Qualitative and quantitative analysis of amino acids by capillary electrophoresis-electrospray ionization-tandem mass spectrometry

Determination of amino acids and peptides without their pre-column derivatization by capillary electrophoresis with ultraviolet and contactless conductivity detection. An overview

This review provides an overview of recent works focusing on the determination of amino acids (AAs) and peptides using capillary electrophoresis with contactless conductivity detection and ultraviolet (UV) detection, which is the most widespread detection in capillary electromigration techniques, without pre-capillary derivatization. Available options for the UV detection of these analytes, such as indirect detection, complexation with transition metal ions, and in-capillary derivatization are described. Developments in the field of direct detection of UV-absorbing AAs and peptides as well as progress in chiral separation are described. A separate section is dedicated to using on-line sample preconcentration methods combined with capillary electrophoresis-UV.

Robust and versatile assembly for emitter positioning, observation, and heating in atmospheric pressure field desorption mass spectrometry

Atmospheric pressure field desorption (APFD) mass spectrometry (MS) has recently been introduced as a new variant of field desorption (FD) mass spectrometry. The development aimed at providing the basic characteristics of FD-MS in combination with instruments equipped with an atmospheric pressure (AP) interface. Hitherto, APFD has been demonstrated to yield both positive and negative even electron ions of highly polar or ionic compounds as well as to enable the generation of positive molecular ions, M+•, of polycyclic aromatic compounds. The prototype setup for APFD was based on a nano-electrospray ionization (nanoESI) source slightly modified to allow for emitter positioning in front of the AP interface of a Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometer. The entrance electrode of the interface was set to negative or positive high voltage with respect to the emitter at ground potential, thereby permitting the formation of positive or negative ions, respectively. This work describes a custom-built device for quicker and more reproducible sample loading on and positioning of field emitters at the entrance electrode of the atmospheric pressure interface of a mass spectrometer. In addition, the device provides means for observation of the emitter during operation and for resistive emitter heating as employed in traditional FD-MS. Emitter heating both speeds up the desorption of the analytes and allows for the desorption/ionization of analytes of higher molecular weight than without emitter heating. In some cases, the signal-to-noise ratio of APFD mass spectra is improved due to higher ion currents effected by compressing the entire process into shorter periods of spectral acquisition. The new setup enables robust and reliable operation in APFD-MS. Moreover, it has been designed as to allow for use on a range of instruments as it can either be used on an FT-ICR mass spectrometer or in combination with a trapped ion mobility-quadrupole-time-of-flight (TIMS-Q-TOF) instrument.

Application of atmospheric pressure field desorption for the analysis of anionic surfactants in commercial detergents

Recent work has shown that field desorption (FD) and field ionization (FI) using activated field emitters may be performed at atmospheric pressure, too. While some limitations apply to atmospheric pressure field desorption (APFD) mass spectrometry (MS), the method can deliver both positive and negative even electron ions of highly polar or ionic compounds. Furthermore, APFD even permits the generation of positive molecular ions of polycyclic aromatic compounds. Here, an application of negative-ion APFD for the analysis of anionic surfactants contained in commercial detergent products for body care, household, and technical uses is presented. The samples include liquid soaps and shower gels, dishwashing liquids, and cooling lubricants. Surfactant solutions in methanol/water or pure methanol at 2-10 µl ml-1 were deposited on commercial 13-µm activated tungsten emitters. The emitters were positioned in front of the atmospheric pressure interface of a Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometer by means of a slightly modified nano-electrospray ionization (nanoESI) source. The entrance electrode of the interface was set to positive high voltage with respect to the emitter at ground potential. Under these conditions, negative-ion desorption was achieved. The surfactant anions, organic sulfates and organic sulfonates, were characterized by accurate mass-based formula assignments, and in part, by tandem mass spectrometry. The negative-ion APFD spectra were compared to results by negative-ion electrospray ionization (ESI) either obtained using the FT-ICR mass spectrometer or by using a trapped ion mobility-quadrupole-time-of-flight (TIMS-Q-TOF) instrument when product ions of low m/z needed to be detected in tandem MS.

