Masshunter software

Manufactured by Agilent Technologies

Sourced in United States, Germany, United Kingdom

MassHunter is a software suite developed by Agilent Technologies for the analysis and processing of mass spectrometry data. It provides tools for data acquisition, qualitative and quantitative analysis, and reporting.

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MassHunter workstation software version B.02.00 (4 citations) MassHunter BioConfirm software (13 citations) Agilent MassHunter Workstation Qualitative Analysis Software (4 citations) MassHunter data processing software (2 citations) MassHunter Workstation Data Acquisition software (32 citations) MassHunter software (version 4.4) (2 citations) MassHunter LCMS Acquisition software 10.0 (2 citations) MassHunter Mass Profiler software (3 citations) MassHunter Qualitative Analysis software V.7 (3 citations) MassHunter Profinder software (27 citations)

440 protocols using masshunter software

Metabolite Profiling of Plant Leaves

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Approximately 50 mg of ground leaf material was used to obtain extracts for metabolite profiling by gas chromatography-mass spectrometry (GC-MS) as described by Fiehn et al. (2000) . Data analysis was performed using MassHunter Software, version B.07.00 (Agilent). For relative quantification, all metabolite peak areas were normalized to the peak area of the internal standard ribitol added prior to extraction and the amount of leaf material. From each sample, two extracts were prepared and analysed.
Amino acids were measured by liquid chromatography-mass spectrometry (LC-MS). Extracts were prepared in 80% (v/v) ethanol (Fisher Scientific) as described by Di Martino et al. (2003) , and data analysis was conducted using MassHunter Software, version B.07.00 (Agilent). From each sample, two extracts were prepared and analysed. Metabolites analysed by both methods are listed in Supplementary Dataset S3.

Maleckova E., Brilhaus D., Wrobel T.J, & Weber A.P. (2019). Transcript and metabolite changes during the early phase of abscisic acid-mediated induction of crassulacean acid metabolism in Talinum triangulare. Journal of Experimental Botany, 70(22), 6581-6596.

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Bioactive Compound Identification in MED

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The bioactive compounds in MED were identified as previously described by Lee et al. (4 (link)). Liquid chromatography-mass spectrometry (LC-MS) analysis was performed with a BEH C18 Column (2.1 × 100 mm, 1.7 μm) (Waters, Milford, MA, USA) using an Agilent 1290 Infinity HPLC system (Agilent Technologies, Waldbronn, Germany). Mass spectra were obtained in the negative mode electrospray ionization (ESI) using MassHunter software (Agilent Technologies).

Roh Y.J., Lee S.J., Kim J.E., Jin Y.J., Seol A., Song H.J., Park J., Park S.H., Douangdeuane B., Souliya O., Choi S.I, & Hwang D.Y. (2023). Dipterocarpus tuberculatus as a promising anti-obesity treatment in Lep knockout mice. Frontiers in Endocrinology, 14, 1167285.

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Leaf Metabolite Analysis by GC-MS

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The homogenized leaf material was extracted for metabolite analysis by gas chromatography-mass spectrometry (GC-MS) according to Fiehn et al. (2000) using a 7200 GC-QTOF (Agilent, Santa Clara, USA). Data analysis was conducted with the Mass Hunter Software (Agilent, Santa Clara, USA). For relative quantification, all metabolite peak areas were normalized to the peak area of an internal standard of ribitol added prior to extraction. The same homogenised leaf material was used for determination of δ¹³C and CN ratios. After lyophilisation, the material was analysed using an Isoprime 100 isotope ratio mass spectrometer coupled to an ISOTOPE cube elemental analyzer (both from Elementar, Hanau, Germany) according to Gowik et al. (2011) (link). Measurements were always done on ten biological replicates. Statistical significance was analysed using Student’s t-test.

Schlüter U., Bräutigam A., Gowik U., Melzer M., Christin P.A., Kurz S., Mettler-Altmann T, & Weber A.P. (2016). Photosynthesis in C3–C4 intermediate Moricandia species. Journal of Experimental Botany, 68(2), 191-206.

