A strategy for examining complex mixtures of deoxyoligonucleotides using ion-pair-reverse-phase high-performance liquid chromatography,matrix-assisted laser desorption ionization time-of-flight mass spectrometry,and informatics

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and ion-pair-reverse-phase high-performance liquid chromatography (IP-RP HPLC) techniques were combined to determine the sequence identity of short single-stranded deoxyoligonucleotides. This methodology is demonstrated using a commercially available multiplex set of eight primer pairs. The primer pairs were separated and collected by IP-RP HPLC. Partial sequence information for IP-RP HPLC fractions was obtained from analyzing exonuclease digestion products by MALDI-TOF MS. IP-RP HPLC, MALDI-TOF MS, exonuclease digests, and a simple computational algorithm provide an integrated strategy for determining the sequence of short nucleic acid oligomers.     

Rapid identification of acetic acid bacteria using MALDI-TOF mass spectrometry fingerprinting

Acetic acid bacteria (AAB) are widespread microorganisms characterized by their ability to transform alcohols and sugar-alcohols into their corresponding organic acids. The suitability of matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS) for the identification of cultured AAB involved in the industrial production of vinegar was evaluated on 64 reference strains from the genera Acetobacter, Gluconacetobacter and Gluconobacter. Analysis of MS spectra obtained from single colonies of these strains confirmed their basic classification based on comparative 16S rRNA gene sequence analysis. MALDI-TOF analyses of isolates from vinegar cross-checked by comparative sequence analysis of 16S rRNA gene fragments allowed AAB to be identified, and it was possible to differentiate them from mixed cultures and non-AAB. The results showed that MALDI-TOF MS analysis was a rapid and reliable method for the clustering and identification of AAB species.     

Laccase-catalyzed polymerization of two phenolic compounds studied by matrix-assisted laser desorption/ionization time-of-flight and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry with collision-induced dissociation experiments

Enzymatic oxidation of two phenolic compounds [syringic acid (3,5-dimethoxy-4-hydroxybenzoic acid) and 2,6-dimethylphenol] was studied. The products of laccase- and laccase-mediator-catalyzed oxidation reactions were monitored by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and further analyzed by electrospray ionization Fourier transform ion cyclotron resonance (ESI-FTICR) MS with collision-induced dissociation (CID) experiments. For the oligomers of syringic acid, some variability was observed in MALDI-TOF analysis. However, the origin of this variability could not be resolved on the basis of MALDI-TOF spectra due to the poor resolution of the instrument in use. The strength of ESI-FTICR MS was the high-resolution data provided from oligomers of syringic acid. The CID experiments were extremely useful for structural studies of oligomers and verified that the variability of the products was due to the end groups; the phenolic hydroxyl group was modified during the oxidation.     

An analytical system for the characterization of highly heterogeneous mixtures of N-linked oligosaccharides

A novel system for characterizing complex N-linked oligosaccharide mixtures that uses a combination of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), capillary electrophoresis (CE), and high-performance liquid chromatography (HPLC) has been developed. In this study, oligosaccharides released from recombinant TNK-tPA (tissue plasminogen activator) were derivatized with 5-amino-2-naphthalenesulfonic acid (ANSA). The negative charge imparted by the ANSA label facilitated the analysis of the oligosaccharides by MALDI-TOF MS by allowing the observation of both neutral and sialylated oligosaccharides in a single negative ion mode spectrum. Labeling with ANSA was also determined to be advantageous in the characterization of oligosaccharides by both HPLC and CE. The ANSA label was demonstrated to provide superior resolution over the commonly used label 8-aminopyrene-1,3,6-trisulfonic acid (APTS) in both the CE and HPLC analysis of oligosaccharides. To date, no other labels that enable the analysis of complex oligosaccharide mixtures in a single mass spectral mode, while also enabling high-resolution chromatographic and electrophoretic separation of the oligosaccharides, have been reported. By integrating the structural information obtained by MALDI-TOF MS analysis with the ability of CE and HPLC to discriminate between structural isomers, the complete characterization of complex oligosaccharide mixtures is possible.     