Decoding Metabolic Symbiosis between Pancreatic Cancer Cells and Cancer-Associated Fibroblasts Using Cultured Tumor Microenvironment

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with a poor prognosis, largely due to its unique tumor microenvironment (TME) and dense fibrotic stroma. Cancer-associated fibroblasts (CAFs) play a crucial role in promoting tumor growth and metastasis, contributing to the metabolic adaptation of PDAC cells. However, the metabolic interactions between PDAC cells and CAFs are not well-understood. In this study, an in vitro co-culture model was used to investigate these metabolic interactions. Metabolomic analysis was performed under monoculture conditions of Capan-1 PDAC cells and CAF precursor cells, as well as co-culture conditions of PDAC cells and differentiated inflammatory CAF (iCAF). Co-cultured Capan-1 cells displayed significant metabolic changes, such as increased 2-oxoglutaric acid and lauric acid and decreased amino acids. The metabolic profiles of co-cultured Capan-1 and CAFs revealed differences in intracellular metabolites. Analysis of extracellular metabolites in the culture supernatant showed distinct differences between Capan-1 and CAF precursors, with the co-culture supernatant exhibiting the most significant changes. A comparison of the culture supernatants of Capan-1 and CAF precursors revealed different metabolic processes while co-culturing the two cell types demonstrated potential metabolic interactions. In conclusion, this study emphasizes the importance of metabolic interactions between cancer cells and CAFs in tumor progression and highlights the role of TME in metabolic reprogramming.

Augmented region of interest for untargeted metabolomics mass spectrometry (AriumMS) of multi-platform-based CE-MS and LC-MS data

In mass spectrometry (MS)-based metabolomics, there is a great need to combine different analytical separation techniques to cover metabolites of different polarities and apply appropriate multi-platform data processing. Here, we introduce AriumMS (augmented region of interest for untargeted metabolomics mass spectrometry) as a reliable toolbox for multi-platform metabolomics. AriumMS offers augmented data analysis of several separation techniques utilizing a region-of-interest algorithm. To demonstrate the capabilities of AriumMS, five datasets were combined. This includes three newly developed capillary electrophoresis (CE)-Orbitrap MS methods using the recently introduced nanoCEasy CE-MS interface and two hydrophilic interaction liquid chromatography (HILIC)-Orbitrap MS methods. AriumMS provides a novel mid-level data fusion approach for multi-platform data analysis to simplify and speed up multi-platform data processing and evaluation. The key feature of AriumMS lies in the optimized data processing strategy, including parallel processing of datasets and flexible parameterization for processing of individual separation methods with different peak characteristics. As a case study, Saccharomyces cerevisiae (yeast) was treated with a growth inhibitor, and AriumMS successfully differentiated the metabolome based on the augmented multi-platform CE-MS and HILIC-MS investigation. As a result, AriumMS is proposed as a powerful tool to improve the accuracy and selectivity of metabolome analysis through the integration of several HILIC-MS/CE-MS techniques.

The Role of Branched-Chain Amino Acids and Branched-Chain α-Keto Acid Dehydrogenase Kinase in Metabolic Disorders

Branched-chain amino acids (BCAAs), composed of leucine, isoleucine, and valine, are important essential amino acids in human physiology. Decades of studies have revealed their roles in protein synthesis, regulating neurotransmitter synthesis, and the mechanistic target of rapamycin (mTOR). BCAAs are found to be related to many metabolic disorders, such as insulin resistance, obesity, and heart failure. Also, many diseases are related to the alteration of the BCAA catabolism enzyme branched-chain α-keto acid dehydrogenase kinase (BCKDK), including maple syrup urine disease, human autism with epilepsy, and so on. In this review, diseases and the corresponding therapies are discussed after the introduction of the catabolism and detection methods of BCAAs and BCKDK. Also, the interaction between microbiota and BCAAs is highlighted.

