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Profinder b 0

Manufactured by Agilent Technologies

Profinder B.0.800 software is a data analysis tool designed for Agilent instruments. It provides functionality for processing and analyzing data generated by Agilent's analytical equipment. The software's core function is to enable users to view, manipulate, and interpret the data collected from their experiments or measurements.

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2 protocols using profinder b 0

1

Metabolomic Analysis of Cellular Samples

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Extracted metabolites were separated on a Cogent Diamond Hydride Type C column (gradient 3) (Microsolve Technologies) and the mobile phase consisted of solution A (ddH2O with 0.2% formic acid) and solution B (acetonitrile with 0.2% formic acid). The mass spectrometer used was an Agilent Mass 6230 time of flight (TOF) coupled with an Agilent 1290 liquid chromatography (LC) system. Detected ions were deemed metabolites on the basis of unique accurate mass-retention time identifiers for masses exhibiting the expected distribution of accompanying isotopologs. The abundance of extracted metabolites was measured using Agilent Qualitative Analysis B. 08.00 software and Profinder B.0.800 software (Agilent Technologies) with a mass tolerance of <0.005 Da. All data obtained by metabolomics were the average of three independent samples of each condition tested. Analysis was performed on metabolite intracellular concentration per milligram of total proteins (IC/mg) taken from GC-MS. The normalized metabolomic data used in this study are listed in Table S2. The variance of metabolome data was analyzed by 2D Principal Component Analysis and heatmap using Clustvis (https://biit.cs.ut.ee/clustvis/) (Metsalu and Vilo, 2015 (link)). Statistical significance was calculated using GraphPad PRISM using a two-way ANOVA with HSD Tukey post-hoc analysis.
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2

Quantitative Metabolomics Analysis of 2D and 3D Cultured TIME Cells

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2D monolayer cultured TIME cells were collected and washed twice with cold PBS and fixed in 80% methanol (Fisher Chemical, LC-MS glade) precooled in dry ice. Cells were detached by scrapping and then transferred to a 2 mL screw cap tube. 3D cultured TIME cells are incubated with Cell Recovery Solution (Corning) for 20 min on ice for depolymerize the Matrigel matrix before fixation. Lysate of cells were quantified by BCA and pelleted by centrifugation (12000 rpm for 10 min at 4°C). The supernatant was transferred into a new 2 mL screw cap tube and driedusing a vacuum concentrator. Dried metabolites were resuspended in acetonitrile/methanol/water(40:40:20).Before applying LC-MS, metabolites were mixed with acetonitrile containing 0.2% folic acid solution and spun down at 12,000 rpm for 10min at 4°C. The supernatant was injected into Agilent Accurate Mass 6230 time of flight (TOF) coupled with Agilent 1290 liquid chromatography (LC) system. Detected ions were deemed metabolites on the basis of unique accurate mass-retention time identifiers for masses exhibiting the expected distribution of accompanying isotopologues. The abundance of metabolites was extracted using Agilent Qualitative Analysis B.07.00 and Profinder B.08.00 software (Agilent Technologies) with a mass tolerance of <0.005 Da.
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