Reference compounds

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Sourced in Italy, United States, Germany

Reference compounds are a collection of well-characterized chemical substances used as standards for analytical and research applications. These compounds serve as references to verify the identity, purity, and performance of other samples or test materials.

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Reference compounds of theobromine (2 citations) Reference antibacterial and antifungal compounds (2 citations) Authentic reference compounds (2 citations)

10 protocols using reference compounds

Cell Culture Supplies from Sigma-Aldrich

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Reference compounds, the medium, and other cell culture reagents were purchased from Sigma-Aldrich (Milan, Italy).

Yasmin S., Capone F., Laghezza A., Piaz F.D., Loiodice F., Vijayan V., Devadasan V., Mondal S.K., Atlı Ö., Baysal M., Pattnaik A.K., Jayaprakash V, & Lavecchia A. (2017). Novel Benzylidene Thiazolidinedione Derivatives as Partial PPARγ Agonists and their Antidiabetic Effects on Type 2 Diabetes. Scientific Reports, 7, 14453.

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Quantification of Citrus Leaf Volatiles

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The citrus leaf VOCs and polar metabolites were separated by gas chromatography-mass spectrometry (GC-MS) using the same chromatographic conditions as reported in our previous study [9 (link)]. Peaks of interest were identified by comparing their mass spectra to those of authentic standards and by matching them to one of two mass spectral libraries with a score of at least 700 (Wiley Flavor and Fragrances of Synthetic and Natural Compounds or NIST 2011 Mass Spectral Database). Reference compounds were purchased from Sigma-Aldrich (St. Louis, MO, USA) at the highest available purity, and injected into the GC-MS under the same conditions as experimental samples to establish their retention time on the column. Peak areas were integrated using TurboMass software v. 5.4.2 (Perkin Elmer, Waltham, MA, USA), and were normalized to the area of the internal standard, trans-2-nonenal for VOCs and ribitol for polar metabolites. Quantification of compounds was based on the peak areas obtained from a dilution series of reference standards at known concentrations. Calibration curves were constructed from the linear regressions obtained by plotting the concentration vs. peak area for each reference compound at each concentration.

Killiny N., Jones S.E., Hijaz F., Kishk A., Santos-Ortega Y., Nehela Y., Omar A.A., Yu Q., Gmitter FG J.r., Grosser J.W, & Dutt M. (2020). Metabolic Profiling of Hybrids Generated from Pummelo and Citrus latipes in Relation to Their Attraction to Diaphorina citri, the Vector of Huanglongbing. Metabolites, 10(12), 477.

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Reagents Purchased from Sigma-Aldrich

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Reference compounds, media, and other cell culture reagents were purchased from Sigma–Aldrich (Milan, Italy).

Brusotti G., Montanari R., Capelli D., Cattaneo G., Laghezza A., Tortorella P., Loiodice F., Peiretti F., Bonardo B., Paiardini A., Calleri E, & Pochetti G. (2017). Betulinic acid is a PPARγ antagonist that improves glucose uptake, promotes osteogenesis and inhibits adipogenesis. Scientific Reports, 7, 5777.

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GC-MS Analysis of Volatile Compounds

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The profile of volatile compounds was mainly determined using headspace solid-phase micro-extraction (HS-SPME) [24 (link)] combined with gas chromatography-mass spectrometry (GC-MS) (Agilent 7890-B/5977A MS system, Agilent Technologies, Little Falls, DE, USA). The sample treatment and instrument operating parameters were carried out according to the methods described in our previous study [25 (link)]. The chromatographic peaks were qualitatively determined by matching the NIST 17s mass spectral library and Kovats index, which was calculated by the analysis of the C7–C40 n-alkane standard (Sigma-Aldrich, St. Louis, MO, USA) under the same chromatographic conditions as the samples. The concentration of each volatile compound was calculated quantitatively by the normalized method based on the peak area of the internal standard compound (2-octanol, 10 mg/L) and the correction factor of the reference compounds purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO, USA).

Yang Z., Li W., Yuan Y., Liang Z., Yan Y., Chen Y., Ni L, & Lv X. (2023). Metagenomic Insights into the Regulatory Effects of Microbial Community on the Formation of Biogenic Amines and Volatile Flavor Components during the Brewing of Hongqu Rice Wine. Foods, 12(16), 3075.

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FAAH Inhibition Assay Protocol

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Reference compounds, cell culture mediums and other reagents, along with plates and other physical supports for cell culture and enzyme assays were purchased from Merck Sigma (Milan, Italy) and Invitrogen (Basel, Switzerland). The FAAH enzyme, the substrate AMC-AA and the reference compound JZL-195 for the FAAH inhibition assay were obtained from Cayman Chemical (Ann Arbor, MI, USA).

Brunetti L., Carrieri A., Piemontese L., Tortorella P., Loiodice F, & Laghezza A. (2020). Beyond the Canonical Endocannabinoid System. A Screening of PPAR Ligands as FAAH Inhibitors. International Journal of Molecular Sciences, 21(19), 7026.