Amino acids in inflammatory bowel diseases: Modern diagnostic tools and methodologies

Amino acids are crucial building blocks of living organisms. Together with their derivatives, they participate in many intracellular processes to act as hormones, neuromodulators, and neurotransmitters. For several decades amino acids have been studied for their potential as markers of various diseases, including inflammatory bowel diseases. Subsequent improvements in sample pretreatment, separation, and detection methods have enabled the specific and very sensitive determination of these molecules in multicomponent matrices-biological fluids and tissues. The information obtained from targeted amino acid analysis (biomarker-based analytical strategy) can be further used for early diagnostics, to monitor the course of the disease or compliance of the patients. This review will provide an insight into current knowledge about inflammatory bowel diseases, the role of proteinogenic amino acids in intestinal inflammation and modern analytical techniques used in its diagnosis and disease activity monitoring. Current advances in the analysis of amino acids focused on sample pretreatment, separation strategy, or detection methods are highlighted, and their potential in clinical laboratories is discussed. In addition, the latest clinical data obtained from the metabolomic profiling of patients suffering from inflammatory bowel diseases are summarized with a focus on proteinogenic amino acids.

Potential Metabolite Markers for Pancreatic Cancer Identified by Metabolomic Analysis of Induced Cancer-Associated Fibroblasts

Simple Summary

Fibroblasts in normal tissues conduct energy metabolism via oxidative phosphorylation (OXPHOS). However, cancer-associated fibroblasts (CAFs) produce energy (i.e., ATP) via glycolysis. Nonetheless, whether intracellular metabolism transitions from OXPHOS to glycolysis when normal tissue fibroblasts differentiate into CAFs remains to be determined. Here, we established an experimental system and induced the in vitro differentiation of mesenchymal stem cells to CAFs and performed detailed metabolomic and RNA sequencing analyses. We found that the intracellular metabolic pathway was reprogrammed to the glycolytic pathway when mesenchymal stem cells were co-cultured with pancreatic cancer cells. Furthermore, we identified CAF-specific metabolites that were expressed post reprogramming. These metabolites have also been observed in pancreatic cancer mouse models, suggesting their potential as cancer biomarkers.

Abstract

Cancer-associated fibroblasts (CAFs) in the tumor microenvironment perform glycolysis to produce energy, i.e., ATP. Since the origin of CAFs is unidentified, it is not determined whether the intracellular metabolism transitions from oxidative phosphorylation (OXPHOS) to glycolysis when normal tissue fibroblasts differentiate into CAFs. In this study, we established an experimental system and induced the in vitro differentiation of mesenchymal stem cells (MSCs) to CAFs. Additionally, we performed metabolomic and RNA-sequencing analyses before and after differentiation to investigate changes in the intracellular metabolism. Consequently, we discovered that OXPHOS, which was the primary intracellular metabolism in MSCs, was reprogrammed to glycolysis. Furthermore, we analyzed the metabolites in pancreatic tumor tissues in a mice model. The metabolites extracted as candidates in the in vitro experiments were also detected in the in vivo experiments. Thus, we conclude that normal tissue fibroblasts that differentiate into CAFs undergo a metabolic reprogramming from OXPHOS to glycolysis. Moreover, we identified the CAF-specific metabolites expressed during metabolic reprogramming as potential future biomarkers for pancreatic cancer.

