds is restricted by spectral interferences in the low m/z region, which are produced by conventional organic matrices. Several strategies regarding sample preparation have been investigated to overcome this problem. A different rationale is centred on developing new matrices which not only meet the fundamental requirements of good absorption and high ionization efficiency, but are also vacuum stable and "MALDI silent", i. e., do not give matrix-related signals in the LMW area. This review gives an overview on the rational design strategies used to develop matrix systems for the analysis of LMW compounds, focusing on (i) the modification of well-known matrices, (ii) the search for high molecular weight matrices, (iii) the development of binary, hybrid and nanomaterial-based matrices, (iv) the advance of reactive matrices and (v) the progress made regarding matrices for negative or dual polarity mode.

Screening for potential interaction partners with surface plasmon resonance imaging coupled to MALDI mass spectrometry

We coupled SPR imaging (SPRi) with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) to identify new potential RNA binders. Here, we improve this powerful method, especially by optimizing the proteolytic digestion (type of reducing agent, its concentration, and incubation time), to work with complex mixtures, specifically a lysate of the rough mitochondrial fraction from yeast. The advantages of this hyphenated method compared to column-based or separate analyses are (i) rapid and direct visual readout from the SPRi array, (ii) possibility of high-throughput analysis of different interactions in parallel, (iii) high sensitivity, and (iv) no sample loss or contamination due to elution or micro-recovery procedures. The model system used is a catalytically active RNA (group IIB intron from Saccharomyces cerevisiae, Sc.ai5γ) and its cofactor Mss116. The protein supports the RNA folding process and thereby the subsequent excision of the intronic RNA from the coding part. Using the novel approach of coupling SPR with MALDI MS, we report the identification of potential RNA-binding proteins from a crude yeast mitochondrial lysate in a non-targeted approach. Our results show that proteins other than the well-known cofactor Mss116 interact with Sc.ai5γ (Dbp8, Prp8, Mrp13, and Cullin-3), suggesting that the intron folding and splicing are regulated by more than one cofactor in vivo.

Quench me if you can: Alpha-2-macroglobulin trypsin complexes enable serum biomarker analysis by MALDI mass spectrometry

One of the main functions of alpha-2-macroglobulin (A2M) in human blood serum is the binding of all classes of protease. It is known that trypsin, after such interaction, possesses modified proteolytic activity. Trypsin first hydrolyzes two bonds in A2M's 'bait region', and the peptide ⁷⁰⁵VGFYESDVMGR⁷¹⁵ is released from A2M. In this work, specifics of the A2M-trypsin interaction were used to determine A2M concentration directly in human blood serum using MALDI mass-spectrometry. Following exogenous addition of trypsin to human blood serum in vitro, the concentration of the VGFYESDVMGR peptide was measured, using its isotopically-labeled analogue (¹⁸O), and A2M concentration was calculated. The optimized mass spectrometric approach was verified using a standard method for A2M concentration determination (ELISA) and the relevant statistical analysis methods. It was also shown that trypsin's modified proteolytic activity in the presence of serum A2M can be used to analyze other serum proteins, including potential biomarkers of pathological processes. Thus, this work describes a promising approach to serum biomarker analysis that can be technically extended in several useful directions.

C60-based chemical labeling strategy for the determination of polyamines in biological samples using matrix-assisted laser desorption/ionization mass spectrometry

Bioactive polyamines play important roles in many biological processes such as gene expression, cell growth, protein synthesis, and signal transduction. Accurate determination of polyamines is helpful for studying their biological functions. Herein, a C₆₀-based chemical labeling strategy was proposed for the determination of polyamines (putrescine, cadaverine, spermidine, and spermine) in biological samples using matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). An N-hydroxysuccinimide ester functionalized C₆₀ (NHS-C₆₀) was used as a labeling reagent and the m/z of the labeled polyamines reached up to more than 900 Da, which avoided matrix interferences in the low m/z region. In addition, as NHS-C₆₀ derivatives, mono- and bis-substituted polyamines were produced simultaneously, which benefited the qualitative analysis of polyamines. The analytical method was validated using NHS-C₆₀ labeled polyamines in cells and mice feces samples. Good linearities were obtained with correlation coefficients ranging from 0.9786 to 0.9982. The limits of quantification were in the range of 0.68-1.48 pmol. Good reproducibility and reliability of our proposed method were confirmed by intra- and inter-day precisions ranged from 2.8 to 16.6%, and the recoveries ranged between 81.8 and 119.9%. Finally, the proposed method was applied to determine polyamines in cells and mice feces. Three polyamines were detected in the cells, and the contents of cadaverine and spermidine in the feces of high-fat diet mice were found to be significantly lower than those in the normal diet mice. The results show that the proposed NHS-C₆₀ labeling coupled with MALDI MS strategy is suitable for the determination of polyamines in biological samples.

Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics

The ability to quantitatively probe diverse panels of proteins and their post-translational modifications (PTMs) across multiple samples would aid a broad spectrum of biological, biochemical and pharmacological studies. We report a novel, microarray analytical technology that combines immuno-affinity capture with Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS), which is capable of supporting highly multiplexed, targeted proteomic assays. Termed "Affinity-Bead Assisted Mass Spectrometry" (Affi-BAMS), this LC-free technology enables development of highly specific and customizable assay panels for simultaneous profiling of multiple proteins and PTMs. While affinity beads have been used previously in combination with MS, the Affi-BAMS workflow uses enrichment on a single bead that contains one type of antibody, generally capturing a single analyte (protein or PTM) while having enough binding capacity to enable quantification within approximately 3 orders of magnitude. The multiplexing capability is achieved by combining Affi-BAMS beads with different protein specificities. To enable screening of bead-captured analytes by MS, we further developed a novel method of performing spatially localized elution of targets from individual beads arrayed on a microscope slide. The resulting arrays of micro spots contain highly concentrated analytes localized within 0.5 mm diameter spots that can be directly measured using MALDI MS. While both intact proteins and protein fragments can be monitored by Affi-BAMS, we initially focused on applying this technology for bottom-up proteomics to enable screening of hundreds of samples per day by combining the robust magnetic bead-based workflow with the high throughput nature of MALDI MS acquisition. To demonstrate the variety of applications and robustness of Affi-BAMS, several studies are presented that focus on the response of 4EBP1, RPS6, ERK1/ERK2, mTOR, Histone H3 and C-MET to stimuli including rapamycin, H2O2, EPO, SU11274, Staurosporine and Vorinostat.

Nano electrospray differential mobility analysis based size-selection of liposomes and very-low density lipoprotein particles for offline hyphenation to MALDI mass spectrometry

Gas-phase electrophoresis of single-charged analytes (nanoparticles) enables their separation according to the surface-dry particle size (Electrophoretic Mobility Diameter, EMD), which corresponds to the diameter of spherical shaped particles. Employing a nano Electrospray Differential Mobility Analyzer (nES DMA), also known as nES Gas-phase Electrophoretic Mobility Molecular Analyzer (nES GEMMA), allows sizing/size-separation and determination of particle-number concentrations. Separations are based on a constant high laminar sheath flow and a tunable, orthogonal electric field enabling scanning of EMDs in the nanometer size range. Additionally, keeping the voltage constant, only nanoparticles of a given EMD pass the instrument and can be collected on corresponding supporting materials for subsequent nanoparticle analyses applying e.g. microscopic, immunologic or spectroscopic techniques. In our proof-of-concept study we now focus for the first time on mass spectrometric (MS) characterization of DMA size-selected material. We carried out size-selection of liposomes, vesicles consisting of a lipid bilayer and an aqueous lumen employed as carriers in e.g. pharmaceutic, cosmetic or nutritional applications. Particles of 85 nm EMD were collected on gold-coated silicon wafers. Subsequently, matrix was applied and Matrix-Assisted Laser Desorption / Ionization (MALDI) MS carried out. However, we not only focused on plain liposomes but also demonstrated the applicability of our approach for very heterogeneous low density lipoprotein (VLDL) particles, a transporter of lipid metabolism. Our novel offline hyphenation of gas-phase electrophoresis (termed nES DMA or nES GEMMA) and MALDI-MS opens the avenue to the molecular characterization of size-select nanoparticles of complex nature.

Quantitative Assessment of Anti-Cancer Drug Efficacy From Coregistered Mass Spectrometry and Fluorescence Microscopy Images of Multicellular Tumor Spheroids

Spheroids-three-dimensional aggregates of cells grown from a cancer cell line-represent a model of living tissue for chemotherapy investigation. Distribution of chemotherapeutics in spheroid sections was determined using the matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI). Proliferating or apoptotic cells were immunohistochemically labeled and visualized by laser scanning confocal fluorescence microscopy (LSCM). Drug efficacy was evaluated by comparing coregistered MALDI MSI and LSCM data of drug-treated spheroids with LSCM only data of untreated control spheroids. We developed a fiducial-based workflow for coregistration of low-resolution MALDI MS with high-resolution LSCM images. To allow comparison of drug and cell distribution between the drug-treated and untreated spheroids of different shapes or diameters, we introduced a common diffusion-related coordinate, the distance from the spheroid boundary. In a procedure referred to as "peeling", we correlated average drug distribution at a certain distance with the average reduction in the affected cells between the untreated and the treated spheroids. This novel approach makes it possible to differentiate between peripheral cells that died due to therapy and the innermost cells which died naturally. Two novel algorithms-for MALDI MS image denoising and for weighting of MALDI MSI and LSCM data by the presence of cell nuclei-are also presented.

