Qualitative analysis b 07

Manufactured by Agilent Technologies

Sourced in United States

Qualitative Analysis B.07.00 is a software application developed by Agilent Technologies for the analysis of spectroscopic data. The core function of the software is to provide users with the ability to perform qualitative analysis of samples.

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Lab products found in correlation

El maven, by Agilent Technologies (2 mentions) Spss statistics 21, by IBM (1 mentions) Salicin, by Merck Group (1 mentions) Accurate mass 6230 tof, by Agilent Technologies (1 mentions) Profinder b 06, by Agilent Technologies (1 mentions) Agilent 6520 quadrupole time of flight mass spectrometer, by Agilent Technologies (1 mentions) 1290 liquid chromatography system, by Agilent Technologies (1 mentions) 6520 quadrupole time of flight mass spectrometer, by Agilent Technologies (1 mentions)

7 protocols using qualitative analysis b 07

GC-MS Metabolite Identification Protocol

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Gas chromatography–mass spectrometry data were acquired by using the software Qualitative Analysis B.07.00 (Agilent Technologies, Santa Clara, CA, United States) and following procedures established in our previous research (Fiehn et al., 2007 (link) and Hu et al., 2019 (link)). All detected metabolites were identified by comparing spectra with the NIST14 library and Fiehn database (Kanani et al., 2008 (link)). Instrumental stability was evaluated by analyzing the percentage of relative standard deviation (RSD) of the internal standard substance (>99% salicin, Sigma-Aldrich) in the six repeated tests. The SPSS Statistics 21 software (IBM, Armonk, United States) was used to analyze metabolites with one-way ANOVA followed by a Tukey test at a significance level of P < 0.05. HCA was carried out based on average areas calculated from principal ions of all the compounds.

Liang L., Cheng X., Dai T., Wang Z., Li J., Li X., Lei B., Liu P., Hao J, & Liu X. (2020). Metabolic Fingerprinting for Identifying the Mode of Action of the Fungicide SYP-14288 on Rhizoctonia solani. Frontiers in Microbiology, 11, 574039.

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Amyloid-β Protein Fibrillization Studied by IM-MS

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Fifty micromolar αSA53T was prepared for IM-MS experiments in 50 mM ammonium acetate buffer in the absence and presence of each compound at a molar ratio of 1:2 (protein: compound). Samples were allowed to fibrillize by incubation at 37°C with constant shaking at 300 rpm. IM-MS analysis was performed on an Agilent 6560 Ion Mobility Q-ToF spectrometer with samples introduced by nanoelectrospray ionization through platinum-coated capillaries (made in-house). Ions were analyzed in the positive mode, with parameters systematically selected to achieve optimal signal while avoiding any analysis induced structural transitions (full details of optimization will be reported in a manuscript currently in preparation). Typical instrument parameters included; capillary voltage 1,700 V, fragmentor voltage 400 V, gas temperature 0°C, gas flow 2 l/min, trap fill time 20000.0 μs, trap release time 4000.0 μs and CCS measurement was made using a multifield approach varying the IM drift tube voltage between 1,200 and 1,700 V. The acquired spectra were processed using Qualitative Analysis B.07.00 and IM-MS browser B.07.01 (both Agilent, Santa Clara, USA).

Das S., Pukala T.L, & Smid S.D. (2018). Exploring the Structural Diversity in Inhibitors of α-Synuclein Amyloidogenic Folding, Aggregation, and Neurotoxicity. Frontiers in Chemistry, 6, 181.

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Comprehensive Metabolite Profiling Using QTOF-MS/MS and Orbitrap-MS

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The analysis of the flow injection-QTOF-MS/MS and HPLC-QTOF-MS/MS data was performed using the Qualitative Analysis B.07.00 software from Agilent. Compounds were found by molecular features. The data range was restricted to retention times between 3 and 28 min and to m/z between 100 and 1200 with a minimum signal height of 10,000 counts to qualify as a compound. The formulas were generated using only C, H, and O atoms in anticipation of cucurbitacins and their glycosides. The signal spacing tolerance was set to 5 ppm.
The analysis of the HPLC-Orbitrap-MS data was performed using the Thermo Xcali-bur 3.0.63.3 software from Thermo Fisher Scientific. Compounds were found manually.

Benka M., Görlitz K., Schöttgen M.C., Lagies S., Mohl D.A., Kather M., Du Preez-Bruwer I., Mumbengegwi D., Teufel R., Kowarschik S., Huber R., Plattner D.A, & Kammerer B. (2023). Mass Spectrometric Analysis of Cucurbitacins and Dihydrocucurbitacins from the Tuber of Citrullus naudinianus. Biomolecules, 13(8), 1168.

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Metabolomics Analysis of Mycobacterial Strains

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Liquid chromatography mass spectrometry (LC-MS) differentiation and detection of WT Mtb, ICL knock-down, BCG, M. bovis, and ΔRD1 metabolites were performed with an Agilent Accurate Mass 6230 TOF coupled with an Agilent 1290 Liquid Chromatography system using a Cogent Diamond Hydride Type C column (Microsolve Technologies, Long Branch, NJ, USA) using solvents and configuration as previously described^{68 (link)}. An isocratic pump was used for continuous infusion of a reference mass solution to allow mass axis calibration. Detected ions were classified as metabolites based on unique accurate mass-retention time identifiers for masses showing the expected distribution of accompanying isotopologues. Metabolites were analyzed using Agilent Qualitative Analysis B.07.00 and Profinder B.06.00 software (Agilent Technologies, Santa Clara, CA, USA) with a mass tolerance of <0.005 Da. Standards of authentic chemicals of known amounts were mixed with bacterial lysates and analyzed to generate the standard curves used to quantify metabolite levels. All data obtained by metabolomics were the average of at least two independent triplicates for each condition tested.

