Improvement of peak shape in aqueous normal phase analysis of anionic metabolites

LC-MS/MS quantification of bacterial and fungal signal peptides via direct injection: a case study of cross-kingdom communication

Bacteria and yeast use secreted signal peptides, also known as pheromones, for cell-cell communication within their respective species. Recently, genetic modification has allowed for the extension and exploitation of this type of communication, to communication between organisms from different species and even from different kingdoms. This innovative approach is intended to allow for the large-scale production of specific compounds for applications in medicine and biotechnology while producing reduced amounts of by-products. Until now, the detection of signal peptides, which are often short-lived and only present in small amounts, is usually qualitative, non-selective, and time-consuming and/or requires the presence of additional cell types. Here, an ESI-LC-MS/MS method for the specific quantification of signal peptides from yeast (α- and P-factor) and bacteria (CSF) using a TSKgel column operating under HILIC conditions has been demonstrated. The influence of different matrices, their adsorption behavior, and their stability were investigated. In matrix, LOQs of 0.05 µM, 0.03 µM, and 0.02 µM were obtained for CSF, α-factor, and P-factor, respectively. Subsequently, the developed method was applied to the detection of yeast- and bacteria-specific peptides secreted by genetically modified yeasts. It could be demonstrated that under overexpressing conditions, α-factor and P-factor concentrations of 1 µM were measured, while for CSF concentrations as high as 2.5 µM was reached. Finally, the established method permits the simultaneous, quantitative detection of signal peptides in different matrices and without pre-concentration in near-real time, thus advancing the possibility of tracking cross-kingdom communication.

Advanced Liquid Chromatography with Tandem Mass Spectrometry Method for Quantifying Glyphosate, Glufosinate, and Aminomethylphosphonic Acid Using Pre-Column Derivatization

Analytical limitations make it challenging to develop effective methodologies for understanding glyphosate-based herbicide levels in drinking water and groundwater. Due to their lack of chromophores and zwitterionic nature, glyphosate-based herbicides are difficult to detect using traditional methods. This paper offers a straightforward method for quantifying glyphosate, glufosinate, and aminomethylphosphonic acid (AMPA) via 9-fluorenylmethylchloroformate (FMOC-Cl) pre-column derivatization and analysis by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Method development was focused on optimizing the critical variables for optimal derivatization using a 24-factorial design. We found that complete derivatization significantly depends on the inclusion of borate buffer to create the alkaline conditions necessary for aminolysis. Ethylenediaminetetraacetic acid (EDTA) addition was critical to minimize metallic chelation and ensure reproducible retention times and peaks. However, EDTA concentrations ≥5% decreased peak intensity due to ion suppression. The FMOC-Cl concentration and derivatization time exhibited a direct proportional relationship, with the complete reaction achieved with 2.5 mM FMOC-Cl after 4 h. Concentrations of FMOC-Cl greater than 2.5 mM led to the formation of oxides, which interfere with the detection sensitivity and selectivity. Desirable results were achieved with 1% EDTA, 5% borate, and 2.5 mM FMOC-Cl, which led to complete derivatization after 4 h.

Bioinertization of nanoLC/MS/MS systems by depleting metal ions from the mobile phases for phosphoproteomics

We have successfully developed a bioinertized nanoflow liquid chromatography/tandem mass spectrometry (nanoLC/MS/MS) system for the highly sensitive analysis of phosphopeptides by depleting metal ions from the mobile phase. We found that not only direct contact of phosphopeptides with metal components, but also indirect contact with nanoLC pumps through the mobile phase causes significant losses during the recovery of phosphopeptides. Moreover, electrospray ionization was adversely affected by the mobile phase containing multiple metal ions as well as by the sample solvents contaminated with metal ions used in immobilized metal ion affinity chromatography for phosphopeptide enrichment. To solve these problems, metal ions were depleted by inserting an on-line metal ion removal device containing metal-chelating membranes between the gradient mixer and the autosampler. As a result, the peak areas of the identified phosphopeptides increased an average of 9.9-fold overall and 77-fold for multiply phosphorylated peptides with the insertion of the on-line metal ion removal system. This strategy would be applicable to highly sensitive analysis of other phosphorylated biomolecules by microscale-LC/MS/MS.