Phytochemical analysis of Ficus carica L. active compounds possessing anticonvulsant activity

The anticonvulsant potential of Ficus carica methanol-extract (Fc) has been studied. It was found that Fc most active fraction is rich in oligosaccharides (OFG). ¹H, ¹³C NMR and Nano-ESI, MALDI MS, and LC-MS techniques proved that OFG contains alpha-glucopyranoside oligomer in high amounts. Both Fc and OFG reduced strychnine (STR) convulsion-action. Fc and OFG fully protected the experimental-animals from STR-lethality. The intracerebroventricular-administration (ICV) of Fc or OFG in combination with glycine in ethanol-treated mice caused a dose-dependent returning to a 2nd-loss of righting-reflex (LORR), and was antagonized by STR. FC and OFG ICV injection counteracted STR-inhibition, confirming that Fc/OFG anticonvulsant mechanism of action was mediated by potentiation of glycine receptor. These results support Fc and OFG potential anticonvulsant-activity with good safety-profile.

Novel Prognostic Markers in Triple-Negative Breast Cancer Discovered by MALDI-Mass Spectrometry Imaging

There are no widely-accepted prognostic markers currently available to predict outcomes in patients with triple-negative breast cancer (TNBC), and no targeted therapies with confirmed benefit. We have used MALDI mass spectrometry imaging (MSI) of tryptic peptides to compare regions of cancer and benign tissue in 10 formalin-fixed, paraffin-embedded sections of TNBC tumors. Proteins were identified by reference to a peptide library constructed by LC-MALDI-MS/MS analyses of the same tissues. The prognostic significance of proteins that distinguished between cancer and benign regions was estimated by Kaplan-Meier analysis of their gene expression from public databases. Among peptides that distinguished between cancer and benign tissue in at least 3 tissues with a ROC area under the curve >0.7, 14 represented proteins identified from the reference library, including proteins not previously associated with breast cancer. Initial network analysis using the STRING database showed no obvious functional relationships except among collagen subunits COL1A1, COL1A2, and COL63A, but manual curation, including the addition of EGFR to the analysis, revealed a unique network connecting 10 of the 14 proteins. Kaplan-Meier survival analysis to examine the relationship between tumor expression of genes encoding the 14 proteins, and recurrence-free survival (RFS) in patients with basal-like TNBC showed that, compared to low expression, high expression of nine of the genes was associated with significantly worse RFS, most with hazard ratios >2. In contrast, in estrogen receptor-positive tumors, high expression of these genes showed only low, or no, association with worse RFS. These proteins are proposed as putative markers of RFS in TNBC, and some may also be considered as possible targets for future therapies.

CSF N-Glycoproteomics Using MALDI MS Techniques in Neurodegenerative Diseases

CSF diagnostics has proved to be a formidable testing ground for N-glycoproteomic analysis of neurological diseases. To characterize specific N-glycan profiles of CSF in early and advanced phases of Alzheimer's disease, as well as in lysosomal storage disorders such as Tay-Sachs disease, we set up in our lab a robust and feasible protocol by coupling bioanalytical methods and mass spectrometry analysis.Starting from a few microliters of CSF, after protein denaturation, reduction, and alkylation, N-glycans are released from glycoproteins using the peptide-N-glycosidase F (PNGase F) and purified. The analysis of permethylated N-glycans by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and MALDI-TOF MS/MS allowed us to identify specific glyco-structures and also to distinguish between isobaric N-glycans.

Superhydrophobic candle soot/PDMS substrate for one-step enrichment and desalting of peptides in MALDI MS analysis

Superhydrophobic substrate is applied in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) detection due to its confinement effect. The weak interaction of superhydrophobic surface with water/salts makes it potential in one-step enrichment and desalting of peptide in MALDI MS analysis. We fabricate a superhydrophobic substrate by spin-coating poly(dimethyl siloxane) (PDMS) on a candle soot layer. On this substrate, the peptide analytes can be confined and enriched in a small area due to the confinement effect and its strong hydrophobic interactions with PDMS. Meanwhile, the desalting can be easily realized by removing the residual solution after the absorption of analyst molecules due to the weak interaction between water/salt contaminants and the superhydrophobic surface. Using this substrate, angiotensin III (Ang III) in the presence of salt with high concentration (2 M or saturated) can be analyzed, and the peptide sequence coverage of 10 μg/mL myoglobin (MYO) and bovine serum albumin (BSA) digests is enhanced to 51% and 26%, which is 37% and 21% analyzed with the commercial ZipTipC₁₈ pipette tips. The LOD of bacitracin A (Bac A) in milk with this substrate is 100 pM and nearly 360 times lower than the LOD of standard testing method. This substrate has potential practical applications in proteomics research and actual sample analysis.