Genetic Background Negates Improvements in Rice Flour Characteristics and Food Processing Properties Caused by a Mutant Allele of the PDIL1-1 Seed Storage Protein Gene

Phenotypic differences among breeding lines that introduce the same superior gene allele can be a barrier to effective development of cultivars with desirable traits in some crop species. For example, a deficient mutation of the Protein Disulfide Isomerase Like 1-1 (PDIL1-1) gene can cause accumulation of glutelin seed storage protein precursors in rice endosperm, and improves rice flour characteristics and food processing properties. However, the gene must be expressed to be useful. A deficient mutant allele of PDIL1-1 was introduced into two rice cultivars with different genetic backgrounds (Koshihikari and Oonari). The grain components, agronomic traits, and rice flour and food processing properties of the resulting lines were evaluated. The two breeding lines had similar seed storage protein accumulation, amylose content, and low-molecular-weight metabolites. However, only the Koshihikari breeding line had high flour quality and was highly suitable for rice bread, noodles, and sponge cake, evidence of the formation of high-molecular-weight protein complexes in the endosperm. Transcriptome analysis revealed that mRNA levels of fourteen PDI, Ero1, and BiP genes were increased in the Koshihikari breeding line, whereas this change was not observed in the Oonari breeding line. We elucidated part of the molecular basis of the phenotypic differences between two breeding lines possessing the same mutant allele in different genetic backgrounds. The results suggest that certain genetic backgrounds can negate the beneficial effect of the PDIL1-1 mutant allele. Better understanding of the molecular basis for such interactions may accelerate future breeding of novel rice cultivars to meet the strong demand for gluten-free foods.

Infrared pulsed fiber laser-produced silver-109-nanoparticles for laser desorption/ionization mass spectrometry of amino acids

Application of monoisotopic cationic 109Ag nanoparticles (109AgNPs) obtained by pulsed fiber laser (PFL) 2D galvo-scanner (GS) laser generated nanomaterial (LGN) for both high resolution laser desorption/ionization mass spectrometry and mass spectrometry imaging of amino acids is presented. Four amino acids, alanine, isoleucine, lysine, and phenylalanine were used as test compounds for quantification with matrix-assisted laser desorption/ionization mas (MALDI)-type mass spectrometer. Comparison of commonly made manual measurements with semiautomatic mass spectrometry imaging (MSI) was performed providing very interesting findings. Amino acids were directly tested in 1 000 000-fold concentration change conditions ranging from 1 mg/ml to 1 ng/ml, which equates to 500 ng to 500 fg of amino acid per measurement spot. Methods were also tested on samples of human blood plasma for quantification of endogenous amino acids.

Poly(2-vinylpyridine) as a reference compound for mass calibration in positive-ion matrix-assisted laser desorption/ionization-mass spectrometry on different instrumental platforms

Butyl-terminated poly(2-vinylpyridine) (P2VP), C₄H₉(C₇H₇N)_nH, is evaluated for use as an external and internal mass calibrant in positive-ion matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). P2VP oligomers covering the m/z 450-4500 range are employed to calibrate a time-of-flight (TOF) mass spectrometer in linear and reflector mode, an ion mobility-quadrupole-time-of-flight (IM-Q-TOF) mass spectrometer, and a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The proton affinity of P2VPs introduced by the numerous pyridyl groups leads to the almost exclusive formation of [M + H]⁺ ions with common acidic matrices like α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB) as well as with the non-acidic and aprotic matrices 1,8-dihydroxy-10H-anthracen-9-on (dithranol) and 2-[(2E)-3-(4-tert-butylphenyl)-2-methylprop-2-enylidene]malonitrile (DCTB). This prevalence of [M + H]⁺ ions evenly spaced at Δ(m/z) = 105.0578 renders butyl-terminated P2VP oligomers as convenient mass calibrants. The mass accuracies achieved across various m/z ranges with different mass analyzers and modes of operation are evaluated by using established standard compounds. Results as obtained by internal or external calibration are presented. Further, the compilation of mass reference lists tailored to suit the respective analyzer modes is discussed and those reference files are provided.