Lee J.J., Lim J., Gao S., Lawson C.P., Odell M., Raheem S., Woo J., Kang S.H., Kang S.S., Jeon B.Y, & Eoh H. (2018). Glutamate mediated metabolic neutralization mitigates propionate toxicity in intracellular Mycobacterium tuberculosis. Scientific Reports, 8, 8506.

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Comprehensive Metabolomic Annotation Pipeline

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Features obtained by LC-MS and CE-MS representing significant differences between the class were annotated using CEU Mass Mediator Online Platform as the database source [24 (link)]. Accurate masses, retention time, protonation, deprotonation, adducts formation, neutral loss, isotopic distribution and formula calculation tool Qualitative Analysis B.07.00 (Agilent Technologies), were used to annotate the metabolites. Additionally, CE-MS features were annotated using an in-house library developed at CEMBIO (Madrid, Spain) to match the fragmentation profile and the relative migration time (RMT). Features annotation by GC-MS was performed by using the Fienh 15 [25 (link)] Library using retention time information, the in house CEMBIO library and the NIST 17 mass spectra library using retention index determination obtained from n-alkanes (C8–C28). Biochemical pathway was created from the metabolites annotated using Pathway Analysis of MetaboAnalyst 4.0 with the following parameters: Hypergeometric Test and Relative-betweenness Centrality Algorithms and Homo sapiens (KEGG) pathway library [23 (link)].

Mendes-Frias A., Santos-Lima B., Furtado D.Z., Ruperez F.J., Assunção N.A., Matias M.J., Gomes V., Gaifem J., Barbas C., Castro A.G., Capela C, & Silvestre R. (2020). Dysregulation of glycerophospholipid metabolism during Behçet’s disease contributes to a pro-inflammatory phenotype of circulating monocytes. Journal of Translational Autoimmunity, 3, 100056.

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Metabolomics profiling of biological samples

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Analyses on Agilent 1290 liquid chromatography system coupled to Agilent 6520 quadrupole time-of- flight mass spectrometer as previously described [29 (link)]. The mass spectrometer, equipped with a dual- electrospray ionization source, was run in negative ion and then positive ion mode. The scan range was 50–1600 m/z. Source settings; drying gas flow rate: 11 L/min; nebulizer: 40 pounds per square inch gauge; gas temperature: 350 °C; capillary voltage: 3000 V (neg), 2500 V (pos). Metabolites were identified using MS/MS, with fragments compared against Agilent Metlin Metabolomics Database and Library. Liquid chromatography–mass spectrometry data were analyzed using Agilent Qualitative Analysis B.07.00, El-MAVEN (Elucidata), and Metabolomic Analysis and Visualization ENgine (MAVEN). Five biological replicates completed in each treatment group.

Parkhurst A., Wang S.Z., Findlay T.R., Malebranche K.J., Odabas A., Alt J., Maxwell M.J., Kaur H., Peer C.J., Figg W.D., Warren K.E., Slusher B.S., Eberhart C.G., Raabe E.H, & Rubens J.A. (2022). Dual mTORC1/2 inhibition compromises cell defenses against exogenous stress potentiating Obatoclax-induced cytotoxicity in atypical teratoid/rhabdoid tumors. Cell Death & Disease, 13(4), 410.

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Stable Isotope Tracing of Metabolites

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Stable isotope experiments were completed after cells were treated 24 hours with DON and incubated 2 hours with 4mM glutamine (¹³C₅, ¹⁵N₂, 99% purity) from Cambridge Isotope (Cat#: CNLM-1275-H-0.5). Cell samples were washed with ice-cold PBS, pelleted, and metabolites extracted with chilled 80% HPLC grade methanol (MeOH) as previously described (30 (link)). Analyses were completed on an Agilent 1290 liquid chromatography system coupled to an Agilent 6520 quadrupole time of flight mass spectrometer. The mass spectrometer, equipped with a dual electrospray ionization source, was run in negative ion and then positive ion mode. The scan range was 50–1600 m/z. The source settings consisted of: drying gas flow rate: 11 L/min; nebulizer: 40 pounds per square inch gauge; gas temp: 350ºC; capillary voltage: 3000 V (neg), 2500 V (pos). Metabolite identification was determined using MS/MS, with fragments compared against the Agilent Metlin Metabolomics Database and Library.
Liquid chromatography-mass spectrometry data were analyzed using Agilent Qualitative Analysis B.07.00, El-MAVEN (Elucidata), and Metabolomic Analysis and Visualization ENgine (MAVEN) as previously described (31 (link)).

Wang S.Z., Poore B., Alt J., Price A., Allen S.J., Hanaford A.R., Kaur H., Orr B.A., Slusher B.S., Eberhart C.G., Raabe E.H, & Rubens J.A. (2019). Unbiased metabolic profiling predicts sensitivity of high MYC-expressing atypical teratoid/rhabdoid tumors to glutamine inhibition with 6-diazo-5-oxo-L-norleucine. Clinical cancer research : an official journal of the American Association for Cancer Research, 25(19), 5925-5936.

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