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37 protocols using lc 20ad hplc

1

LC-MS Analysis of Nucleosides

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LC–MS analysis of nucleosides was performed on the LC-ESI-MS/MS system consisting of a Shimadzu LC-20AD HPLC (Tokyo, Japan) and an AB 3200 QTRAP mass spectrometer (Applied Biosystems, Foster City, CA) with an electrospray ionization source (Turbo Ionspray). Data acquisition and processing were performed using AB SCIEX Analyst 1.5 Software (Applied Biosystems, Foster City, CA, USA). The LC separation was performed on a Shimadzu VP-ODS column (250 mm × 2.1 mm i.d., 5 μm, Tokyo, Japan) with a flow rate of 0.2 ml/min at 35°C. 2 mM NH4HCO3 in water (solvent A) and methanol (solvent B) were employed as mobile phase. A gradient of 0–5 min 5% B, 5–15 min 5–25% B, 15–28 min 25–70% B and 30–40 min 5% B was used.
The mass spectrometry detection was performed under positive electrospray ionization (ESI) mode. The nucleosides were monitored by multiple reaction monitoring (MRM) mode. The MRM parameters of all nucleosides were optimized to achieve maximal detection sensitivity. The mass transitions of nucleosides are listed in Table S1 in Supporting Information. Quantification of measured nucleosides was carried out according to previously described method (28 ) and detailed information can be found in the Supporting Information.
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2

Quantitative Lipid Mediator Profiling

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Supernatant from the inflammatory lesions were placed in ice cold methanol containing deuterated internal standards (d8-5S-hydroxyeicosatetraenoic acid (HETE), d4-leukotriene (LT) B4, d4-prostaglandin (PG)E2 and d5-lipoxin (LX) A4; 500pg each) and homogenized using a PTFE dounce (Kimble Chase). Proteins were allowed to precipitate (4°C), and lipid mediators were extracted using C18 solid-phase cartridges and a Biotage RapidTrace®. Measurement of lipid mediators was carried out by liquid chromatography-tandem mass spectrometry using a QTrap 5500 (ABSciex, Framingham, MA) equipped with a Shimadzu LC-20AD HPLC and a Shimadzu SIL-20AC autoinjector (Shimadzu, Kyoto, Japan). An Agilent Eclipse Plus C18 column (100mm × 4.6 mm × 1.8 μm) maintained at 50°C was used with a gradient of methanol/water/acetic acid of 55:45:0.01 (v/v/v) to 100:0:0.01 at 0.4 ml/min flow rate. Multiple reactions monitoring (MRM) was used to monitor lipid mediator profiles with more than 60 bioactive products from specific biosynthetic pathway including their pathway markers. Identification was carried out with signature ion fragments for each target lipid mediator (pro-inflammatory mediators PG, LT as well as SPM) using a minimum of six diagnostic ions. Quantification was achieved using calibration curves (Colas et al., 2014 (link)).
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3

Quantitative Lipidomics of Mouse Hearts

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After cardiac function analysis, mice were then deeply anesthetized with 3% isoflurane, and were euthanized with CO2. Hearts were placed in ice cold MeOH containing deuterated internal standards (d4-LTB4, d8-5S-HETE, d4-PGE2, d5-LXA4, and d5-RvD2, 500 pg each). These were gently homogenized, kept at −20°C for 45 min to allow for protein precipitation the subjected to solid phase extraction (18 (link)). Methyl formate fractions were brought to dryness using a TurboVap LP (Biotage) and products suspended in water-methanol (50:50 vol:vol) for LC-MS/MS. Here a Shimadzu LC-20AD HPLC and a Shimadzu SIL-20AC autoinjector (Shimadzu, Kyoto, Japan), paired with a QTrap 5500 (ABSciex, Warrington, UK) was utilized and operated as described previously (18 (link)). To monitor each LM and respective pathways, an MRM method was developed with diagnostic ion fragments (Table S1) and identification using recently published criteria (18 (link)), including matching retention time (RT) to synthetic and authentic materials and at least six diagnostic ions for each LM. Calibration curves were obtained for each using authentic compound mixtures and deuterium labeled LM at 3.12, 6.25, 12.5, 25, 50, 100, and 200 pg. Linear calibration curves were obtained for each LM, which gave r2 values of 0.98–0.99.
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4