Isotopic tracing of glucose metabolites in human monocytes to assess changes in inflammatory conditions

Differences in metabolic profiles can link to functional changes of immune cells in disease conditions. Here, we detail a protocol for the detection and quantitation of 19 metabolites in one analytical run. We provide the parameters for chromatographic separation and mass spectrometric analysis of isotopically labeled and unlabeled metabolites. We include steps for incubation and sample preparation of PBMCs and monocytes. This protocol overcomes the chromatographic challenges caused by the chelating properties of some metabolites.

Assessing the impact of nonspecific binding on oligonucleotide bioanalysis

Aim: Accurate and reliable quantification of oligonucleotides can be difficult, which has led to an increased focus on bioanalytical methods for more robust analyses. Recent advances toward mitigating sample losses on liquid chromatography (LC) systems have produced recovery advantages for oligonucleotide separations. Results & methodology: LC instruments and columns constructed from MP35N metal alloy and stainless steel columns were compared against LC hardware modified with hybrid inorganic-organic silica surfaces. Designed to minimize metal-analyte adsorption, these surfaces demonstrated a 73% increase in 25-mer phosphorothioate oligonucleotide recovery using ion-pairing reversed-phase LC versus standard LC surfaces, most particularly upon initial use. Conclusion: Hybrid silica chromatographic surfaces improve the performance, detection limits and reproducibility of oligonucleotide bioanalytical assays.

An exploratory approach for an oriented development of an untargeted hydrophilic interaction liquid chromatography-mass spectrometry platform for polar metabolites in biological matrices

The analysis of polar metabolites based on liquid chromatography-mass spectrometry (LC-MS) methods should take into consideration the complexity of interactions in LC columns to be able to cover a broad range of metabolites of key biological pathways. Therefore, in this study, different chromatographic columns were tested for polar metabolites including reversed-phase and hydrophilic interaction liquid chromatography (HILIC) columns. Based on a column screening, two new generations of zwitterionic HILIC columns were selected for further evaluation. A tree-based method optimization was applied to investigate the chromatographic factors affecting the retention mechanisms of polar metabolites with zwitterionic stationary phases. The results were evaluated based on a scoring system which was applied for more than 80 polar metabolites with a high coverage of key human metabolic pathways. The final optimized methods showed high complementarity to analyze a wide range of metabolic classes including amino acids, small peptides, sugars, amino sugars, phosphorylated sugars, organic acids, nucleobases, nucleosides, nucleotides and acylcarnitines. Optimized methods were applied to analyze different biological matrices, including human urine, plasma and liver cell extracts using an untargeted approach. The number of high-quality features (< 30% median relative standard deviation) ranged from 3,755 for urine to 5,402 for the intracellular metabolome of liver cells, showing the potential of the methods for untargeted purposes.

Oligonucleotide quantification and metabolite profiling by high-resolution and accurate mass spectrometry

Aim: Advancements in RNA interference therapeutics have triggered development of improved bioanalytical methods for oligonucleotide metabolite profiling and high-throughput quantification in biological matrices. Results & methodology: HPLC coupled with high-resolution mass spectrometry (LC-HRMS) methods were developed to investigate the metabolism of a REVERSIR™ molecule in vivo. Plasma and tissue samples were extracted using solid-phase extraction followed by LC-HRMS analysis for metabolite profiling and quantification. The method was qualified from 10 to 5000 ng/ml (plasma) and 100 to 50000 ng/g (liver and kidney). In rat liver, intra and interday accuracy ranged from 80.9 to 118.5% and 88.4 to 111.9%, respectively, with acceptable precision (<20% CV). Conclusion: The LC-HRMS method can be applied for metabolite profiling and quantification of oligonucleotides in biological matrices.

