MetaboMSDIA: A tool for implementing data-independent acquisition in metabolomic-based mass spectrometry analysis.

Data-dependent acquisition (DDA) is the most widely used mode in untargeted metabolomic analysis despite its limited tandem mass spectrometry (MS2) detection coverage. We present MetaboMSDIA for complete processing of data-independent acquisition (DIA) files by the extraction of multiplexed MS2 spectra and further identification of metabolites in open libraries. In the analysis of polar extracts from lemon and olive fruits, DIA allows one to obtain multiplexed MS2 spectra for 100% of precursor ions compared to 64% of precursor ions from average MS2 acquisition in DDA. MetaboMSDIA is compatible with MS2 repositories and homemade libraries prepared by analysis of standards. An additional option is based on filtering molecular entities by searching for selective fragmentation patterns according to selective neutral losses or product ions to target the annotation of families of metabolites. Combining both options, the applicability of MetaboMSDIA was tested by annotating 50 and 35 metabolites in polar extracts from lemon and olive fruit, respectively. MetaboMSDIA is particularly proposed to increase the acquisition coverage in untargeted metabolomics and to improve spectral quality, which are two critical pillars for the tentative annotation of metabolites. The R script used in MetaboMSDIA workflow is available at github repository (https://github.com/MonicaCalSan/MetaboMSDIA).

Determination of vitamin D3 conjugated metabolites: a complementary view on hydroxylated metabolites.

Experts typically define vitamin D deficiency levels by the determination of a circulating 25-hydroxyvitamin D3-calcifediol prohormone. A large part of the population is characterized by deficient vitamin D levels (calcifediol < 20 ng mL-1) despite individuals not being affected by any disorder. Cholecalciferol (vitamin D3) and/or calcifediol supplementation is a common practice for vitamin D-deficient individuals as recommended by international scientific societies and official agencies. In the last few years, several studies have reported the presence of conjugated vitamin D3 metabolites, mainly glucuronidation and sulfation derivatives, although simultaneous quantitative measurements involving phase I and II vitamin D metabolites have not been carried out. A quantitative method based on tandem mass spectrometry detection is proposed here for the combined determination of phase I and phase II vitamin D3 metabolites in human serum. As phase I and phase II metabolites are preferentially ionized in different modes, a switching polarity mode was adopted to determine both groups of compounds in serum at high sensitivity levels (pg mL-1). The validation of this proposal was successfully accomplished by following the Center for Drug Evaluation and Research (CDER) guidelines. Its applicability was tested in a cohort of volunteers with mostly deficient baseline levels. Considering the sulfated form of calcifediol, the sum of its concentrations showed sufficient baseline vitamin D levels in all individuals, suggesting that this could be a novel strategy for vitamin D deficiency definition. Therefore, phase II metabolites are proposed to be included when evaluating the vitamin D status since they provide more information about the overall status of the vitamin D endocrine system. Nevertheless, further studies are required to confirm the biological activity of these conjugated metabolites and the suitability of this strategy for the description of vitamin D deficiency.

Profiling analysis of phospholipid fatty acids in serum as a complement to the comprehensive fatty acids method.

Fatty acids (FAs) are mostly found in blood as triglycerides, phospholipids (PLs) and cholesteryl esters. Determination of FAs is typically carried out in serum or plasma by a comprehensive method (known as the classical FAMEs method since FAs are determined as Fatty Acids Methyl Esters), which is based on liquid-liquid extraction, derivatization by transesterification, and determination by gas chromatography (GC) coupled to a suited detection technique. However, this method does not favor the determination of FAs that are chemically conjugated in PLs due to kinetics impediment. For this reason, we have developed a selective method to determine the FAs profile of PLs in serum based on solid-phase extraction (SPE) for isolation of PLs and determination of the FAME derivatives by GC-mass spectrometry (GC-MS). The method was applied to serum samples collected from twenty-five individuals to compare the FAs profile versus that provided by the non-selective protocol based on liquid-liquid extraction of lipid families. Statistical analysis revealed compositional changes in the FAs profile with special emphasis on the content of saturated (SFAs) and monounsaturated FAs (MUFAs). Thus, SFAs passed from 34.0% with the classical method to 49.3% in PLs while MUFAs went from 24.4% to 11.4%. This study proves that the proposed method provides complementary results to the comprehensive method and, therefore, both methods can be combined to evaluate the effect of intervention diets and their connection to metabolic diseases.

Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4.

We applied multi-omics approaches (transcriptomics, proteomics and metabolomics) to study the effect of iron starvation on the Gram-positive human pathogen Streptococcus pneumoniae to elucidate global changes in the bacterium in a condition similar to what can be found in the host during an infectious episode. We treated the reference strain TIGR4 with the iron chelator deferoxamine mesylate. DNA microarrays revealed changes in the expression of operons involved in multiple biological processes, with a prevalence of genes coding for ion binding proteins. We also studied the changes in protein abundance by 2-DE followed by MALDI-TOF/TOF analysis of total cell extracts and secretome fractions. The main proteomic changes were found in proteins related to the primary and amino sugar metabolism, especially in enzymes with divalent cations as cofactors. Finally, the metabolomic analysis of intracellular metabolites showed altered levels of amino sugars involved in the cell wall peptidoglycan metabolism. This work shows the utility of multi-perspective studies that can provide complementary results for the comprehension of how a given condition can influence global physiological changes in microorganisms.

Untargeted analysis to monitor metabolic changes of garlic along heat treatment by LC-QTOF MS/MS.

Black garlic is increasing its popularity in cuisine around the world; however, scant information exists on the composition of this processed product. In this study, polar compounds in fresh garlic and in samples taken at different times during the heat treatment process to obtain black garlic have been characterized by liquid chromatography coupled to tandem mass spectrometry in high resolution mode. Ninety-five compounds (mainly amino acids and metabolites, organosulfur compounds, and saccharides and derivatives) were tentatively identified in all the analysed samples and classified as a function of the family they belong to. Statistical analysis of the results allowed establishing that the major changes in garlic occur during the first days of treatment, and they mainly affect to the three representative families. The main pathways involved in the synthesis of the compounds affected by heat treatment, and their evolution during the process were studied.

High-resolution mass spectrometry to evaluate the influence of cross-breeding segregating populations on the phenolic profile of virgin olive oils.

BACKGROUND: The growing demand for high-quality virgin olive oils (VOOs) has increased the interest in olive breeding programs. Cross-breeding is considered, within these programs, the best strategy to generate new cultivars as an attempt to improve the present cultivars. In this research, the phenolic profile of VOOs from target crosses (Arbequina × Arbosana, Picual × Koroneiki and Sikitita × Arbosana) and their corresponding genitors (Arbequina, Arbosana, Koroneiki, Picual and Sikitita) has been evaluated using a targeted metabolomics approach. RESULTS: The phenolic profiles were obtained by liquid chromatographic-hybrid quadrupole time-of-flight mass spectrometric targeted analysis of 37 phenols or compounds involved in the main pathways for their biosynthesis. Statistical multivariate analysis by principal component analysis was applied to study the influence of genotype on phenol composition. Phenolic compounds with the highest contribution to explain the observed variability associated to genotype were identified through fold change algorithms (cut-off > 2.0) and t-test analysis. CONCLUSION: A total of nine phenols (viz. quercetin, ligstroside aglycon (p-HPEA-EA), demethyl oleuropein aglycon, oleuropein aglycon (3,4-DHPEA-EA), hydroxypinoresinol, hydroxytyrosol and phenolic acids such as p-coumaric acid, ferulic acid and protocatechuic acid) contributed to explain the observed variability with 99% confidence (P<0.01).

Global metabolomic profiling of human serum from obese individuals by liquid chromatography-time-of-flight/mass spectrometry to evaluate the intake of breakfasts prepared with heated edible oils.

The metabolic profile of human serum after intake of breakfasts prepared with different heated vegetable oils has been studied. Four oils (olive and sunflower oils, pure and enriched with natural and artificial oxidation inhibitors) were subjected to a simulated heated process prior to breakfast preparation. A metabolomics global profiling approach performed on post-basal serum samples revealed statistical differences among individuals based on breakfast intake, and identified compounds responsible for such differences. Serum samples obtained in basal state (control samples) and 2 and 4h after programmed intakes were analyzed by LC-TOF/MS. The resulting fingerprints were compared and differences between basal and post-basal states evaluated, observing that the intake of different breakfasts altered the metabolic signature of serum. Analysis models based on PLS algorithms were developed to discriminate individuals in post-basal state for each intervention breakfast. Then, Volcano tests enabled to detect significant molecular entities explaining the variability associated to each breakfast. It is worth emphasizing the importance of fatty acids, their derivatives and phospholipids for tentative identification.