Disposable MoS2-Arrayed MALDI MS Chip for High-Throughput and Rapid Quantification of Sulfonamides in Multiple Real Samples

In this work, we demonstrate, for the first time, the development of a disposable MoS₂-arrayed matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) chip combined with an immunoaffinity enrichment method for high-throughput, rapid, and simultaneous quantitation of multiple sulfonamides (SAs). The disposable MALDI MS chip was designed and fabricated by MoS₂ array formation on a commercial indium tin oxide (ITO) glass slide. A series of SAs were analyzed, and clear deprotonated signals were obtained in negative-ion mode. Compared with MoS₂-arrayed commercial steel plate, the prepared MALDI MS chip exhibited comparable LDI efficiency, providing a good alternative and disposable substrate for MALDI MS analysis. Furthermore, internal standard (IS) was previously deposited onto the MoS₂ array to simplify the experimental process for MALDI MS quantitation. 96 sample spots could be analyzed within 10 min in one single chip to perform quantitative analysis, recovery studies, and real foodstuff detection. Upon targeted extraction and enrichment by antibody conjugated magnetic beads, five SAs were quantitatively determined by the IS-first method with the linear range of 0.5-10 ng/mL ( R² > 0.990). Good recoveries and repeatability were obtained for spiked pork, egg, and milk samples. SAs in several real foodstuffs were successfully identified and quantified. The developed method may provide a promising tool for the routine analysis of antibiotic residues in real samples.

A matrix-assisted laser desorption/ionization mass spectroscopy method for the analysis of small molecules by integrating chemical labeling with the supramolecular chemistry of cucurbituril

Although several methods have realized the analysis of low molecular weight (LMW) compounds using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) by overcoming the problem of interference with MS signals in the low mass region derived from conventional organic matrices, this emerging field still requires strategies to address the issue of analyzing complex samples containing LMW components in addition to the LMW compounds of interest, and solve the problem of lack of universality. The present study proposes an integrated strategy that combines chemical labeling with the supramolecular chemistry of cucurbit [n]uril (CB [n]) for the MALDI MS analysis of LMW compounds in complex samples. In this strategy, the target LMW compounds are first labeled by introducing a series of bifunctional reagents that selectively react with the target analytes and also form stable inclusion complexes with CB [n]. Then, the labeled products act as guest molecules that readily and selectively form stable inclusion complexes with CB [n]. This strategy relocates the MS signals of the LMW compounds of interest from the low mass region suffering high interference to the high mass region where interference with low mass components is absent. Experimental results demonstrate that a wide range of LMW compounds, including carboxylic acids, aldehydes, amines, thiol, and cis-diols, can be successfully detected using the proposed strategy, and the limits of detection were in the range of 0.01-1.76 nmol/mL. In addition, the high selectivity of the labeling reagents for the target analytes in conjunction with the high selectivity of the binding between the labeled products and CB [n] ensures an absence of signal interference with the non-targeted LMW components of complex samples. Finally, the feasibility of the proposed strategy for complex sample analysis is demonstrated by the accurate and rapid quantitative analysis of aldehydes in saliva and herbal medicines. As such, this work not only provides an alternative method for the detection of various LMW compounds using MALDI MS, but also can be applied to the selective and high-throughput analysis of LMW analytes in complex samples.

Neuropeptidomics of the Rat Habenular Nuclei

Conserved across vertebrates, the habenular nuclei are a pair of small symmetrical structures in the epithalamus. The nuclei functionally link the forebrain and midbrain by receiving input from and projecting to several brain regions. Each habenular nucleus comprises two major asymmetrical subnuclei, the medial and lateral habenula. These subnuclei are associated with different physiological processes and disorders, such as depression, nicotine addiction, and encoding aversive stimuli or omitting expected rewarding stimuli. Elucidating the functions of the habenular nuclei at the molecular level requires knowledge of their neuropeptide complement. In this work, three mass spectrometry (MS) techniques-liquid chromatography (LC) coupled to Orbitrap tandem MS (MS/MS), LC coupled to Fourier transform (FT)-ion cyclotron resonance (ICR) MS/MS, and matrix-assisted laser desorption/ionization (MALDI) FT-ICR MS-were used to uncover the neuropeptide profiles of the rodent medial and lateral habenula. With the assistance of tissue stabilization and bioinformatics, a total of 262 and 177 neuropeptides produced from 27 and 20 prohormones were detected and identified from the medial and lateral habenula regions, respectively. Among these neuropeptides, 136 were exclusively found in the medial habenula, and 51 were exclusively expressed in the lateral habenula. Additionally, novel sites of sulfation, a rare post-translational modification, on the secretogranin I prohormone are identified. The results demonstrate that these two small brain nuclei have a rich and differentiated peptide repertoire, with this information enabling a range of follow-up studies.