Quantitative Profiling of Endogenous Metabolites Using Hydrophilic Interaction Liquid Chromatography-Tandem Mass Spectrometry (HILIC-MS/MS)

Dynamic modeling of metabolic reaction networks requires absolute quantification of intracellular and extracellular metabolite concentrations with high precision and accuracy. This chapter presents a robust HILIC-ESI-MS/MS procedure for targeted quantitative profiling of more than 50 polar key metabolites in multicomponent endogenous extracts. Without using ion-pairing-agents or prior derivatization protocols, organic acids, amino acids, sugar phosphates, coenzymes, and nucleotides are measured on a triple quadrupole platform in positive and negative electrospray ionization modes with preoptimized MRM transitions. Robust polymer-based zwitterionic stationary phases (ZIC®-pHILIC) support alkaline mobile phase conditions (pH 9.2) for enhancing retention and chromatographic performance of polar analytes in bicratic elution mode without unfavourable column bleed. The quality of the method was extensively validated and demonstrated by absolute metabolite quantification in endogenous Escherichia coli extracts by comparative use of standard-based external calibration, isotope dilution, and standard addition as quantification strategies. In sum, alkaline ZIC®-pHILIC chromatography emerged as an efficient approach providing high selectivity and sensitivity for comprehensive metabolic studies.

Improved LC/MS Methods for the Analysis of Metal-Sensitive Analytes Using Medronic Acid as a Mobile Phase Additive

Phosphorylated compounds and organic acids with multiple carboxylate groups are commonly observed to have poor peak shapes and signal in LC/MS experiments. The poor peak shape is caused by the presence of trace metals, particularly iron, contributed from a variety of sources within the chromatographic system. To ameliorate this problem, different solvent additives were investigated to reduce the amount of metal in the flow path to achieve better analytical performance for these metal-sensitive compounds. Here, we introduce the use of a solvent additive that can significantly improve the peak shapes and signal of metal-sensitive metabolites for LC/MS analysis. Moreover, the additive is shown to be amenable for other metal-sensitive applications, such as the analysis of phosphopeptides and polar phosphorylated pesticides, where the instruments could be used in either positive or negative analysis mode.

Novel and potent anti-tumor and anti-metastatic di-2-pyridylketone thiosemicarbazones demonstrate marked differences in pharmacology between the first and second generation lead agents

Di(2-pyridyl)ketone 4,4-dimethyl-3-thiosemicarbazone (Dp44mT) and di(2-pyridyl)ketone 4-cyclohexyl-4-methyl-3-thiosemicarbazone (DpC) are novel, highly potent and selective anti-tumor and anti-metastatic drugs. Despite their structural similarity, these agents differ in their efficacy and toxicity in-vivo. Considering this, a comparison of their pharmacokinetic and pharmaco/toxico-dynamic properties was conducted to reveal if these factors are involved in their differential activity. Both compounds were administered to Wistar rats intravenously (2 mg/kg) and their metabolism and disposition were studied using UHPLC-MS/MS. The cytotoxicity of both thiosemicarbazones and their metabolites was also examined using MCF-7, HL-60 and HCT116 tumor cells and 3T3 fibroblasts and H9c2 cardiac myoblasts. Their intracellular iron-binding ability was characterized by the Calcein-AM assay and their iron mobilization efficacy was evaluated. In contrast to DpC, Dp44mT undergoes rapid demethylation in-vivo, which may be related to its markedly faster elimination (T_1/2 = 1.7 h for Dp44mT vs. 10.7 h for DpC) and lower exposure. Incubation of these compounds with cancer cells or cardiac myoblasts did not result in any significant metabolism in-vitro. The metabolism of Dp44mT in-vivo resulted in decreased anti-cancer activity and toxicity. In conclusion, marked differences in the pharmacology of Dp44mT and DpC were observed and highlight the favorable pharmacokinetics of DpC for cancer treatment.