Biological investigations on macro-morphological characteristics,polyphenolic acids,antioxidant activity of Perilla frutescens (L) Britt. grown under open field

Perilla frutescens, perilla is a functional food, spice and medicinal herb and ornamental plant in the family of Lamiaceae. Thus, macro-morphological characteristics, phenolic acids, antioxidants of twelve accessions of P. frutescens grown under open field were studied. High polymorphism was found among the perilla accessions and macroscopic features of perilla genotypes showed variable results. Perilla can be classified into two clearly phenotypes green and purple, within these two other colours were appeared. A good level of biomass production was recorded for JTD3, 203P, PS2, 203P respectively. Principal component analysis was performed to cluster phenolic acids. GB phenotype exhibited the major content of polyphenols, followed by JTD3 then J1. Regarding antioxidant capacity, JTD3 showed the highest value followed by 203P and GB respectively. The HPLC analysis showed that the most abundant phenolic acids were ellagic acid which is accumulated in a higher percentage in NP606, 588P and JTD3 cultivars respectively, followed by salicylic acid and gallic acid. This is the first report of cultivation of various Perilla varieties under open field environmental conditions, not only to increase productivity but also to improve the quality. Therefore, the present study results confirm the importance of the Perilla species for human consumption, therapeutic and ornamental purposes.     

Metabolic profiling and antioxidant activity during flower development in Agastache rugosa

Our previous study showed that flowers of Agastache rugosa had higher phenolic levels and higher antibacterial and antioxidant capacity compared to those of the leaves and stems. The aim of this study was to provide information on the variation in primary and secondary metabolites during flower development in A. rugosa by using high performance liquid chromatography (HPLC) and assays of total anthocyanin (TAC), flavonoid (TFC), and phenolic content (TPC), as well as gas chromatography time-of-flight mass spectrometry (GC-TOFMS) analysis. Assays of TPC, TAC, and TFC showed that the floral bud (stage I) contained higher TPC than did the partially open flower (stage II) and fully open flower (stage III). However, the TFC was the highest at stage II, and the highest TAC was observed at stage III. Furthermore, HPLC analysis revealed that the level of total phenylpropanoids, including rosmarinic acid, tilianin, acacetin, 4-hydroxybenzoic acid, caffeic acid, chlorogenic acid, trans-cinnamic acid, rutin, (-)-epicatechin, quercetin, and kaempferol, was higher in stages I and II, but the concentrations of rutin and rosmarinic acid were highest in stage III. A total of 43 compounds, including amino acids, organic acids, phenolic compounds, sugars, photorespiration-related compounds, and intermediates of the tricarboxylic acid cycle, were identified through GC-TOFMS analysis. Of these compounds, most amino acids decreased during flower development. In contrast, the increase in concentrations of glucose and sucrose were observed from stages I to III. In this study, health-beneficial compounds were identified and quantified in flowers of A. rugosa. Accordingly, our results suggests that A. rugosa flowers can potentially be used as biomaterials for pharmaceuticals, cosmetics, food, and related industries.Supplementary informationThe online version contains supplementary material available at (10.1007/s12298-021-00945-z).     

MALDI-TOF MS analysis of the extracellular polysaccharides released by the diatom Thalassiosira pseudonana

The extracellular polysaccharides (ECPS) released by diatoms have significant roles in marine ecosystems and have potential applications including drug-discovery and biopharmaceutical precursors. In this study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technology was used in the structural analysis of the ECPS released by Thalassiosira pseudonana (Bacillariophyta). Three different deproteinization methods, the Sevag method, the trichloroacetic acid (TCA) method, and the enzymolysis method, were compared in the purification of ECPS. Our results suggested that TCA was the best deproteinization method among the three methods for subsequent MALDI-TOF MS investigation because of its high ECPS yield, protein removal ability and reliable MALDI-TOF MS fingerprint. The degree of polymerization (d.p.) profiles, the molecular weight of the ECPS and the distribution pattern of the polymers with different molecular mass were described from the MALDI-TOF MS spectra. This work represents the whole-level composition of the ECPS released by the diatom and has improved our knowledge of the structural characterization of ECPS.     

Athenolide A,a New Steroidal Lactone from the Leaves of Athenaea martiana (Solanaceae) Determined by Means of HPLC‐HR‐MS‐SPE‐NMR Analysis

Athenaea (Solanaceae) is an endemic genus belonging to the Brazilian Atlantic Rainforest. Recently, botanical investigations suggested the re‐evaluation of the generic status of the genus Athenaea as a synonym of Aureliana. In this study, the first investigation of the Athenaea genus performed on Athenaea martiana by means of HPLC‐HR‐MS‐SPE‐NMR combined with high‐resolution radical scavenging profile led to identification of several phenolic acids as radical scavengers: protocatechuic acid ( 1 ), 4‐hydroxybenzoic acid ( 2 ), caffeic acid ( 3 ), vanillic acid ( 4 ), and ferulic acid ( 6 ). Additional analysis revealed a new steroidal lactone, named athenolide A ( 9 ). Their structures were elucidated by extensive use of NMR spectroscopy as well as HR‐MS. Chemotaxonomic considerations based on these results supported the chemical relationships between the Athenaea and Aureliana genera, in agreement with the recent botanical findings.     