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Enzyme Inhibition Activity Assay

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Enzymes, substrates, and reference compounds were from Sigma-Aldrich (St. Louis, MO, United States). The activity of enzymes was measured spectrophotometrically, as described in detail in (Makhaeva et al., 2017 (link)) using ATCh iodide, BTCh iodide, and 4-NPA as substrates for AChE, BChE, and CES, respectively. Experimental conditions: K,Na-phosphate buffer (100 mM), 25°С, pH 7.5 for AChE and BChE and pH 8.0 for CES assay. Measurements were carried out on a BioRad Benchmark Plus microplate spectrophotometer (Hercules, CA, United States).
Test compounds were dissolved in DMSO; final concentration of solvent in the incubation mixture was 2% (v/v). Initial assessment of inhibitory activity was carried out by determining the degree of enzyme inhibition at a compound concentration of 20 µM. For the most active compounds (inhibition ≥35%), IC₅₀ values were determined.
Mechanism of BChE inhibition was assessed by a detailed analysis of enzyme kinetics with three increasing concentrations of inhibitor and six substrate concentrations as described in detail in Makhaeva et al. (2017) (link).

Makhaeva G.F., Kovaleva N.V., Rudakova E.V., Boltneva N.P., Lushchekina S.V., Astakhova T.Y., Timokhina E.N., Serebryakova O.G., Shchepochkin A.V., Averkov M.A., Utepova I.A., Demina N.S., Radchenko E.V., Palyulin V.A., Fisenko V.P., Bachurin S.O., Chupakhin O.N., Charushin V.N, & Richardson R.J. (2023). Derivatives of 9-phosphorylated acridine as butyrylcholinesterase inhibitors with antioxidant activity and the ability to inhibit β-amyloid self-aggregation: potential therapeutic agents for Alzheimer’s disease. Frontiers in Pharmacology, 14, 1219980.

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Cell Culture Supplies from Sigma-Aldrich

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Reference compounds, the medium, and other cell culture reagents were purchased from Sigma-Aldrich (Milan, Italy).

Capelli D., Cerchia C., Montanari R., Loiodice F., Tortorella P., Laghezza A., Cervoni L., Pochetti G, & Lavecchia A. (2016). Structural basis for PPAR partial or full activation revealed by a novel ligand binding mode. Scientific Reports, 6, 34792.

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Preparation of LC-MS Compound Mix

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Acetonitrile and water (both LC-MS grade) were purchased from Fluka (Buchs, Switzerland). Reference compounds with a purity of > 99% were purchased from Sigma-Aldrich (Seelze, Germany). First, they were dissolved individually into stock solutions of 1 mM in either acetonitrile (nonpolar compounds) or in acetonitrile/water (50/50, v/v) (polar or very polar compounds). Afterwards, they were combined into a standard working mixture of 10 μM per compound.

Minkus S., Grosse S., Bieber S., Veloutsou S, & Letzel T. (2020). Optimized hidden target screening for very polar molecules in surface waters including a compound database inquiry. Analytical and Bioanalytical Chemistry, 412(20), 4953-4966.

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Comprehensive Analytical Reagents for Metabolomic Studies

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Water (LC-MS grade), acetonitrile (LC-MS grade, ≥99.95 %), hexane (UV/IR grade, ≥99.5 %), methanol (LC-MS grade ≥ 99.95 %), isopropanol (LC-MS grade, ≥99.95 %), acetone (LC-MS grade, ≥99.9 %), butanol (for synthesis, ≥99.5 %), trichloromethane/chloroform (UV/IR grade, ≥99.8 %) and citric acid (≥99.5 % p.a.) were purchased from Carl Roth (Karlsruhe, Germany), ethyl acetate (Reag. Ph. Eur. ≥ 99.9 %) was purchased from Biosolve (Valkenswaard, Netherlands), formic acid (98 %) and acetic acid (100 %) from Fisher Scientific (Schwerte, Germany), hydrochloric acid (Reag. Ph. Eur., 37 %) and disodium hydrogen phosphate (NormaPur) from VWR Chemicals (Darmstadt, Germany), and 2,6-di-tert-butyl-4-methylphenol (BHT, 99 %) from Sigma-Aldrich (Munich, Germany). Reference compounds and isotopically labeled internal standards (IS) were purchased from Cayman Chemicals (Ann Arbor, MI, USA) for endocannabinoids and oxylipins, or Avanti Polar Lipids (Alabaster, AL, USA) for sphingolipids, LPAs, and lipids analyzed by LC-HRMS. For polar compounds, tryptophan and related metabolites, isotopically labeled IS and Reference compounds were purchased from Sigma-Aldrich or Cambridge Isotope Laboratories (Tewksbury, MA, USA). Detailed descriptions can be found in the supplementary material.

Sens A., Rischke S., Hahnefeld L., Dorochow E., Schäfer S.M., Thomas D., Köhm M., Geisslinger G., Behrens F, & Gurke R. (2023). Pre-analytical sample handling standardization for reliable measurement of metabolites and lipids in LC-MS-based clinical research. Journal of Mass Spectrometry and Advances in the Clinical Lab, 28, 35-46.

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Analytical Reagents for LC-MS Metabolomics

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Ultra LC-MS grade acetonitrile (ACN) and methanol (MeOH) were purchased from Carl Roth GmbH & Co KG (Germany). Ammonium acetate (AmAc) was purchased from Sigma-Aldrich (Taufkirchen, Germany). Pure water was obtained from a Milli-Q system (Millipore, USA) and used for the preparation of aqueous solvents. Reference compounds were purchased from Sigma Aldrich (Taufkirchen, Germany) unless otherwise indicated (Supplementary Table S1).

Lackner M., Neef S.K., Winter S., Beer-Hammer S., Nürnberg B., Schwab M., Hofmann U, & Haag M. (2022). Untargeted stable isotope-resolved metabolomics to assess the effect of PI3Kβ inhibition on metabolic pathway activities in a PTEN null breast cancer cell line. Frontiers in Molecular Biosciences, 9, 1004602.

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