Comprehensive Evaluation of Amino Acids and Polyphenols in 69 Varieties of Green Cabbage (Brassica oleracea L. var. capitata L.) Based on Multivariate Statistical Analysis

The biological activities of the primary metabolites and secondary metabolites of 69 green cabbage varieties were tested. The LC-MS detection method was used to determine the content of 19 free amino acids (lysine, tryptophan, phenylalanine, methionine, threonine, isoleucine, leucine, valine, arginine, asparagine, glycine, proline, tyrosine, glutamine, alanine, aspartic acid, serine, and glutamate). The content of 10 polyphenols (chlorogenic acid, gallic acid, 4-coumaric acid, ferulic acid, gentisic acid, cymarin, erucic acid, benzoic acid, rutin, and kaempferol) was determined by the HPLC detection method. Considering the complexity of the data obtained, variance analysis, diversity analysis, correlation analysis, hierarchical cluster analysis (HCA), and principal component analysis (PCA) were used to process and correlate amino acid or polyphenol data, respectively. The results showed that there were significant differences between the different amino acids and polyphenols of the 69 cabbage varieties. The most abundant amino acids and polyphenols were Glu and rutin, respectively. Both amino acids and polyphenols had a high genetic diversity, and multiple groups of significant or extremely significant correlations. The 69 cabbage varieties were divided into two groups, according to 19 amino acid indexes, by PCA. Among them, seven varieties with high amino acid content all fell into the fourth quadrant. The HCA of amino acids also supports this view. Based on 10 polyphenols, the 69 cabbage varieties were divided into two groups by HCA. Based on 29 indexes of amino acids and polyphenols, 69 cabbage varieties were evaluated and ranked by PCA. Therefore, in this study, cabbage varieties were classified in accordance with the level of amino acids and polyphenols, which provided a theoretical basis for the genetic improvement of nutritional quality in cabbage.

Determination of Branched-Chain Amino Acids in Food Supplements and Human Plasma by a CE-MS/MS Method with Enhanced Resolution

In the presented study, a capillary electrophoresis-mass spectrometry method combining high separation efficiency and sensitive detection has been developed and validated, for the first time, to quantify branched chain amino acids (valine, isoleucine, leucine) in commercial food and sport supplement samples and human plasma samples. The separations were performed in a bare fused silica capillary. The background electrolyte was composed of 500 mM formic acid with pH 2.0. The plasma sample pretreatment was realized by simple protein precipitation with acetonitrile. Injection of a short zone of highly basic electrolyte before the sample injection and application of the negative pressure on the separation were accompanied by enhanced resolution of the isobaric amino acids—isoleucine and leucine. The developed method was characterized by favorable validation parameters, such as linearity (r² > 0.99), accuracy and precision, the limit of detection, lower limit of quantification, or robustness. These parameters were more than sufficient for the quantification of branched chain amino acids in various samples. The determined concentrations of branched chain amino acids in food and sports supplements were in very good agreement with the content declared by the manufacturer. The investigated concentrations of branched chain amino acids were in the range 294.68–359.24 µM for valine, 91.76–95.67 µM for isoleucine, and 196.78–251.24 µM for leucine. These concentrations fall within the physiological limits. The developed CE-MS/MS method represents a suitable alternative to traditional approaches used in branched chain amino acid quality control and bioanalysis.

Direct detection of inorganic ions and underivatized amino acids in seconds using high-speed capillary electrophoresis coupled with back-scatter interferometry

