High-Resolution MS (HRMS) for Quantitation of Oligonucleotides
HRMS in full-scan mode provides selectivity and can improve the detection limit considerably. Therefore, HRMS is especially advantageous for the analysis of oligonucleotides. The method achieved a 5–10 ng/ml lower limit of quantitation (LLOQ) for double stranded oligonucleotides with an 18–22-mer oligonucleotide in each strand using TripleTOF mass spectrometer system.
Materials
Chemicals such as 1,1,1,3,3,3-hexafluoro-isopropanol (HFIP), diisopropylamine (DIPA), tetrahydrofuran, ammonium acetate and ammonium bicarbonate, were purchased from Sigma-Aldrich Inc. (MO, USA). HPLC grade methanol and acetonitrile were obtained from Fisher Scientific (PA, USA). Clarity OTX lysis buffer and SPE cartridges were obtained from Phenomenex Inc. (CA, USA).
Preparation of stock & working solutions
Oligonucleotide solution was prepared in deionized water to give a final concentration of 2 mg/ml. IS stock solution concentration was 300 μg/ml. Working solutions of the oligonucleotides were prepared by spiking stock solutions into plasma. The calibration samples were prepared with concentrations of 10, 20, 100, 300, 1000, 3000, 9000 and 10,000 ng/ml and QC samples with concentrations of 10, 30, 400, 4000 and 8000 ng/ml.
For calibration standards 100 μl of these solutions were then spiked with 50 μl of IS working solution before extraction.
Sample preparation for plasma & urine samples
The equilibration buffer consisted of ammonium acetate, NaN3 and K2EDTA in water and the pH was adjusted with acetic acid to 5.5. The washing buffer 1 consisted of ammonium acetate in 50:50 water:acetonitrile and pH was adjusted with acetic acid to 5.5. The washing buffer 2 consisted of ammonium acetate in 10:90 water:acetonitrile and the pH was adjusted to 5.5 with acetic acid. The elution buffer contained ammonium bicarbonate, pH adjusted to 8.8 with ammonium hydroxide, acetonitrile and tetrahydrofuran.
Extraction was performed using a semi-automated TomTec Quadra 4 SPE 96-well format liquid handler. The SPE cartridges were conditioned using methanol and equilibration buffer sequentially.
Plasma samples were then mixed with IS and Clarity OTX buffer and loaded onto the column. The cartridges were washed using washing buffer 1 and 2 and the analytes were eluted using elution buffer into a plate containing RNA recovery solution.
The collected solutions were evaporated to dryness and reconstituted with reconstitution solution. The reconstitution solvent contained water, methanol, DIPA, HFIP, EDTA in water, acetonitrile and ammonium hydroxide. A total of 10 μl of the reconstituted solution was injected into the uHPLC–TOF system for analysis.
Sample preparation for tissue samples
Tissue samples underwent disruption to produce a frozen powder using a SPEX Geno/Grinder (Spex Sample Prep LLC, NJ, USA). Tissue powder was homogenized by adding Clarity OTX Lysis-Loading buffer (Phenomenex, CA, USA) to produce a 100 mg/ml mixture of tissue homogenate. After mixing for 3 h at ambient temperature, the tissue homogenate was centrifuged. The tissue lysate was separated out and used for standard and QC preparations.
The calibration standards in tissue lysate ranged from 10–10,000 ng/ml and 100–100,000 ng/g in terms of tissue concentration. The extraction, LC–TOF–MS and quantitation methods for tissue were similar to plasma methods.
Instrumentation LC–TOF–MS conditions
Samples were analyzed using reversed-phase uHPLC with ESI TOF–MS detection using high resolution TripleTOF™ system (AB Sciex LLC, MA, USA).
In TOF-MS quantitation, each peak in the isotopic envelope of the [M-4]4-and [M-3]3- charged states was extracted using a 50–75 mDa extraction window. Accurate mass of ten most intense ions (m/z) for each strand of the analyte, antisense and sense and each strand of IS, antisense and sense were monitored in the negative ion mode.
The peak area for the analyte or IS was the sum of the response from the respective ten ions. Waters Acquity BEH C18 column (2.1 × 50 mm, 1.7 μm, Waters Corporation, MA, USA) was used with a flow rate of 0.85 ml/min and the following mobile phases: Mobile phase A is H2O:DIPA:HFIP (100:0.15:0.264 v/v/v) and mobile phase B is H2O:MeOH: DIPA:HFIP (50:50:0.15:0.264, v/v/v/v). The gradient was from 30%B increased to 50%B in 1.6 min, then to 100%B in 0.1 min and maintained for 0.5 min, followed by re-equilibration with 30%B for 0.6 min. The column temperature was maintained at 70◦C.
Method validation in plasma
Plasma calibration curves were constructed using peak area ratios of the oligonucleotide to the IS and applying a weighted (1/x2) quadratic regression. The following parameters were assessed during method validations.
- Precision and accuracy
- Interday accuracy and precision .
- Evaluation of method selectivity
- Relative extraction recovery
- Matrix effects
- Linearity of dilution
- Carryover evaluations
The validation workflow includes acquisition of full scan TOF MS spectra and use of high resolution extracted ion (XIC) for quantitation, summing multiple ions (m/z) to achieve sensitivity. The post-acquisition data mining is a significant advantage of this workflow and it allowed us to easily identify and mine metabolites. Data were acquired using Analyst TF™1.7 and quantitation was performed using MultiQuant™ software.
Summary Results:
Calibration standards met acceptance criteria that a minimum of 75% of the total number of calibration standards in the calibration range (between and including the LLOQ and the ULOQ [upper limit of quantification]) were ±15.0% (±20.0% at the method LLOQ concentration) from their nominal values.
The method was accurate and precise and met all the validation criteria.
For urine and tissue samples, the slightly higher acceptance criteria for %recovery were deemed acceptable for fit for purpose use.
Reference and Related Publication
https://doi.org/10.4155/bio-2019-0134