Two-dimensional liquid chromatography coupled to mass spectrometry for impurity analysis of dye-conjugated oligonucleotides

Modulation optimization when using a splitter pump after the first dimension in comprehensive two- dimensional liquid chromatography

The rapid growth in the use of two dimensional liquid chromatography (2D-LC) applied to the analysis of moderately to highly complex mixtures, has been fueled by continuous improvements in performance and robustness of the instrument components, as well as the ease-of-use of software necessary for controlling the 2D-LC instrument hardware, and analysis of the large data files that result from this type of work. This work has focused on the evaluation of the performance of an online full comprehensive mode (LC×LC), when an active modulation is implemented using a flow splitter pump placed after the 1D effluent. Two different types of splitting pumps were evaluated: a binary ultra-high pressure liquid chromatography (UHPLC) pump and a high precision syringe pump. We analyzed the performance (reproducibility in peak area and retention times and the 2D peak dispersion) as a function of the location of the active pump Before or After the modulation valve, and the influence of connecting tubes (based on internal diameter and length) necessary between the interface, waste, and the splitting pump. The effect on the flow direction on the filling and flushing of the injection loops at the modulation valve was also analyzed for each pump. In this study, we demonstrate that flow-splitting LCxLC assembly can be performed using either a UHPLC binary pump or a simple syringe pump. Flow splitting after the first dimension is a straightforward strategy to: (i) independently select the 1D column and flow rates with respect to the second dimension; (ii) consciously dilute the eluate according to the solvent characteristics of the second dimension, thereby avoiding 2D peak distortions; and (iii) adapt the injected amount to the second column according to the relative concentration of the components in a complex sample. However, careful consideration of the system setup is necessary. It is demonstrated how experimental results can be significantly affected in terms of peak broadening and reproducibility if optimization of the interface is not taken into account. In addition, under the optimized conditions, the reproducibility in peak area and dispersion in the 2D dimension were evaluated as a function of the amount of sample transferred in terms of percentage of filled loop.

Certification and long-term stability monitoring of low-content folic acid and 5-methyltetrahydrofolate in human plasma certified reference material by isotope dilution ultra-high performance liquid chromatography/tandem mass spectrometry

A reliable measurement of blood folate levels is necessary in the clinical field to prevent serious diseases such as cognitive impairment and neural tube defects. Herein, the certification of the low-content folic acid (FA) and 5-methyltetrahydrofolate (5-Me-THF) in human plasma certified reference material (KRISS CRM 111-01-018) was performed. A human plasma pool obtained from the Korean Red Cross was used as a CRM candidate. The certification of the human plasma CRM was performed by isotope dilution ultra-performance liquid chromatography/tandem mass spectrometry. Two-dimensional liquid chromatography was employed to confirm the validity of the analytical method for FA due to the susceptibility of FA to matrix effects because of its limited quantity. The CRM stability was evaluated at -20 °C for 2 months and at -70 °C for up to 12 months to determine the certified value of the CRM. The certified value of the CRM was (84.6 ± 4.3) ng kg-1 and (5.80 ± 0.47) μg kg-1 for FA and 5-Me-THF, respectively. The homogeneity of the CRM was 1.64% and 3.10% for FA and 5-Me-THF, respectively. Further long-term stability assessments were conducted, indicating that the CRM remains valid for at least 58 months at -70 °C for FA and 48 months for 5-Me-THF. Compared to other blood-based CRMs, this CRM has lower folate levels, making it helpful in establishing analytical methods for a broader range of folate levels.

Improved lipid analysis using a 2D-LC-MS system with a novel injection procedure

The aim of this study was to improve analysis of nonpolar lipidomics sample extracts using reversed phase (RP) chromatography. A 4/3/3 (v/v/v) mixture of methanol/methyl tert-butyl ether/chloroform (MeOH/MTBE/CHCl3, MMC) was chosen for sample extraction solvent based on its proven extraction capability for several lipid classes. To avoid carry over, loss of analytes and peak distortion the loops and all capillaries of the presented LC system were flushed and filled up with methanol until the analytical column. The choice of methanol was due to its weak elution strength and being infinitely miscible with MMC and several other nonpolar solvents. This allowed injection of a 100 μl sample that was 20 μl nonpolar extraction solvent diluted fivefold with methanol. All lipids of 25 lipid classes were transferred quantitatively to the column head where the online dilution of methanol was carried out with aqueous eluent for focusing the lipid analytes. The weak elution strength of methanol prevented peak distortions. The consecutive reversed phase elution resulted in remarkably narrow peaks (full width at half maximum was 0.07-0.08 min typically) and enhanced sensitivity (limit of detection usually in sub nM region) because of increased sample injection volume and narrow peaks. Calibration and quality control samples made by diluting commercial lipid standards 200-50000 times confirmed the applicability of this approach both for targeted lipid quantification and for untargeted quantitative comparison of lipids from different sources.