High speed capillary electrophoresis (HSCE) combined with refractive index (RI) detection is developed for the rapid separation and detection of inorganic ions and amino acids. A mixture of three inorganic ions (K⁺, Na⁺, Li⁺) and eight amino acids (Lys, Arg, Ala, Gly, Val, Thr, Trp, Asp) are detected using back scatter interferometry (BSI), without the need for chemical modifications or contrast. A thin-walled separation capillary (50 μm i.d. by 80 μm o.d.) helps mitigate Joule heating at the high field strengths required for rapid separations. This, combined with a short 8 cm length-to-detector (10 cm total length), enables separations on the seconds time scale. Using a background electrolyte (BGE) of 4 M acetic acid (pH 1.6) and a field strength of 900 V cm^-1, all 11 analytes are separated in less than 40 s. Moreover, peaks in the BSI signal arising from the sample injection and EOF, enable electrophoretic mobilities to readily be obtained from apparent mobilities. This leads to excellent repeatability, with analyte electrophoretic mobilities varying from 0.39 to 1.56 % RSD over eight consecutive separations. The universal detection of inorganic ions and amino acids without prior chemical modification or additives in the BGE is an advantage of refractive index detection. A disadvantage arises from modest detection limits. Here, however, we show that submicromolar detection is possible with careful thermostatting of the thin separation capillary. A series of electropherograms are used to quantify arginine concentrations from 700 nM to 500 μM, using 50 μM Li⁺ as an internal standard. The resulting calibration curve leads to a calculated LOD of 376 nM and a LOQ of 1.76 μM. Diagnostically relevant amino acid panels are also separated, illustrating the potential for future applications in neurodegenerative and metabolic disease diagnostics. HSCE combined with BSI detection, therefore, is shown to be a rapid, sensitive, and universal approach for analyzing sample mixtures.

Determination of amino acids by capillary and microchip electrophoresis with contactless conductivity detection - Theory, instrumentation and applications

This review article summarises aspects of the determination of amino acids using capillary and chip electrophoresis in combination with contactless conductivity detection from their historical beginnings to the present time. Discussion is included of the theory of conductivity detection in electromigration techniques, the design of contactless conductivity cells for detection in capillaries and on microchips, including the use of computer programs for simulation of the conductivity response and the process of the electrophoretic separation of amino acids. Emphasis is placed on optimisation of the background electrolyte composition, chiral separation, multidimensional separation, stacking techniques and the use of multidetection systems. There is also a description of clinical applications, the determination of amino acids in foodstuffs, waters, soils and composts with emphasis on modern techniques of sample treatment, such as microdialysis, liquid membrane extraction and many other techniques.

Saccharose cluster ions as mass calibrants in positive-ion direct analysis in real time-mass spectrometry

In positive-ion direct analysis in real time-mass spectrometry (DART-MS), mono-, di, and trisaccharides form [M+NH₄]⁺ ions. Some of them, in addition, yield abundant [M_n+NH₄]⁺ cluster ions (n = 1-6)), and thus, can serve for mass calibration. Saccharose, C₁₂H₂₂O₁₁, the most common sugar, also termed sucrose, is among the [M_n+NH₄]⁺ cluster ion forming species. Saccharose may therefore be employed as a cheap and ubiquitous mass calibration standard. The extent of saccharose cluster ion formation depends on the temperature of the DART gas, sample load, and instrumental parameters like trapping conditions of ions prior to mass analysis. This study identifies optimized experimental conditions and demonstrates the application of saccharose cluster ion-based mass calibration for accurate mass measurements in DART mode on a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer.

Profiling of Amino Acids in Urine Samples of Patients Suffering from Inflammatory Bowel Disease by Capillary Electrophoresis-Mass Spectrometry

Urine represents a convenient biofluid for metabolomic studies due to its noninvasive collection and richness in metabolites. Here, amino acids are valuable biomarkers for their ability to reflect imbalances of different biochemical pathways. An impact of amino acids on pathology, prognosis and therapy of various diseases, including inflammatory bowel disease (IBD), is therefore the subject of current clinical research. This work is aimed to develop a capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) method for the quantification of the 20 proteinogenic amino acids in human urine samples obtained from patients suffering from IBD and treated with thiopurines. The optimized CE-MS/MS method, with minimum sample preparation (just “dilute and shoot”), exhibited excellent linearity for all the analytes (coefficients of determination were higher than 0.99), with inter-day and intra-day precision yielding relative standard deviations in the range of 0.91–15.12% and with accuracy yielding relative errors in the range of 85.47–112.46%. Total analysis time, an important parameter for the sample throughput demanded in routine practice, was shorter in ca. 17% when compared to established CE-MS methods. Favorable performance of the proposed CE-MS/MS method was also confirmed by the comparison with corresponding ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) method. Consistent data for the investigated amino acid metabolome were obtained using both methods. For the first time, the amino acid profiling by CE-MS approach was applied on the clinical IBD samples. Here, significant differences observed in the concentration levels of some amino acids between IBD patients undergoing thiopurine treatment and healthy volunteers could result from the simultaneous action of the disease and the corresponding therapy. These findings indicate that amino acids analysis could be a valuable tool for the study of mechanism of the IBD treatment by thiopurines.