Quantification of Lipid Mediators by LC-MS/MS

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Media and lysate samples were stored at −80 °C prior to analysis. 2 volumes of ice cold MeOH containing deuterated internal standards (d4-LTB4, d8-5S-HETE, d4-PGE2, d5-LXA4 and d5-RvD2, 500 pg each) were added to the samples. These were then kept at −20 °C for 45 minutes to allow for protein precipitation and subjected to solid phase extraction as per previous publication26 (link). Methyl formate fractions were then brought to dryness using a TurboVap LP (Biotage) and products suspended in water-methanol (50:50 vol:vol) for LC-MS-MS. A Shimadzu LC-20AD HPLC and a Shimadzu SIL-20AC autoinjector (Shimadzu, Kyoto, Japan), paired with a QTrap 5500 (ABSciex, Warrington, UK) were utilised and operated as described26 (link). To monitor each lipid mediator and respective pathways, a Multiple Reaction Monitoring (MRM) method was developed with diagnostic ion fragments and identification using recently published criteria26 (link), including matching retention time (RT) to synthetic and authentic materials and at least six diagnostic ions for each lipid mediator. Calibration curves were obtained for each using authentic compound mixtures and deuterium labeled lipid mediator at 0.78, 1.56, 3.12, 6.25, 12.5, 25, 50, 100, and 200 pg. Linear calibration curves were obtained for each lipid mediator, which gave r2 values of 0.98–0.99.
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5

LC-MS/MS Analysis of DNA Nucleosides

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LC-MS/MS analysis of nucleosides was carried out on a LC-MS/MS system consisting of an AB 3200 QTRAP mass spectrometer (Applied Biosystems, Foster City, CA, USA) and a Shimadzu LC-20AD HPLC (Tokyo, Japan). LC separation was conducted on a Hisep C18-T column (150 mm × 2.1 mm i.d., 5 μm, Weltech Co., Ltd., Wuhan, China) with a flow rate of 0.2 mL min−1 at 35 °C. Water (solvent A) and methanol (solvent B) were employed as mobile phases with a gradient of 5–50% B for 25 min. Mass spectrometry detection was carried out in the positive electrospray ionization mode, and nucleosides were monitored in the multiple reaction monitoring (MRM) mode. Mass transitions (precursor ions → product ions) of dC (228.1 → 112.1), dT (243.1 → 127.1), dA (252.1 → 136.1), dG (268.1 → 152.1), 5mC (242.1 → 126.1), 5hmC (258.1 →142.1), and 5gmC (268.1 → 142.1) were utilized to determine these nucleosides.
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6

Lipidomic Analysis of Inflammatory Mediators

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Samples were taken to solid-phase extraction (SPE) using Isolute C18 SPE 3 mL cartridges (Biotage, USA), as in Colas et al.15 (link). Briefly, internal standards (d8-5-HETE, d5-RvD2, d5-LXA4, d4-LTB4, d4-PGE2; 500 pg each; Cayman Chemicals, USA) were added along with four volumes of methanol before SPE, and covered on ice for 30-60 minutes to allow for protein precipitation. During SPE, 6 mL of water was eluted through each cartridge, followed by elution of 6 mL of hexane. Lipid mediators were collected by elution and collection of 6 mL of methyl formate. Methyl formate fractions from SPE were analyzed by a liquid chromatography-tandem mass spectrometry system, QTrap 5500 (AB Sciex) equipped with a Shimadzu LC-20AD HPLC (Tokyo, Japan). A Poroshell 120 EC-18 column (100 mm × 4.6 mm × 2.7 μm; Agilent Technologies, USA) was kept in a column oven maintained at 50°C, and lipid mediators (LMs) were eluted in a gradient of methanol/water/acetic acid from 55:45:0.01 (v/v/v) to 98:2:0.01 at 0.5 mL/min flow rate. In order to monitor and quantify the levels of targeted LMs, multiple reaction monitoring (MRM) was used with MS/MS matching signature ion fragments for each molecule (at least six diagnostic ions; ~0.1 pg limits of detection) and standard curves (r2>0.98 for each lipid mediator and pathway marker).
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7