Liquid Chromatography Methods for Analysis of mRNA Poly(A) Tail Length and Heterogeneity

Messenger RNA (mRNA) is a new class of therapeutic compounds. The current advances in mRNA technology require the development of efficient analytical methods. In this work, we describe the development of several methods for measurement of mRNA poly(A) tail length and heterogeneity. Poly(A) tail was first cleaved from mRNA with the RNase T1 enzyme. The average length of a liberated poly(A) tail was analyzed with the size exclusion chromatography method. Size heterogeneity of the poly(A) tail was estimated with high-resolution ion-pair reversed phase liquid chromatography (IP RP LC). The IP RP LC method provides resolution of poly(A) tail oligonucleotide variants up to 150 nucleotide long. Both methods use a robust ultraviolet detection suitable for mRNA analysis in quality control laboratories. The results were confirmed by the LC-mass spectrometry (LC MS) analysis of the same mRNA sample. The poly(A) tail length and heterogeneity results were in good agreement.

Quantification of 10 B vitamins in mouse colon by LC-MS/MS: Application on breast cancer mice treated with doxorubicin

B vitamins play important roles in various physiological processes, including cell metabolism and DNA synthesis. The intestine is critical for the absorption and utilization of B vitamins, but few analytical methods for detecting intestinal B vitamins are currently available. In this study, we developed a novel liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the simultaneous quantification of 10 B vitamins in mouse colon tissue, including thiamin (B1), riboflavin (B2), nicotinic acid (B3), niacinamide (B3-AM), pantothenic acid (B5), pyridoxine (B6), pyridoxal 5'-phosphate (B6-5P), biotin (B7), folic acid (B9), and cyanocobalamin (B12). The method was thoroughly validated following the U.S. Food and Drug Administration (FDA) guidelines and yielded good results in terms of linearity (r² > 0.9928), lower limit of quantification (40-600 ng/g), accuracy (88.9-119.80 %) and precision (relative standard deviation ≤ 19.71 %), recovery (87.95-113.79 %), matrix effect (91.26-113.78 %), and stability (85.65-114.05 %). Furthermore, we applied our method to profile B vitamins in the colons of mice with breast cancer after doxorubicin chemotherapy treatment, which revealed that the doxorubicin treatment led to significant colon damage and accumulation of several B vitamins including B1, B2 and B5. We also confirmed the capability of this method for quantifying B vitamins in other intestinal tissues like the ileum, jejunum, and duodenum. The newly developed method is simple, specific, and useful for targeted profiling of B vitamins in mouse colon, with a potential for future studies on the role of these micronutrients in healthy and diseased states.

On-line Sequencing of CRISPR Guide RNAs and Their Impurities via the Use of Immobilized Ribonuclease Cartridges Attached to a 2D/3D-LC-MS System

In this study, for the first time, the automated digestion and sequencing of an RNA molecule via the use of immobilized RNase cartridges attached to a multidimensional liquid chromatography (LC)-mass spectrometry (MS) system are presented. We first developed an on-line digestion-HILIC two-dimensional (2D)-LC-MS method in order to sequence CRISPR guide RNAs for gene editing. Three RNases (T1, A, and U2) were immobilized on polyetheretherketone cartridges, and their performance was evaluated. Ultrafast digestions were performed within 2.3 min with the on-line approach versus 30 min via the conventional off-line approach. The higher sequence coverage was achieved by the RNase T1 (71%), which is the same as the off-line mode. A 20-fold reduction in the gRNA sample amount was achieved with the on-line digestion approach (6.5 μg) in comparison to that with the off-line approach (130 μg). In the second step, a three-dimensional (3D)-LC-MS method was developed for the sequencing of fractions collected on-line across the main peak and the partially separated tail by the reference ion-pairing RPLC method. Additional insights were gained in order to better understand the cause of the main peak tailing.

