Molecular characterization of root exudates using Fourier transform ion cyclotron resonance mass spectrometry.

The release of root exudates (REs) provides an important source of soil organic carbon. This work revealed the molecular composition of REs of different plant species including alfalfa (Medicago sativa L.), bean (Phaseolus vulgaris L.), barley (Hordeum vulgare L.), maize (Zea mays), wheat (Triticum aestivum L.), ryegrass (Lolium perenne L.) and pumpkin (Cucurbita maxima) using electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS). The combination of positive ion mode (+ESI) and negative ion mode (-ESI) increased the number of the molecules detected by ESI FT-ICR MS, and a total of 8758 molecules were identified across all the samples. In detail, lipids and proteins and unsaturated hydrocarbons were more easily detected in +ESI mode, while aromatic compounds with high O/C were readily ionized in -ESI mode, and only 38% of the total assigned formulas were shared by -ESI and +ESI modes. Multivariate statistical analysis of the formulas indicated that the close related plants species secreted REs with similar molecular components. Moreover, the unsaturation degree and nitrogen content were the two key parameters able to distinguish the similarities and differences of molecular components of REs between plant species. The results provided a feasible analysis method for characterization of the molecular components of REs and for the first time characterized the molecular components of REs of a variety of plant species using ESI FT-ICR MS.

A boronic acid modified binary matrix consisting of boron nitride and α-cyano-4-hydroxycinnamic acid for determination of cis-diols by MALDI-TOF MS.

A MALDI-TOF mass spectrometric method is described for the determination of small molecule compounds with cis-diol. It is based on the use of a binary matrix consisting of boron nitride (BN) and α-cyano-4-hydroxycinnamic acid that was modified with the derivatization reagent of (3-(acridin-9-ylamino)phenyl)boronic acid which can recognize cis-diols. The binary matrix is used for desorption/ionization (DI) in the positive ion mode. The mechanism leading to DI enhancement was investigated. The results imply that BN is beneficial for the DI because it induces an enhancement in the positive ion mode. The boronic acid-functionalized binary matrix was successfully applied to capture the glucose, shikimic acid and quinic acid. The method was applied to the determination of 3-chloro-1,2-propanediol in plant oil. Graphical abstract Schematic representation of a method for detecting the cis-diol compounds on matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) using the binary matrix of boron nitride (BN)/α-cyano-4-hydroxycinnamic acid (CHCA) that was modified with (3-(acridin-9-ylamino)phenyl) boronic acid (AYPBA).

An HPLC-tandem mass spectrometry method for simultaneous detection of alkylated base excision repair products.

DNA glycosylases excise a broad spectrum of alkylated, oxidized, and deaminated nucleobases from DNA as the initial step in base excision repair. Substrate specificity and base excision activity are typically characterized by monitoring the release of modified nucleobases either from a genomic DNA substrate that has been treated with a modifying agent or from a synthetic oligonucleotide containing a defined lesion of interest. Detection of nucleobases from genomic DNA has traditionally involved HPLC separation and scintillation detection of radiolabeled nucleobases, which in the case of alkylation adducts can be laborious and costly. Here, we describe a mass spectrometry method to simultaneously detect and quantify multiple alkylpurine adducts released from genomic DNA that has been treated with N-methyl-N-nitrosourea (MNU). We illustrate the utility of this method by monitoring the excision of N3-methyladenine (3 mA) and N7-methylguanine (7 mG) by a panel of previously characterized prokaryotic and eukaryotic alkylpurine DNA glycosylases, enabling a comparison of substrate specificity and enzyme activity by various methods. Detailed protocols for these methods, along with preparation of genomic and oligonucleotide alkyl-DNA substrates, are also described.

Analysis of Volatile Esters and Alkanoic Acids by an Atmospheric Pressure Corona Discharge Ionization Collision-Induced Dissociation Mass Spectrometry in Positive-Ion Mode: Ionization, Fragmentation Patterns, and Discrimination between Isomeric Compounds.

The ionization and fragmentation patterns of 24 compounds with elemental composition of CmH2mO2, including isomeric esters and alkanoic acids, were investigated by atmospheric pressure corona discharge ionization collision-induced dissociation (CID) mass spectrometry in the positive-ion mode. All compounds were ionized as protonated molecules and NH4+ adducts. In addition, fragment ions were observed in mass spectra of esters other than methyl esters, which are owing to the dissociation of the alkyl group in the alcohol side from the protonated molecules. In CID spectra, protonated alkanoic acids/methyl esters split off H2O/CH3OH and CO or the alkyl group in the acid side, depending on the carbon chain length. Protonated esters (other than methyl esters) mainly fragmented the alkyl group in the alcohol side. These general rules on ionization and fragmentation patterns can provide relevant information on the discrimination of isomers.