Improving detection sensitivity of amino acids in thyroid tissues by using phthalic acid as a mobile phase additive in hydrophilic interaction chromatography-electrospray ionization-tandem mass spectrometry

In this work, 0.08 mmol L(-1) of phthalic acid was introduced as a mobile phase additive to quantify free amino acids (AAs) by hydrophilic interaction liquid chromatography (HILIC) coupled with electrospray ionization tandem mass spectrometry (ESI-MS/MS). The addition of phthalic acid significantly increased the signal intensity of protonated AA ions, resulting from the decrease of the relative abundance of AA sodium adducts. Meanwhile, the chromatographic peak shapes of AAs were optimized. As a consequence, there was a noticeable increase in the sensitivity of detection for AAs. The limits of detection (LOD) and quantification (LOQ) of the AAs ranged from 0.0500 to 20.0 ng mL(-1) and from 0.100 to 50.0 ng mL(-1), respectively, which were 4-50 times lower compared to the values measured without the addition of phthalic acid. The enhanced detection and separation of AAs were obtained by merely adding phthalic acid to the mobile phase without changing other conditions. Eventually, this simple method was validated and successfully applied to the analysis of twenty-four kinds of free AAs in human thyroid carcinoma and para-carcinoma tissues, demonstrating a significant increase of most AAs in thyroid carcinoma tissues (p<0.05).

Silica, hybrid silica, hydride silica and non-silica stationary phases for liquid chromatography

Free silanols on the surface of silica are the "villains", which are responsible for detrimental interactions of those compounds and the stationary phase (i.e., bad peak shape, low efficiency) as well as low thermal and chemical stability. For these reasons, we began this review describing new silica and hybrid silica stationary phases, which have reduced and/or shielded silanols. At present, in liquid chromatography for the majority of analyses, reversed-phase liquid chromatography is the separation mode of choice. However, the needs for increased selectivity and increased retention of hydrophilic bases have substantially increased the interest in hydrophilic interaction chromatography (HILIC). Therefore, stationary phases and this mode of separation are discussed. Then, non-silica stationary phases (i.e., zirconium oxide, titanium oxide, alumina and porous graphitized carbon), which afford increased thermal and chemical stability and also selectivity different from those obtained with silica and hybrid silica, are discussed. In addition, the use of these materials in HILIC is also reviewed.

Accurate mass-time tag library for LC/MS-based metabolite profiling of medicinal plants

We report the development and testing of an accurate mass-time (AMT) tag approach for the LC/MS-based identification of plant natural products (PNPs) in complex extracts. An AMT tag library was developed for approximately 500 PNPs with diverse chemical structures, detected in electrospray and atmospheric pressure chemical ionization modes (both positive and negative polarities). In addition, to enable peak annotations with high confidence, MS/MS spectra were acquired with three different fragmentation energies. The LC/MS and MS/MS data sets were integrated into online spectral search tools and repositories (Spektraris and MassBank), thus allowing users to interrogate their own data sets for the potential presence of PNPs. The utility of the AMT tag library approach is demonstrated by the detection and annotation of active principles in 27 different medicinal plant species with diverse chemical constituents.

Silica hydride-based chromatography of LC–MS response-altering compounds native to human plasma

Background: An investigation was carried out into the chromatographic behavior, on a silica hydride-based phase and a comparator silica-based phase, of an important group of lipids endogenous to human plasma, which are associated with matrix effect and in the context of quantitative peptide analysis. Results: The propensity for aqueous normal phase (ANP) retention on the silica hydride-based phase was strong and extensive in comparison with the silica-based comparator, and the lipophilic interferences in question were readily eluted using the ANP mode, a contrast to over-retention issues with accompanying implications for method ruggedness typically found with silica-based phases. Conclusion: The silica hydride-based phase, with ANP operation, offered selectivity conducive to rapid lipophilic interferent elimination and the bimodal retention involved in suitable gradient elution was appropriate for general peptide analytical application.

A new approach to bioanalysis: aqueous normal-phase chromatography with silica hydride stationary phases

Stationary phases based on silica hydride have demonstrated a number of unique properties that are especially advantageous for bioanalyses. They have excellent retention capabilities for hydrophilic compounds, which have been the most difficult to analyze by standard reversed-phase methods and, in many cases, can outperform newer approaches for the analysis of polar molecules, such as hydrophilic liquid interaction chromatography. In addition, all columns utilizing silica-hydride materials can be used in either the normal-phase or reversed-phase modes, sometimes retaining both polar and nonpolar compounds simultaneously. These stationary phases have a high degree of reproducibility and long-term stability.