Lipid Mediator Extraction and Quantification

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Blister exudates were placed in 2 volumes of ice-cold methanol containing deuterium-labeled standards (Cayman Chemicals). These were then kept at –20°C for 45 minutes to allow for protein precipitation and lipid mediators were extracted using C-18–based solid phase extraction as previously described (24 (link)). Methyl formate fractions were brought to dryness using a TurboVap LP (Biotage) and products suspended in water/methanol (50:50 vol/vol) for LC-MS/MS–based profiling. A Shimadzu LC-20AD HPLC and a Shimadzu SIL-20AC autoinjector, paired with a QTrap 5500 (ABSciex) were utilized and operated as previously described (24 (link)). To monitor each lipid mediator and deuterium-labeled internal standard, a multiple reaction monitoring (MRM) method was developed using parent ions and characteristic diagnostic ion fragments as previously described (24 (link)). This was coupled to an information-dependent acquisition and an enhanced product ion scan. Identification criteria included matching retention time to synthetic standards and at least 6 diagnostic ions in the MS/MS spectrum for each molecule. Calibration curves were obtained for each molecule using authentic compound mixtures and deuterium-labeled lipid mediator at 0.78, 1.56, 3.12, 6.25, 12.5, 25, 50, 100, and 200 pg. Linear calibration curves were obtained for each lipid mediator, which gave r2 values of 0.98–0.99.
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8

Mangosteen Pericarp Fractionation and Analysis

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Maceration and fractionation of the mangosteen pericarp were carried out using a procedure similar to that reported by Mulia et al. [15 ]. Dried mangosteen pericarp powder was mixed with 96% ethanol at a ratio of 1:3 (w/v) and macerated for 14 days with continuous stirring. The fractionation of extracts obtained from maceration was performed using a mixture of ethyl acetate and water (volume ratio of 1:1) in a separating funnel. The ethyl acetate fraction was separated and solvent was evaporated using a rotary evaporator.
The uv-spectrophotometry and high-performance liquid chromatography (HPLC) were used to determine the total mangostin and the α-mangostin content, respectively. The total mangostin in the ethyl acetate fraction was quantified as α-mangostin equivalent, based on the absorbance curve of α-mangostin standard solutions measured at a wavelength of 316 nm. The α-mangostin content was determined using a Shimadzu LC 20AD HPLC equipped with a reversed-phase C18 column (250nm×4.6nm, 5μm) at maintained at 30°C, and, a UV detector set at a wavelength of 244 nm. The mobile phase consisted of 95% acetonitrile and 5% buffer (0.1% H3PO4) was used with a flow rate of 1 mL/min and elution time of 8 min [16 ].
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9

Quantification and Profiling of Biomolecules by LC-MS/MS

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The LC-MS/MS system included a Shimadzu LC-20AD HPLC and a Shimadzu SIL-20AC autoinjector (Shimadzu) paired with a QTrap 5500 (ABSciex) coupled to a Poroshell 120 EC column (100 mm × 4.6 mm × 2.7 µm; Agilent) maintained at 50 °C using a column oven (ThermaSphere TS-130; Phenomenex) employed for identification and quantification. For product profiling the following mobile phase was employed: MeOH/H2 O/acetic acid of 55:45:0.1 (vol:vol:vol) with a gradient ramped to 80:20:0.1 (vol:vol:vol) for 8 min, that was held for 3 min and then ramped to 98:2:0.1 (vol:vol:vol) for the next 0.1 min and maintained at 98:2:0.1 (vol:vol:vol) for 4 min, with a flow rate maintained at 0.6 mL/min. The QTrap 5500 was operated in negative ionization mode using scheduled multiple reaction monitoring coupled with information-dependent acquisition (IDA) and an enhanced product ion scan (EPI).
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10

Lipidomics Analysis by LC-MS/MS

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All samples for LC-MS-MS-based lipidomics were subject to solid-phase extraction as described [11 (link)]. Prior to sample extraction, d4-LTB4 and d4-PGE2 internal standards (500 pg each) were added to facilitate quantification. Extracted samples were analyzed by a liquid chromatography-ultraviolet-tandem mass spectrometry system, QTrap 5500 (AB Sciex) equipped with a Shimadzu LC-20AD HPLC (Tokyo, Japan). A Poroshell 120 EC-18 column (100 mm × 4.6 mm × 2.7 µm; Agilent Technologies, Santa Clara, CA, USA) was kept in a column oven maintained at 50°C, and lipid mediators (LMs) were eluted with a gradient of methanol/water/acetic acid from 55:45:0.01 (v/v/v) to 100:0:0.01 at 0.5 mL/min flow rate. To monitor and quantify the levels of targeted LMs, multiple reaction monitoring (MRM) was used with MS/MS matching signature ion fragments for each molecule (six diagnostic ions and calibration curves) as in [11 (link)].
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