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Fatty Acid Methylation and GC Analysis

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A volume of 50 µL of total lipid extract was evaporated and resolubilized in 500 µL toluen-methanol (1:1, v/v) for methylation. The methylation reaction was performed in the presence of 500 µL BF₃/methanol (14%) used as catalyzer, under N₂ atmosphere, by heating at 100 °C for 90 min. The reaction was stopped by fast cooling of the samples and the addition of K₂CO₃ (10% in water). Isooctane was further added to extract the methylated fatty acids—the upper organic phase; the extraction was performed 2 times. The samples were dried under N₂ and re-solubilized in isooctane for GC analysis.
GC was performed on an HP 6890 (Agilent Technologies) instrument equipped with a fused silica capillary BPX70 column (Trajan, SGE; 60 m × 0.25 mm). The carrier gas was hydrogen (1 mL/min). The temperatures of the flame ionization detector and the split/splitless injector were set at 250 and 230 °C, respectively. The oven temperature program was as follows: 50 °C for 2 min, followed by 20 °C/min up to 140 °C, and 2 °C/min up to 240 °C (for 5 min). The samples were injected in a splitless mode. Peak detection, integration and quantitative analyses were executed using MassHunter software (Agilent Technologies, Santa Clara, CA, USA).

Lazar A.N., Hanbouch L., Boussicaut L., Fourmaux B., Daira P., Millan M.J., Bernoud-Hubac N, & Potier M.C. (2022). Lipid Dys-Homeostasis Contributes to APOE4-Associated AD Pathology. Cells, 11(22), 3616.

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GC-MS Analysis of Aroma Compounds

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Identification of aroma compounds was performed on an Agilent 7890B GC, coupled with an Agilent 5977B MS (Agilent Technologies, USA). The DB-Wax column (30 m × 0.25 mm ID, 0.25 m film thickness) was used to perform the chromatographic separations. Helium was used as the carrier gas with a constant flow mode of 0.7 mL/min. The injector temperature was kept at 260 °C. The oven temperature program was hold at 45 °C for 1.5 min, raised to 85 °C at a rate of 6 °C, then, sequentially increased at a rate 4 °C/min to 225 °C for 15 min, along with quadrupole mass filter was at 150 °C, the transfer line temperature was at 250 °C and ion source temperature at 230 °C. The MS parameters included electron impact ionization with electron energy of 70 eV, and mass range of m/z 50-550, using the selective ion monitoring (SIM) mode. The area of each peak was determined by MassHunter software (Agilent Technologies).

Zhou R., Chen X., Xia Y., Chen M., Zhang Y., Li Q., Zhen D., & Fang S. (2020). Research on the application of liquid-liquid extraction-gas chromatography-mass spectrometry (LLE-GC-MS) and headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS) in distinguishing the Baiyunbian aged liquors. International Journal of Food Engineering, 17(2), 83-96.

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Phenolic Compound Analysis Using UHPLC-MS/MS

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The analyses of phenolic compounds were carried out using a 1260 Infinity UHPLC (Agilent Technologies). The UHPLC system was coupled to a 6430 triple quadrupole mass spectrometer from Agilent Technologies. Four µL were injected into a Zorbax SB-C₁₈ column (2.1 × 100 mm, 1.8 µm) (Agilent Technologies, Les Ulis, France). Two different solvents were used as a mobile phase: solvent A (water/formic acid 99.9:0.1, v/v) and solvent B (acetonitrile/formic acid 99.9:0.1, v/v), at a flow rate of 0.3 mL/min and a gradient as follows in solvent A: 0 min 1% B, 2 min 5% B, 3 min 25% B, 6 min 25% B, 8 min 40% B, 11.5 min 95% B, 14 min 95% B, and 16 min 1% B. The MS/MS parameters were set as follows: negative ion mode, capillary tension 3000 V, nebulizer 15 psi, dry gas 11 L/min, dry temperature 350 °C, and acquisition in multiple reaction monitoring (MRM), see Supplementary Table S1 for further details. The data were processed using MassHunter software (Agilent Technologies).

Wauquier F., Boutin-Wittrant L., Krisa S., Valls J., Langhi C., Otero Y.F., Sirvent P., Peltier S., Bargetto M., Cazaubiel M., Sapone V., Bouchard-Mercier A., Roux V., Macian N., Pickering G, & Wittrant Y. (2023). Circulating Human Metabolites Resulting from TOTUM-070 Absorption (a Plant-Based, Polyphenol-Rich Ingredient) Improve Lipid Metabolism in Human Hepatocytes: Lessons from an Original Ex Vivo Clinical Trial. Nutrients, 15(8), 1903.

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ESI-MS Analysis of Solvent Extracts

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High-resolution electrospray mass spectrometry (ESI-MS) was performed in the positive ion mode on Agilent 6210A HPLC-TOF/MS. Agilent Mass Hunter software was used for analysing the data and operating the instrument. Pure acetonitrile was used as mobile phase. All samples were stored in dry toluene (with the 1–4 volume ratio of sample to toluene).

Liu M., Wang K., Wang L., Han S., Fan H., Rowell N., Ripmeester J.A., Renoud R., Bian F., Zeng J, & Yu K. (2017). Probing intermediates of the induction period prior to nucleation and growth of semiconductor quantum dots. Nature Communications, 8, 15467.