Recent advances in therapeutic nucleic acids and their analytical methods

Therapeutic nucleic acids are various chemically modified RNA or DNA with different functions, which mainly play roles at the gene level. Owing to its accurately targeting at pathogenic genes, nucleic acid based therapeutics have a wide range of application prospects. Recently, the improvement on chemical synthesis and delivery materials accelerated the development of therapeutic nucleic acids rapidly. Up to now, 17 nucleic acid based therapeutics approved by Food and Drug Administration (FDA) or European Medicines Agency (EMA). The development of therapeutics raised higher requirements for analytical methods, both in quality control and in clinical research. The first part of this review introduces different classes of therapeutic nucleic acids, including antisense oligonucleotide (ASO), RNA interference (RNAi) therapy, mRNA, aptamer and other classes which are under research. The second part reviews the therapeutic nucleic acids commercialized from 2019 to now. The third part discusses the analytical methods for nucleic acid based therapeutics, including liquid chromatography-based methods, capillary gel electrophoresis (CGE), hybridization enzyme-linked immunosorbent assay (ELISA) and other infrequently used methods. Finally, the advantages and shortcomings of these methods are summarized, and the future development of analysis methods are prospected.

An Effective QWBA/UHPLC-MS/Tissue Punch Approach: Solving a Pharmacokinetic Issue via Quantitative Met-ID

BACKGROUND

Methods to provide absolute quantitation of the administered drug and corresponding metabolites in tissue in a spatially resolved manner is a challenging but much needed capability in pharmaceutical research. Quantitative Whole-Body Autoradiography (QWBA) after a single- dose intravenous (3 mg/kg) and extravascular (30 mg/kg) administrations of an in vitro metabolically stable test compound (structure not reported here) indicated quick tissue distribution and excretion.

OBJECTIVE

Good bioavailability and short in vivo half-lives were determined formerly for the same test compound. For closing gaps in the understanding of pharmacokinetic data and in vitro results, radioactive hot spots on whole-body tissue sections had been profiled.

METHODS

Punches from selected tissue regions containing high radioactivity in the tissue sections previously analyzed by QWBA were extracted by a highly organic solvent and analyzed without any consecutive sample preparation step, applying Ultra High Performance Liquid Chromatography- Mass Spectrometry (UHPLC-MS) and off-line radioanalysis to maximize signal levels for metabolite identification and profiling.

RESULTS

The analysis revealed that the test compound was metabolized intensively by phase I reactions in vivo and the metabolites formed were excreted in bile and urine. The predominant metabolites showed abundant signal intensities both by MS and by radioanalysis but the MS signal intensities generally underestimated the real abundances of metabolites relative to the unchanged drug.

CONCLUSION

This work illustrates that maximizing the sensitivity of tissue punch radioanalysis and the combination with UHPLC-MS leads to a better insight into pharmacokinetic processes by providing quantitative data with high molecular selectivity.

Multiple heart-cutting mixed-mode chromatography-reversed-phase 2D-liquid chromatography method for separation and mass spectrometric characterization of synthetic oligonucleotides

Until today, ion-pair reversed-phase chromatography is still the dominating method for analytical characterization of synthetic oligonucleotides. Its hyphenation with mass spectrometry, however, has some drawbacks such as ion-suppression in electrospray ionization. To overcome this problem, we present in this work a multiple heart-cutting (MHC) two-dimensional liquid chromatography (2D-LC) method with ultra-violet (UV) and electrospray ionization (ESI) mass spectrometry (MS) detection. A reversed-phase/weak anion-exchange (RP/WAX) stationary phase in the first dimension (¹D) provides the selectivity for separation of structurally closely related oligonucleotide sequences and deletions (shortmers), respectively, using a mixed pH/triethylammonium phosphate buffer gradient at constant organic modifier content. Heart cuts of the oligonucleotide peaks are transferred to the second dimension (²D) via a multiple heart-cutting valve which is equipped with two loop decks. The ²D RP column is used for desalting via a diverter valve. Active solvent modulation enables to refocus the oligonucleotide peak into a sharp zone by ²D RP entirely free of non-volatile buffer components and ion-pair agents. Oligonucleotides can thus be sensitively detected by ESI-QTOF-MS under MS-compatible conditions.