The quest for improved reproducibility in MALDI mass spectrometry

Reproducibility has been one of the biggest hurdles faced when attempting to develop quantitative protocols for MALDI mass spectrometry. The heterogeneous nature of sample recrystallization has made automated sample acquisition somewhat "hit and miss" with manual intervention needed to ensure that all sample spots have been analyzed. In this review, we explore the last 30 years of literature and anecdotal evidence that has attempted to address and improve reproducibility in MALDI MS. Though many methods have been attempted, we have discovered a significant publication history surrounding the use of nitrocellulose as a substrate to improve homogeneity of crystal formation and therefore reproducibility. We therefore propose that this is the most promising avenue of research for developing a comprehensive and universal preparation protocol for quantitative MALDI MS analysis. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:217-228, 2018.

Mass Spectrometry of Gangliosides

This chapter describes protocols for mass spectrometry (MS) applied to the characterization of ganglioside structures and the determination of ganglioside contents. Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) are often used to ionize biological materials and this chapter covers three protocols for atmospheric pressure MALDI MS (AP-MALDI MS), liquid chromatography-ESI MS (LC-ESI MS), and LC-ESI MS with multiple reaction monitoring (MRM). Purified gangliosides were used in AP-MALDI MS analyses while crude preparations of gangliosides were subjected to LC-ESI MS and LC-ESI MS with MRM. The LC protocol includes conditions for both reversed-phase and normal-phase column chromatography.

CSF N-Glycomics Using MALDI MS Techniques in Alzheimer's Disease

In this chapter, we present the methodology currently applied in our laboratory for the structural elucidation of the cerebrospinal fluid (CSF) N-glycome. N-glycans are released from denatured carboxymethylated glycoproteins by digestion with peptide-N-glycosidase F (PNGase F) and purified using both C18 Sep-Pak^® and porous graphitized carbon (PGC) HyperSep™ Hypercarb™ solid-phase extraction (SPE) cartridges. The glycan pool is subsequently permethylated to increase mass spectrometry sensitivity. Molecular assignments are performed through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) analysis considering either the protein N-linked glycosylation pathway or MALDI TOF MS/MS data. Each stage has been optimized to obtain high-quality mass spectra in reflector mode with an optimal signal-to-noise ratio up to m/z 4800. This method has been successfully adopted to associate specific N-glycome profiles to the early and the advanced phases of Alzheimer's disease.

Preliminary study of mechanism of action of SN38 derivatives. Physicochemical data, evidence of interaction and alkylation of DNA octamer d(GCGATCGC)2

The synthesis of water-soluble SN38 derivatives is presented, and their stability in solutions used during drug development studies has been investigated. A preliminary study of mechanism of action of 9-aminomethyl SN38 is presented. Using NMR techniques, the interaction of the oligomer d(GCGATCGC)₂ is studied, showing that the terminal GC base pairs are the main site of interaction. Using pulsed field gradient spin echo and mass spectroscopy, evidence of a spontaneous alkylation reaction of the DNA oligomer with SN38 derivatives is presented. A proposed mechanism of reaction is suggested. Copyright © 2016 John Wiley & Sons, Ltd.

Immune-enrichment of insulin in bio-fluids on gold-nanoparticle decorated target plate and in situ detection by MALDI MS

BACKGROUND

Detection of low-abundance biomarkers using mass spectrometry (MS) is often hampered by non-target molecules in biological fluids. In addition, current procedures for sample preparation increase sample consumption and limit analysis throughput. Here, a simple strategy is proposed to construct an antibody-modified target plate for high-sensitivity MS detection of target markers such as insulin, in biological fluids.

METHODS

The target plate was first modified with gold nanoparticle, and then functionalized with corresponding antibody through chemical conjugation. Clinical specimens were incubated onto these antibody-functionalized target plates, and then subjected to matrix assisted laser desorption ionization mass spectrometry analysis.

RESULTS

Insulin in samples was enriched specifically on this functional plate. The detection just required low-volume samples (lower than 5 µL) and simplified handling process (within 40 min). This method exhibited high sensitivity (limit of detection in standard samples, 0.8 nM) and good linear correlation of MS intensity with insulin concentration (R² = 0.994). More importantly, insulin present in real biological fluids such as human serum and cell lysate could be detected directly by using this functional target plate without additional sample preparations.

CONCLUSIONS

Our method is easy to manipulate, cost-effective, and with a potential to be applied in the field of clinical biomarker detection.