"CORE" a new assay for rapid identification of Klebsiella pneumoniae COlistin REsistant strains by MALDI-TOF MS in positive-ion mode.

Due to the global spread of pan resistant organisms, colistin is actually considered as one of the last resort antibiotics against MDR and XDR bacterial infections. The emergence of colistin resistant strains has been observed worldwide in Gram-negative bacteria, such as Enterobacteriaceae and especially in K. pneumoniae, in association with increased morbidity and mortality. This landscape implies the exploration of novel assays able to target colistin resistant strains rapidly. In this study, we developed and evaluated a new MALDI-TOF MS assay in positive-ion mode that allows quantitative or qualitative discrimination between colistin susceptible (18) or resistant (32) K. pneumoniae strains in 3 h by using the "Autof MS 1000" mass spectrometer. The proposed assay, if integrated in the diagnostic workflow, may be of help for the antimicrobial stewardship and the control of the spread of K. pneumoniae colistin resistant isolates in hospital settings.

A pilot study optimizing metabolomic and lipidomic acquisition in serum for biomarker discovery in nonalcoholic fatty liver disease.

BACKGROUND: The worldwide prevalence of non-alcoholic fatty liver disease (NAFLD) has stimulated work to identify biomarkers and develop effective treatments. Metabolomics is an emerging tool that has been widely applied to discover biomarkers and simultaneously uncover pathological mechanisms. Here, we aim to optimize metabolomic acquisition with the goal of obtaining a systemic metabolic profile to unravel the potential link between dysregulated metabolism and NAFLD. METHODS: We analyzed serum samples collected from healthy subjects (n = 8) and NAFLD patients (n = 8) via an integrative analytical workflow using two orthogonal separation modes with T3 and amide columns and two ionization polarity modes on a UPLC-ESI-Q/TOF. Data dependent acquisition was employed for data acquisition. Differentially expressed metabolites and lipids were identified by comparing the collected metabolic and lipidomic profiles between the healthy subjects and NAFLD patients. RESULTS: The integrative LC-MS/MS analytical workflow employed here features an improved coverage of metabolites and lipids, which leads to the identification of 20 potential biomarkers of NAFLD, including lipids, acylcarnitines, and organic acids. CONCLUSIONS: This pilot study has identified potential biomarkers for NAFLD and revealed corresponding dysregulated metabolic pathways related to NAFLD's occurrence and progression, establishing a molecular basis for NAFLD diagnosis and therapeutic intervention.

Characterization of complex, heterogeneous lipid A samples using HPLC-MS/MS technique III. Positive-ion mode tandem mass spectrometry to reveal phosphorylation and acylation patterns of lipid A.

In this study, we report the detailed analysis of the fragmentation patterns of positively charged lipid A species based on their tandem mass spectra obtained under low-energy collision-induced dissociation conditions of an electrospray quadrupole time-of-flight mass spectrometer. The tandem mass spectrometry experiments were performed after the separation of the compounds with a reversed-phase high performance liquid chromatography method. We found that both, phosphorylated and nonphosphorylated lipid A molecules can be readily ionized in the positive-ion mode by adduct formation with triethylamine added to the eluent. The tandem mass spectra of the lipid A triethylammonium adduct ions showed several product ions corresponding to inter-ring glycosidic cleavages of the sugar residues, as well as consecutive and competitive eliminations of fatty acids, phosphoric acid, and water following the neutral loss of triethylamine. Characteristic product ions provided direct information on the phosphorylation site(s), also when phosphorylation isomers (ie, containing either a C1 or a C4' phosphate group) were simultaneously present in the sample. Continuous series of high-abundance B-type and low-abundance Y-type inter-ring fragment ions were indicative of the fatty acyl distribution between the nonreducing and reducing ends of the lipid A backbone. The previously reported lipid A structures of Proteus morganii O34 and Escherichia coli O111 bacteria were used as standards. Although, the fragmentation pathways of the differently phosphorylated lipid A species significantly differed in the negative-ion mode, they were very similar in the positive-ion mode. The complementary use of positive-ion and negative-ion mode tandem mass spectrometry was found to be essential for the full structural characterization of the C1-monophosphorylated lipid A species.