New Advances in Amino Acid Profiling in Biological Samples by Capillary Electrophoresis-Mass Spectrometry

Capillary electrophoresis-mass spectrometry (CE-MS) offers a high efficiency microseparation platform for amino acid profiling when analyzing volume-restricted biological samples, such as a dried blood spot punch. Direct analysis of amino acids and their analogs is routinely achieved using strongly acidic buffer conditions under positive-ion mode detection with a coaxial sheath liquid interface for electrospray ionization (ESI). New advances in online sample preconcentration, pre-column chemical derivatization, and/or low flow/sheathless CE-MS interface designs can further improve sensitivity while allowing for resolution of amino acid stereoisomers and labile aminothiols with low nanomolar detection limits. Additionally, multiplexed separations in CE-MS based on serial injection of seven or more samples within a single run greatly boosts sample throughput (<2-3 min/sample) without added infrastructure costs while allowing for stringent quality control and signal batch correction. Accurate prediction of the electromigration behavior of amino acids and their analogs offers a convenient approach for structural elucidation that is complementary to high-resolution MS and MS/MS. Simultaneous analysis of amino acids together with other classes of ionic metabolites by CE-MS allows for comprehensive metabolomic screening as required for new advances in clinical medicine, nutritional sciences, and population health.

Direct Analysis of Underivatized Amino Acids in Plant Extracts by LC-MS/MS (Improved Method)

In this chapter we describe a method for quantification of 20 proteinogenic amino acids by liquid chromatography-mass spectrometry which affords neither derivatization nor the use of organic solvents. Analysis of the underivatized amino acids is performed by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) in the positive ESI mode. Separation is achieved on a strong cation exchange (SCX) column (Luna 5 μ SCX 100 Å) with 5% acetic acid in water (A) and 75 mM ammonium acetate in water (B). Quantification is accomplished by use of d₂-phenylalanine as internal standard achieving limits of detection of 5-50 nM. The method was successfully applied for the determination of proteinogenic amino acids in plant extracts.

Ferredoxin/thioredoxin system plays an important role in the chloroplastic NADP status of Arabidopsis

NADP is a key electron carrier for a broad spectrum of redox reactions, including photosynthesis. Hence, chloroplastic NADP status, as represented by redox status (ratio of NADPH to NADP⁺ ) and pool size (sum of NADPH and NADP⁺ ), is critical for homeostasis in photosynthetic cells. However, the mechanisms and molecules that regulate NADP status in chloroplasts remain largely unknown. We have now characterized an Arabidopsis mutant with imbalanced NADP status (inap1), which exhibits a high NADPH/NADP⁺ ratio and large NADP pool size. inap1 is a point mutation in At2g04700, which encodes the catalytic subunit of ferredoxin/thioredoxin reductase. Upon illumination, inap1 demonstrated earlier increases in NADP pool size than the wild type did. The mutated enzyme was also found in vitro to inefficiently reduce m-type thioredoxin, which activates Calvin cycle enzymes, and NADP-dependent malate dehydrogenase to export reducing power to the cytosol. Accordingly, Calvin cycle metabolites and amino acids diminished in inap1 plants. In addition, inap1 plants barely activate NADP-malate dehydrogenase, and have an altered redox balance between the chloroplast and cytosol, resulting in inefficient nitrate reduction. Finally, mutants deficient in m-type thioredoxin exhibited similar light-dependent NADP dynamics as inap1. Collectively, the data suggest that defects in ferredoxin/thioredoxin reductase and m-type thioredoxin decrease the consumption of NADPH, leading to a high NADPH/NADP⁺ ratio and large NADP pool size. The data also suggest that the fate of NADPH is an important influence on NADP pool size.

