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7 protocols using agilent 6460 triple quadrupole ms

1

Sialylated N-Glycan Profiling by LC-MS/MS

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Dried sialylated N-glycans were reconstituted by 50 μl of water and then analyzed using Agilent 1260 LC system coupled to an Agilent 6460 triple quadrupole MS (Agilent Technologies, Santa Clara, CA). A Thermo Hypercarb™ column (3 mm i.d., 100 mm length, and 3 µm particle size) was used for LC separation. Upon injection of 2 μl of sample, sialylated N-glycans were chromatographically separated for 45 min using binary gradient consisting of solvent A of 3% ACN with 0.1% FA (v/v) and solvent B of 90% ACN with 0.1% FA (v/v) at a flow rate of 0.3 ml/min. The LC gradient used was as follows: 0–0.25 min, 7%, 0.3 ml/min B; 0.25–10 min, 7%–15%, 0.3 ml/min B; 10–25 min, 15%–40%, 0.3 ml/min B; 25–30 min, 40%–100%, 0.3 ml/min B; 30–35 min, 100%, 0.3 ml/min B; 35–35.1 min, 100%–7%, 0.3 ml/min B; and 35.1–45 min, 7%, 0.3 ml/min B. MS was operated in the positive mode. The first and third quadrupoles were operated at unit resolution. The optimal parameters used were as follows: dry gas temperature 250°C, dry gas flow 10 l/min, nebulizer pressure 30 psi, sheath gas temperature 300°C, sheath gas flow 12 l/min, and capillary voltage 4,000 V. MRM transitions monitored for the study are listed in Supplementary Table S2.
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2

Eicosanoid Profiling by HPLC-MS/MS

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Eicosanoid analysis was performed using an HPLC Agilent 1290 Infinity on a ZorBAX SB-C18 analytical column (50 × 2.1 mm, 1.8 μm) (Agilent Technologies) maintained at 40 °C. The mobile phases were composed of two solvents: solvent A, H2O with 0.1% (v/v) HCOOH, and solvent B, ACN with 0.1% (v/v) HCOOH. The flow rate of the mobile phase was 0.35 mL.min−1, and the injection volume was 5 µL. The gradient of the elution was as follows: 0% B at 0 min, 85% B at 8.5 min, 100% B at 9.5 min for 1 min.
The liquid chromatography was coupled to an Agilent 6460 triple quadrupole MS with an ESI source in negative mode. The monitoring of fragmentation was executed in Selection Reaction Monitoring (SRM) detection mode. Finally, peak detection, integration and quantitative analysis were obtained using the MassHunter Quantitative analysis software version B.09.00 (Agilent Technologies).
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3

HPLC-MS/MS Analysis of Compounds

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High-performance liquid chromatography was performed using an Agilent 1290 Infinity. The analytical column was a ZorbaxSB-C18 column (2.1 mm, 50 mm, 1.8 μm) (Agilent Technologies) maintained at 40 °C. The mobile phases consisted of water, acetonitrile, and formic acid (75:25:0.1; v/v/v) (A) or (0:100:0.1, v/v) (B). The linear gradient was as follows: 0% B at 0 min, 85% B at 8.5 min, 100% B at 9.5 min, 100% B at 10.5 min, and 0% B at 12 min. The flow rate was 0.35 mL/min and the injection volume was 5 μL. The HPLC system was coupled on-line to an Agilent 6460 triple quadrupole MS (Agilent Technologies). Electrospray ionization was performed in negative ion mode. Analyses were performed in selected reaction monitoring detection mode. Peak detection, integration, and quantitative analysis were conducted using Mass Hunter Quantitative analysis software (Agilent Technologies) via correlation with the IS response.
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4

DMAE-NAC Adduct Identification by LC-MS

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The reaction mixture of NAC and DMAE-CB (in water) after pre-incubation of 48 h was further analyzed using LC-MS to confirm the formation of the DMAE-NAC adduct. LC-MS analysis was performed using an Agilent 6460 triple quadrupole MS (Agilent Technologies) equipped with electrospray ionization source. Electrospray ionization (ESI) was performed in negative ion mode. After optimization, the source parameters used were as follows: source temperature was set at 300°C, nebulizer gas (nitrogen) flow rate was 10 L/min, sheath gas temperature was 400°C, sheath gas (nitrogen) flow rate was 6 L/min and the spray voltage was -3500 V. Data were acquired in MS scanning mode and recorded in the 100–800 m/z region. The analysis was repeated for three times for each group. Peak detection, integration and quantitative analysis were done using Mass Hunter Quantitative analysis software (Agilent Technologies).
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5