Chemosystematics of taxa from the Leontodon section Oporinia

A chemosystematic study of the subgenus Oporinia of the genus Leontodon (Asteraceae) was performed, using flavonoids and phenolic acids in the flowerheads as diagnostic characters. A total of 44 samples from nine different Oporinia taxa were analyzed. Five luteolin-derivatives (luteolin, luteolin 7-O-β-d-gentiobioside, luteolin 7-O-β-d-glucoside, luteolin 7-O-β-d-glucuronide, and luteolin 4′-O-β-d-glucoside) and four caffeic acid derivatives (caffeoyl tartaric acid, chlorogenic acid, cichoric acid, and 3,5-dicaffeoylquinic acid) were identified in crude extracts by means of HPLC retention times, on-line UV spectra and on-line MS spectra. Quantification of these compounds was performed by HPLC, using quercetin as internal standard. The data obtained were processed by Principal Component Analysis, resulting in the formation of five different clusters. These clusters were taxonomically interpretable and are in good agreement with the morphologically based system of the genus Leontodon.     

Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry for Identification of Microorganisms in Clinical Urine Specimens after Two Pretreatments

Rapid identification of microorganisms in urine is essential for patients with urinary tract infections (UTIs). Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been proposed as a method for the direct identification of urinary pathogens. Our purpose was to compare centrifugation-based MALDI-TOF MS and short-term culture combined with MALDI-TOF MS for the direct identification of pathogens in urine specimens. We collected 965 urine specimens from patients with suspected UTIs, 211/965 isolates were identified as positive by conventional urine culture. Compared with the conventional method, the results of centrifugation-based MALDI-TOF MS were consistent in 159/211 cases (75.4%), of which 135/159 (84.9%) had scores ≥ 2.00; 182/211 cases (86.3%) were detected using short-term culture combined with MALDI-TOF MS, of which 153/182 (84.1%) had scores ≥ 2.00. There were no apparent differences among the three methods (p = 0.135). MALDI-TOF MS appears to accelerate the microbial identification speed in urine and saves at least 24 to 48 hours compared with the routine urine culture. Centrifugation-based MALDI-TOF MS is characterized by faster identification speed; however, it is substantially affected by the number of bacterial colonies. In contrast, short-term culture combined with MALDI-TOF MS has a higher detection rate but a relatively slow identification speed. Combining these characteristics, the two methods may be effective and reliable alternatives to traditional urine culture.     

A relative and absolute quantification of neutral N-linked oligosaccharides using modification with carboxymethyl trimethylammonium hydrazide and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Quantification of oligosaccharides is of great importance to investigate variations or changes in the glycans of glycoconjugates. Mass spectrometry (MS) has been widely applied to identification and structural analysis of complex oligosaccharides. However, quantification using MS alone is still quite challenging due to heterogeneous charge states and different ionization efficiency of various types of oligosaccharides. To overcome such shortcomings, derivatization with carboxymethyl trimethylammonium hydrazide (Girard’s reagent T [GT]) was introduced to generate a permanent cationic charge at the reducing end of neutral oligosaccharides, resulting in mainly [M]⁺ ion using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), so that the ambiguities caused by metal adduct peaks such as [M+K]⁺ and [M + Na]⁺ were avoided. To verify our method, the relative and absolute quantification of neutral glycans from human immunoglobulin G (IgG) and ovalbumin with internal standards of dextran ladders using MALDI-TOF MS were compared with those performed by conventional normal-phase high-performance liquid chromatography (NP-HPLC) profiling. The quantification using GT derivatization and MALDI-TOF MS agreed well with the HPLC profiling data and showed excellent reliability and reproducibility with better resolution and sensitivity. This method was further applied to quantify the enzymatically desialylated N-glycans from miniature pig kidney membrane proteins. The results showed that the low-abundance structures that could not be resolved by NP-HPLC were quantified with high sensitivity. Thus, this novel method of using modification of neutral sugars with GT is quite powerful for neutral glycan analysis, especially to quantify minute glycan samples with undetectable levels using HPLC.     