A comparison of PC oxidation products as detected by MALDI-TOF and ESI-IT mass spectrometry

Oxidized (phospho)lipids are of paramount interest for different reasons: besides their in vivo relevance as markers of inflammatory diseases, they are often needed in the laboratory to study the response of selected cells to oxidized lipids. Mass spectrometry (MS) is nowadays one of the most powerful methods to identify lipid oxidation products. Although MALDI and ESI MS are both widely used, it is so far not clear whether all potential phospholipid oxidation products can be detected by both methods This aspect will be studied here using NaMnO₄-oxidized phosphatidylcholine 16:0/18:1 and 16:0/18:2 as simple, but reliable model systems. We will show that chain-shortened products such as aldehydes and carboxylic acids (generated by cleavage at the double bond position) can be easily detected by both ionization methods: without the need of any derivatization. However, primary oxidation products such as hydroperoxides can be predominantly detected by ESI MS while MALDI-TOF MS detects secondary oxidation products derived thereof more sensitively. Potential reasons for these differences will be discussed and put in the context of biological mixture analysis.

MALDI Mass Spectrometry Profiling and Imaging Applied to the Analysis of Latent Fingermarks

Latent fingermarks are derived from a transfer of material from the fingertips to a surface upon contact. Traditionally, fingermarks are employed for biometric identification of individuals based on matching of the pattern of the ridges. However, in recent years, there has been a stark increase in the use of advanced analytical techniques in order to obtain additional information, specifically the chemical composition of the residue. Understanding the complexity of the endogenous and exogenous content of fingermarks could be extremely useful in allowing further development of enhancement techniques currently used in forensic scenarios by identifying potential target molecules. This chemical information could also potentially provide invaluable information on the lifestyle of an individual, including their activities prior to depositing a mark.An analytical tool that has gained notable popularity in this novel area of research is matrix-assisted laser desorption/ionisation mass spectrometry (MALDI MS). This technique can either be employed for rapid chemical profiling or imaging of fingermarks to detect chemical species contained within the residue, with the latter also allowing for physical reconstruction of the fingermark ridges.This chapter will provide an overview of the protocols employed to allow for both MALDI MS profiling and imaging analysis of latent fingermarks, specifically covering the types of fingermarks employed and techniques used to deposit matrices onto samples.

Mesoporous silica chip: enabled peptide profiling as an effective platform for controlling bio-sample quality and optimizing handling procedure

Background

High quality clinical samples are critical for meaningful interpretation of data obtained in both basic and translational medicine. More specifically, optimized pre-analysis handling to bio-sample is crucial for avoiding biased analysis in a clinical setting. A universally applicable method for the evaluation of sample quality and pre-analysis handling is therefore in great demand.

Methods

The fingerprint pattern of low molecular weight (LMW) peptides in sera is directly associated with sample quality and handling process. Previous studies for enrichment/isolation of LMW peptides have shown that LMW peptides can be enriched by silica meso-porous material in a sensitive and high-throughput manner. Here, a peptide profile approach utilizing mesoporous silica chip-based sample preparation combined with MALDI MS analysis was used as a new platform for evaluation of bio-sample quality. Rat sera were selected as model sample and analyzed according to their LMW peptide fingerprint spectra.

Results

This novel method can complete the entire sample preparation procedure in a short period of time (<40 min), requires minimum amounts of sample (<10 µL), is of high sensitivity (LOD 10 ng/mL) as well as high reproducibility (CV% < 15%). According to the acquired LMW peptide spectra, we were able to distinguish the serum samples processed under different conditions (including different storage temperature, time, and freezing/thaw cycles) with the help of bioinformatics tools (principle composition analysis and significant difference analysis), and identify the samples that had significantly changed due to the inappropriate processing. Based on the percentage of significantly changed peaks in LMW peptide mass spectrum after handling, a judgment standard was established that can be used to evaluate the status of preservation of a biological sample. In addition, our principle study established recommendations for storage time, storage temperature and freeze/thaw conditions.

Conclusion

Our novel method for analysis of bio-samples allows for effective identification of variations in composition within samples, and provides a cost-effective tool for simple sample manipulation in a clinical setting.