Quantification of Thyroid and Cortisol Hormones

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T3 was measured by isotope dilution LC-MS/MS using the Agilent 6460 triple quadrupole MS coupled with an ESI source and Agilent 1200 Infinity series HPLC (Agilent Technologies, Santa Clara, CA, USA) as previously described.16 (link),19 (link) FT3 and FT4 were separated from protein-bound hormones by ultrafiltration at 37°C, followed by measurement by isotope dilution LC-MS/MS using an AB Sciex Triple Quad 6500 (AB Sciex, Concord, ON, Canada) and Shimadzu LC-20AD HPLC (Shimadzu Instruments, Columbia, MD, USA) as previously described.36 (link) Complete method validation studies and diurnal reference intervals for thyroid hormones have been established.37 (link)Cortisol was measured by isotope dilution LC-MS/MS using the Agilent 6490 triple quadrupole MS coupled with an atmospheric pressure photoionization source and Agilent 1200 Infinity series HPLC (Agilent Technologies, Santa Clara, CA, USA) as previously described.38 (link),39 (link) Complete method validation studies and diurnal variations have been established.40 (link)
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6

Quantitative Analysis of Adenosine Nucleosides

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Analysis of nucleosides
was performed with Agilent 1290 UHPLC and Agilent 6460 Triple Quadrupole
MS (both from Agilent Technologies Inc., Santa Clara, CA). The injected
sample volume was 5 μL. Chromatographic separation of adenosine
and N6-methylated adenosine was done with a reversed phase column
(2.1 × 100 mm, 1.7 μm Waters). UHPLC eluents were A, 10
mM ammonium formate at pH 5 and B, methanol. Gradient elution was
from 5 to 25% B in 5 min followed by 4 min at 5% MeOH, total flow
being 400 μL/min. Retention times of monitored adenosine nucleosides
were 3.6 and 5.6 min, respectively. A mass spectrometer was set to
the positive electrospray ionization mode with the daughter ion analysis
mode (MS/MS) (Ade 268 → 136 m/z and 6mAde
282 → 150 m/z) using collision energy 7 and
21, respectively. Ion optimization was done using automatic tuning
with source capillary temperature at 400, and 250 °C was used
as transfer line temperature. A mixture of nitrogen and air was used
as electrospray ionization gases, and argon was used as collision
gas. Quantification of sample analysis was done with the instrument’s
quantitation program for adenosine at 1–10,000 nM and for N6-methylated
adenosine at 0.5–3000 μM concentration ranges.
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7

Quantitative Oxylipin Profiling Methodology

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Oxylipins were analyzed within a week following extraction to minimize the potential impact of prolonged storage on lipid oxidation. The samples were stored in a −80°C freezer during this period. Seventy-two oxylipins were analyzed on an Agilent 1290 LC (Agilent Corporation) coupled to an Agilent 6460 Triple Quadrupole MS (Agilent Corporation). Oxylipin species were separated on an Agilent Eclipse Plus C18 column (2.1 × 150 mm, 1.8 μm, Agilent Corporation) with a binary gradient consisting of solvent A (water containing 0.1% acetic acid) and solvent B (Acetonitrile: methanol 80:15 containing 0.1% acetic acid). The autosampler temperate was 4°C and the column temperature was maintained at 45°C. The gradient profile is shown in Supplementary Table 2. Oxylipins were ionized with negative-mode electrospray ionization. The ion source gas temperature was 250°C, gas flow was 10 L/min, sheath gas temperature was 300°C, sheath gas flow was 11 mL/min, nebulizers were at 35 psi, and the capillary gas was at 3500 V/−3500 V. Optimization parameters and ion pairs for each oxylipin are described in Supplementary Table 1. Oxylipins were detected using dynamic multiple reaction monitoring mode.
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