Combining various strategies to increase the coverage of the plant cell wall glycoproteome

Glycoproteomics recently became a very active field, mostly in mammals. The first part of this paper consists of a mini-review on the strategies used in glycoproteomics, namely methods for enrichment in glycoproteins and mass spectrometry (MS) techniques currently used. In a second part, these strategies are applied to the cell wall glycoproteome of etiolated hypocotyls of Arabidopsis thaliana, showing their complementarity. Several sub-glycoproteomes were obtained by: (i) affinity chromatography on concanavaline A (ConA) and analysis of glycoproteins by MALDI-TOF MS; (ii) multidimensional lectin chromatography (using AIL, PNA, ConA and WGA lectins) and subsequent identification of glycoproteins by MALDI-TOF MS and LC-MS/MS; (iii) boronic acid chromatography followed by identification of glycoproteins by MALDI-TOF MS. Altogether, 127 glycoproteins were identified. Most glycoproteins were found to be putative N-glycoproteins and N-glycopeptides were predicted from MS data using the ProTerNyc bioinformatics software.     

Tea prepared from Anastatica hirerochuntica seeds contains a diversity of antioxidant flavonoids, chlorogenic acids and phenolic compounds

HPLC-PDA-MS(2) was used to identify phenolic and polyphenolic compounds in an herbal tea made from seeds of Anastatica hirerochuntica, a plant found in the Sahara-Arabian deserts and used to treat a variety of ailments. Twenty compounds comprising a series of flavone C- and O-linked glycosides, phenolic acids, chlorogenic acids and flavonols were identified or partially identified on the basis of co-chromatography with reference compounds and MS(2) and MS(3) fragmentation patterns. The flavones were the principal components, occurring as luteolin, apigenin and diosmetin conjugates. The antioxidant potential of individual compounds in Anastatica was assessed using HPLC with an on-line ABTS·(+) detection system. This revealed that 14 compounds exhibited antioxidant activity. The highest contribution to the antioxidant capacity of the tea, 56%, came from 3,4-dihydroxybenzoic acid and caffeoyl- and dicaffeoylquinic acids while 6-C-glucosides of luteolin and apigenin contributed 41%.     

Cestric acid,a caffeic acid ester from Cestrum euanthes

Cestric acid, a new phenolic ester was isolated from leaves of Cestrum euanthes. By means of GC, HPLC, mass spectroscopy, GC/MS, and ¹³C NMR, it was shown to be an ester of caffeic acid with glucaric acid. The ester occurs as an equilibrium mixture of four isomers.     

Differentiation of species of the Streptococcus bovis/equinus-complex by MALDI-TOF Mass Spectrometry in comparison to sodA sequence analyses

The Streptococcus bovis/equinus complex is a heterogeneous group within the group D streptococci with important clinical relevance regarding infective endocarditis, sepsis and colon carcinoma. The taxonomic identification of species and sub-species of this complex, by the standard methods remains difficult.In the present study, we compared the cluster analysis of 88 strains of species of the S. bovis/equinus complex by sequence analysis of the manganese-dependent superoxide dismutase gene (sodA) and by Matrix Assisted Laser Desorption/Ionization-Time Of Flight Mass Spectrometry (MALDI-TOF MS). We observed a high congruence of strain grouping by MALDI-TOF MS in comparison with sodA sequence analyses, demonstrating the accuracy and reliability of MALDI-TOF MS in comparison to DNA sequence-based method.By generating mass spectra for each species and sub-species, we were able to discriminate all members of the S. bovis/equinus complex. Furthermore, we demonstrated reliable identifications to the species level by MALDI-TOF MS, independently of cultivation conditions.     

Comparison of the phenolic composition of fruit juices by single step gradient HPLC analysis of multiple components versus multiple chromatographic runs optimised for individual families

After minimal sample preparation, two different HPLC methodologies, one based on a single gradient reversed-phase HPLC step, the other on multiple HPLC runs each optimised for specific components, were used to investigate the composition of flavonoids and phenolic acids in apple and tomato juices. The principal components in apple juice were identified as chlorogenic acid, phloridzin, caffeic acid and p-coumaric acid. Tomato juice was found to contain chlorogenic acid, caffeic acid, p-coumaric acid, naringenin and rutin. The quantitative estimates of the levels of these compounds, obtained with the two HPLC procedures, were very similar, demonstrating that either method can be used to analyse accurately the phenolic components of apple and tomato juices. Chlorogenic acid in tomato juice was the only component not fully resolved in the single run study and the multiple run analysis prior to enzyme treatment. The single run system of analysis is recommended for the initial investigation of plant phenolics and the multiple run approach for analyses where chromatographic resolution requires improvement.     