Carbon Dots and 9AA as a Binary Matrix for the Detection of Small Molecules by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Application of matrix-assisted laser-desorption/ionization mass spectrometry (MALDI MS) to analyze small molecules have some limitations, due to the inhomogeneous analyte/matrix co-crystallization and interference of matrix-related peaks in low m/z region. In this work, carbon dots (CDs) were for the first time applied as a binary matrix with 9-Aminoacridine (9AA) in MALDI MS for small molecules analysis. By 9AA/CDs assisted desorption/ionization (D/I) process, a wide range of small molecules, including nucleosides, amino acids, oligosaccharides, peptides, and anticancer drugs with a higher sensitivity were demonstrated in the positive ion mode. A detection limit down to 5 fmol was achieved for cytidine. 9AA/CDs matrix also exhibited excellent reproducibility compared with 9AA matrix. Moreover, by exploring the ionization mechanism of the matrix, the influence factors might be attributed to the four parts: (1) the strong UV absorption of 9AA/CDs due to their π-conjugated network; (2) the carboxyl groups modified on the CDs surface act as protonation sites for proton transfer in positive ion mode; (3) the thin layer crystal of 9AA/CDs could reach a high surface temperature more easily and lower transfer energy for LDI MS; (4) CDs could serve as a matrix additive to suppress 9AA ionization. Furthermore, this matrix was allowed for the analysis of glucose as well as nucleosides in human urine, and the level of cytidine was quantified with a linear range of 0.05-5 mM (R(2) > 0.99). Therefore, the 9AA/CDs matrix was proven to be an effective MALDI matrix for the analysis of small molecules with improved sensitivity and reproducibility. This work provides an alternative solution for small molecules detection that can be further used in complex samples analysis. Graphical Abstract ᅟ.

Platelet proteomics in thalassemia: Factors responsible for hypercoagulation

PURPOSE

Thalassemias can be defined as a group with inherited hemolytic anemia due to differential expressions of α and β globin genes. Hemoglobin E combined with β thalassemia (HbEβ) creates high oxidative stress in platelets producing different degrees of pathophysiological severity. Numerous cases of thalassemia have been reported with thromboembolic complications due to the hypercoagulable state, the mechanism underlying that is not yet well understood.

EXPERIMENTAL DESIGN

We have used 2DE and DIGE coupled with MALDI TOF/TOF-based MS identification and characterization of altered proteins in both splenectomized and nonsplenectomized HbEβ and β thalassemia to investigate the factors responsible for hypercoagulation.

RESULTS

The study revealed elevated levels of chaperones like HSP70, protein disulfide isomerase; oxidative stress proteins like peroxiredoxin2 and superoxide dismutase1 along with high ROS levels. Upregulation of translation initiation factor 5a observed in thalassemia is a novel finding and plays a protective role toward cell survival under oxidative stress.

CONCLUSIONS AND CLINICAL RELEVANCE

The altered levels of chaperones and oxidative stress proteins indicate toward regulation of integrin binding and platelet activation under oxidative stress. Altogether, this comparative proteomics study of platelets in thalassemia could provide an insight into better understanding of the pathophysiology of the disease.

Proteomics analysis of malignant and benign prostate tissue by 2D DIGE/MS reveals new insights into proteins involved in prostate cancer

BACKGROUND

The key to a more effective diagnosis, prognosis, and therapeutic management of prostate cancer (PCa) could lie in the direct analysis of cancer tissue. In this study, by comparative proteomics analysis of PCa and benign prostate hyperplasia (BPH) tissues we attempted to elucidate the proteins and regulatory pathways involved in this disease.

METHODS

The samples used in this study were fresh surgical tissues with clinically and histologically confirmed PCa (n = 19) and BPH (n = 33). We used two dimensional difference in gel electrophoresis (2D DIGE) coupled with mass spectrometry (MS) and bioinformatics analysis.

RESULTS

Thirty-nine spots with statistically significant 1.8-fold variation or more in abundance, corresponding to 28 proteins were identified. The IPA analysis pointed out to 3 possible networks regulated within MAPK, ERK, TGFB1, and ubiquitin pathways. Thirteen of the identified proteins, namely, constituents of the intermediate filaments (KRT8, KRT18, DES), potential tumor suppressors (ARHGAP1, AZGP1, GSTM2, and MFAP4), transport and membrane organization proteins (FABP5, GC, and EHD2), chaperons (FKBP4 and HSPD1) and known cancer marker (NME1) have been associated with prostate and other cancers by numerous proteomics, genomics or functional studies. We evidenced for the first time the dysregulation of 9 proteins (CSNK1A1, ARID5B, LYPLA1, PSMB6, RABEP1, TALDO1, UBE2N, PPP1CB, and SERPINB1) that may have role in PCa. The UBE2N, PSMB6, and PPP1CB, involved in cell cycle regulation and progression were evaluated by Western blot analysis which confirmed significantly higher abundances of UBE2N and PSMB6 and significantly lower abundance of PPP1CB in PCa.

CONCLUSION

In addition to the identification of substantial number of proteins with known association with PCa, the proteomic approach in this study revealed proteins not previously clearly related to PCa, providing a starting point for further elucidation of their function in disease initiation and progression.