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Metabolite Profiling Using GC-MS and LC-MS

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The metabolites were identified with GC−MS was performed using Agilent Mass Hunter software and the public databases HMDB (Wishart et al., 2007 (link)), Massbank (Horai et al., 2010 (link)), LipidMaps (Sud et al., 2007 (link)), and mzCloud (Abdelrazig et al., 2020 (link)). The metabolites detected with LC−MS were identified using the public HMDB (Wishart et al., 2007 (link)), massbank (Horai et al., 2010 (link)), LipidMaps (Sud et al., 2007 (link)), mzCloud (Abdelrazig et al., 2020 (link)), and KEGG (Kanehisa and Goto, 2000 (link)) databases and the self-built database of BioNovoGene (Chengdu, Sichuan, China) (http://query.biodeep.cn/) with the following parameters: retention time, ppm (<30 ppm), and fragmentation model. Finally, the relative contents of the corresponding metabolites are presented as the percentage of the chromatographic peak area integral relative to the total identified peak area integrals.

Yang H., Zhang S., Gu Y., Peng J., Huang X., Guo H., Chen L., Jiang Y., Liu M., Luo X., Xie J, & Wan X. (2024). Identification and variation analysis of the composition and content of essential oil and fragrance compounds in Phoebe zhennan wood at different tree ages. Frontiers in Plant Science, 15, 1368894.

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Analytical Method for U-47700 and Metabolites

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Plasma was analyzed using our previously validated method (Smith et al) (24 ). Briefly, internal standard was added to plasma (100 μL) and buffered before loading onto solid phase extraction cartridges. Analytes were eluted with dichloromethane:isopropyl alcohol (80:20, v/v) with 5% ammonium hydroxide, then dried under nitrogen and reconstituted in 50 μL of 5 mM ammonium formate with 0.05% formic acid in water: 0.1% formic acid in methanol (60:40, v/v). Samples were analyzed on an Agilent 1290 Infinity II Liquid Chromatograph system equipped with an Agilent 6470 Triple Quadrupole Mass Spectrometer (Santa Clara, CA, USA). Agilent MassHunter Software was used for data acquisition and analysis of U-47700, N-desmethyl-U-47700, and N,N-didesmethyl-U-47700. Linear ranges were 0.1–100 ng/mL for U-47700 and N-desmethyl-U-47700, and 0.5–100 ng/mL for N,N-didesmethyl-U-47700. The limits of detection were 0.05 ng/mL for U-47700 and N-desmethyl-U-47700 and 0.1 ng/mL for N,N-didesmethyl-U-47700.

Truver M.T., Smith C.R., Garibay N., Kopajtic T.A., Swortwood M.J, & Baumann M.H. (2020). Pharmacodynamics and pharmacokinetics of the novel synthetic opioid, U-47700, in male rats. Neuropharmacology, 177, 108195.

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Sensitive UHPLC-MS/MS Microcystins Detection

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UHPLC (Agilent 1290 Infinity II system, USA) coupled to a triple quadrupole mass spectrometer (MS/MS, Agilent 6495, USA) equipped with a Dual Agilent Jet Stream ESI (Agilent, USA). Selective reaction monitoring (SRM) under positive ionization mode was adopted for MS data acquisition, and the MassHunter software (Agilent, USA) was used for data process. The ESI parameters are set as follow: electrospray capillary, 4.0 kV; the sheath gas temperature and flow were 400 o C and 12 L/min, respectively; the gas temperature and flow were 290 o C and 5 L/min, respectively. The precursor and product ions were selected for monitoring all analytes. And the MRM and MIRM parameters for each MCs are available in Table S1, S2 and Table 1, respectively. Chromatographic separation of microcystins was carried out on Poroshell 120 EC-C18 column (2.1 × 100 mm, 2.7 µm; Agilent, USA) using a gradient elution of solvent A (ultra-pure water contains 0.1% formic acid) and solvent B (acetonitrile contains 0.1% formic acid) as follows: 0.0-0.50min, 30% B; 0.5-3.5 min, 30% B to 40% B; 3.5-5.5 min, 40% B to 85% B; 5.5-6.0 min, 85% B to 100% B and maintained for 0.40 min; 6.4-7.5 min, 30% B. The column temperature was keep at 40 o C during the analysis, and the injection volume was set at 20 µL.

Zhang H., Li Y., Abdallah M.F., Tan H., Li J., Liu S., Zhang R., Sun F., Li Y, & Yang S. (2023). Novel one-point calibration strategy for high-throughput quantitation of microcystins in freshwater using LC-MS/MS. The Science of the total environment, 858(Pt 1).

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