MALDI-TOF mass spectrometry for the identification of freshwater snails from Senegal,including intermediate hosts of schistosomes

Freshwater snails of the genera Biomphalaria, Bulinus, and Oncomelania are intermediate hosts of schistosomes that cause human schistosomiasis, one of the most significant infectious neglected diseases in the world. Identification of freshwater snails is usually based on morphology and potentially DNA-based methods, but these have many drawbacks that hamper their use. MALDI-TOF MS has revolutionised clinical microbiology and has emerged in the medical entomology field. This study aims to evaluate MALDI-TOF MS profiling for the identification of both frozen and ethanol-stored snail species using protein extracts from different body parts. A total of 530 field specimens belonging to nine species (Biomphalaria pfeifferi, Bulinus forskalii, Bulinus senegalensis, Bulinus truncatus, Bulinus globosus, Bellamya unicolor, Cleopatra bulimoides, Lymnaea natalensis, Melanoides tuberculata) and 89 laboratory-reared specimens, including three species (Bi. pfeifferi, Bu. forskalii, Bu. truncatus) were used for this study. For frozen snails, the feet of 127 field and 74 laboratory-reared specimens were used to validate the optimised MALDI-TOF MS protocol. The spectral analysis yielded intra-species reproducibility and inter-species specificity which resulted in the correct identification of all the specimens in blind queries, with log-score values greater than 1.7. In a second step, we demonstrated that MALDI-TOF MS could also be used to identify ethanol-stored snails using proteins extracted from the foot using a specific database including a large number of ethanol preserved specimens. This study shows for the first time that MALDI-TOF MS is a reliable tool for the rapid identification of frozen and ethanol-stored freshwater snails without any malacological expertise.     

Metabolite profiling of Neptunia oleracea and correlation with antioxidant and α-glucosidase inhibitory activities using 1H NMR-based metabolomics

Neptunia oleracea is a plant consumed as vegetable and used as a traditional herb to treat several ailments. This study evaluated metabolite variations among N. oleracea leaf and stem subjected to air drying (AD), freeze drying (FD) and oven drying (OD) using proton nuclear magnetic resonance (¹H NMR) based metabolomics. The correlation was also studied for the metabolite content with total phenolic content (TPC), DPPH free radical scavenging and α-glucosidase inhibitory activities. A total of 18 metabolites were identified from N. oleracea extracts, including 10 primary metabolites, 5 flavonoids and 3 phenolic acids using NMR. Ultra-high performance liquid chromatography tandem mass spectrometry analysis (UHPLC-MS/MS) confirmed the presence of the secondary metabolites and revealed the flavonoid derivatives present. All the identified phenolics are first reported from this plant. Multivariate data analysis (MVDA) showed strong correlation between the metabolites with the antioxidant and α-glucosidase inhibitory activities of FD N. oleracea leaves. The compounds suggested to be responsible for the high activity of FD leaves include vitexin-2-O-rhamnoside, catechin, caffeic acid, gallic acid and derivatives of quercetin, kaempferol and myricetin. This study demonstrates that FD N. oleracea leaves are a potential natural source for antioxidant and α-glucosidase inhibitors.     

Defensive role of Gossypium hirsutum L. anti-oxidative enzymes and phenolic acids in response to Spodoptera litura F. feeding

The responses of the cotton plant, Gossypium hirsutum L. to herbivory by Spodoptera litura F. was studied in various laboratory experiments as a measure to understand the defense strategies of certain plant metabolites. Insect feeding damage enhanced the concentration of total phenol content and proteins, whereas amount of carbohydrates and amino acids were reduced. The experiments on estimation of anti-oxidative enzymes revealed stimulation in peroxidase, catalase, and superoxide dismutase levels and reduction in polyphenol oxidase and phenylanine ammonia lyase levels, signifying their defensive role in the plant. Specific phenolic acid changes were further carried out using High Performance Liquid Chromatography (HPLC), and distinct elevations in the gallic acid, catechin, and caffeic acid levels were observed in the infested cotton plant. Feeding assays towards S. litura with these phenolic compounds revealed activated detoxifying enzymes including β-glucosidase, carboxyl esterase, and glutathione-S-transferase in the insect gut indicating the toxicity. The aim of present study is to aid in further use of these specific phenolic acids towards effective management of the cotton pest, S. litura.