A simple method to generate oxidized phosphatidylcholines in amounts close to one milligram

Oxidized (phospho)lipids are of paramount interest from different reasons: beside their significant in vivo relevance, these products are often needed in the laboratory to study the response of selected cells to oxidized lipids. Unfortunately, the commercial availability of oxidized lipids is limited and scientists interested in studying the physiological impact of oxidized lipids are normally forced to prepare the required compounds by themselves. We will show here that chain-shortened products of oxidized phosphatidylcholines (PCs) such as aldehydes and carboxylic acids can be easily (and in nearly quantitative yields) generated by the Fenton reaction (H2O2+Fe(2+)) or the KMnO4-induced oxidation of the PC. Using the Fenton reaction and physiological saline, chlorinated oxidation products such as chlorohydrins are also readily available. Additionally, it will be shown that preparative thin-layer chromatography (TLC) is a convenient but simple method to isolate the individual oxidation products in reasonable yields and high purities: all relevant products could be successfully identified by matrix-assisted laser desorption and ionization (MALDI) mass spectrometry and the amounts of the oxidized products determined by a simple colorimetric assay.

MALDI MS profiling of post-DRE urine samples highlights the potential of β-microseminoprotein as a marker for prostatic diseases

BACKGROUND

To use spectra acquired by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) from pre- and post-digital rectal examination (DRE) urine samples to search for discriminating peaks that can adequately distinguish between benign and malignant prostate conditions, and identify the peaks' underlying biomolecules.

METHODS

Twenty-five participants with prostate cancer (PCa) and 27 participants with a variety of benign prostatic conditions as confirmed by a 10-core tissue biopsy were included. Pre- and post-DRE urine samples were prepared for MALDI MS profiling using an automated clean-up procedure. Following mass spectra collection and processing, peak mass and intensity were extracted and subjected to statistical analysis to identify peaks capable of distinguishing between benign and cancer. Logistic regression was used to combine markers to create a sensitive and specific test.

RESULTS

A peak at m/z 10,760 was identified as β-microseminoprotein (β-MSMB) and found to be statistically lower in urine from PCa participants using the peak's average areas. By combining serum prostate-specific antigen (PSA) levels with MALDI MS-measured β-MSMB levels, optimum threshold values obtained from Receiver Operator characteristics curves gave an increased sensitivity of 96% at a specificity of 26%.

CONCLUSIONS

These results demonstrate that with a simple sample clean-up followed by MALDI MS profiling, significant differences of MSMB abundance were found in post-DRE urine samples. In combination with PSA serum levels, obtained from a classic clinical assay led to high classification accuracy for PCa in the studied sample set. Our results need to be validated in a larger multicenter prospective randomized clinical trial.

Ag44(SeR)30: A Hollow Cage Silver Cluster with Selenolate Protection

Selenolate protected, stable and atomically precise, hollow silver cluster was synthesized using solid state as well as solution state routes. The optical absorption spectrum shows multiple and sharp features similar to the thiolated Ag44 cluster, Ag44(SR)30 whose experimental structure was reported recently. High-resolution electrospray ionization mass spectrometry (HRESI MS) shows well-defined molecular ion features with two, three, and four ions with isotopic resolution, due to Ag44(SePh)30. Additional characterization with diverse tools confirmed the composition. The closed-shell 18 electron superatom electronic structure, analogous to Ag44(SR)30 stabilizes the dodecahedral cage with a large HOMO-LUMO gap of 0.71 eV. The time-dependent density functional theory (TDDFT) prediction of the optical absorption spectrum, assuming the Ag44(SR)30 structure, matches the experimental data, confirming the structure.

MALDI mass spectrometry in prostate cancer biomarker discovery

Matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry (MS) is a highly versatile and sensitive analytical technique, which is known for its soft ionisation of biomolecules such as peptides and proteins. Generally, MALDI MS analysis requires little sample preparation, and in some cases like MS profiling it can be automated through the use of robotic liquid-handling systems. For more than a decade now, MALDI MS has been extensively utilised in the search for biomarkers that could aid clinicians in diagnosis, prognosis, and treatment decision making. This review examines the various MALDI-based MS techniques like MS imaging, MS profiling and proteomics in-depth analysis where MALDI MS follows fractionation and separation methods such as gel electrophoresis, and how these have contributed to prostate cancer biomarker research. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.

Modified MALDI MS fatty acid profiling for bacterial identification

Bacterial fatty acid profiling is a well-established technique for bacterial identification. Ten bacteria were analyzed using both positive- and negative-ion modes with a modified matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) approach using CaO as a matrix replacement (metal oxide laser ionization MS (MOLI MS)). The results show that reproducible lipid cleavage similar to thermal in situ tetramethyl ammonium hydroxide saponification/derivatization had occurred. Principal component analysis showed that replicates from each organism grouped in a unique space. Cross validation (CV) of spectra from both ionization modes resulted in greater than 94% validation of the data. When CV results were compared for the two ionization modes, negative-ion data produced a superior outcome. MOLI MS provides clinicians a rapid, reproducible and cost-effective bacterial diagnostic tool.