Development of a sheathless CE-ESI-MS interface

A sheath-flow interface is the most common ionization technique in CE-ESI-MS. However, this interface dilutes the analytes with the sheath liquid and decreases the sensitivity. In this study, we developed a sheathless CE-MS interface to improve sensitivity. The interface was fabricated by making a small crack approximately 2 cm from the end of a capillary column fixed on a plastic plate, and then covering the crack with a dialysis membrane to prevent metabolite loss during separation. A voltage for CE separation was applied between the capillary inlet and the buffer reservoir. Under optimum conditions, 52 cationic metabolite standards were separated and selectively detected using MS. With a pressure injection of 5 kPa for 15 s (ca. 1.4 nL), the detection limits for the tested compounds were between 0.06 and 1.7 μmol/L (S/N = 3). The method was applied to analysis of cationic metabolites extracted from a small number (12 000) of cancer cells, and the number of peaks detected was about 2.5 times higher than when using conventional sheath-flow CE-MS. Because the interface is easy to construct, it is cost-effective and can be adapted to any commercially available capillaries. This method is a powerful new tool for highly sensitive CE-MS-based metabolomic analysis.

CE-MS for the Analysis of Amino Acids

Amino acids play an important role in clinical analysis. Capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) has proven to possess several characteristics that make it a powerful and useful tool for the analysis of amino acids in clinical studies. Here we present a method for the separation and quantitative analysis of 27 amino acids in urine based on CE-ESI-MS. The method presents an improved resolution between the isomers Leu, Ile, and aIle, in comparison to other CE-ESI-MS methods in the literature. This method is fast, selective, and simple and has improved sensitivity by applying a pH-mediated stacking strategy, showing that it can be successfully used for amino acid analysis and probably for other small cationic metabolites.

Basic poly(propylene glycols) as reference compounds for internal mass calibration in positive-ion matrix-assisted laser desorption/ionization mass spectrometry

Basic poly(propylene glycols), commercially available under the trade name Jeffamine, are evaluated for their potential use as internal mass calibrants in matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry. Due to their basic amino endgroups Jeffamines are expected to deliver [M+H]⁺ ions in higher yields than neutral poly(propylene glycols) or poly(ethylene glycols). Aiming at accurate mass measurements and molecular formula determinations by matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry, four Jeffamines (M-600, M-2005, D-400, D-230) were thus compared. As a result, Jeffamine M-2005 is introduced as a new mass calibrant for positive-ion matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry in the range of m/z 200-1200 and the reference mass list is provided. While Jeffamine M-2005 is compatible with α-cyano-4-hydroxycinnamic acid, 2,5-dihydroxybenzoic acid, and 2-[(2 E)-3-(4- tert-butylphenyl)-2-methylprop-2-enylidene]malonitrile matrix, its use in combination with 2-[(2 E)-3-(4- tert-butylphenyl)-2-methylprop-2-enylidene]malonitrile provides best results due to low laser fluence requirements. Applications to PEG 300, PEG 600, the ionic liquid trihexyl(tetradecyl)-phosphonium tris(pentafluoroethyl)-trifluorophosphate, and [60]fullerene demonstrate mass accuracies of 2-5 ppm.

Ninhydrin-sodium molybdate chromogenic analytical probe for the assay of amino acids and proteins

A sensitive method has been proposed for the quantification of amino acids and proteins using ninhydrin and sodium molybdate as chromogenic substrates in citrate buffer of pH5.6. A weak molybdate-hydrindantin complex plays the role in the formation of Ruhemann's purple. The linear response for the amino acid, amino acid mixture and Bovine serum albumin is between 0.999 and 66.80μM, 1.52 and 38μM and 5 and 100μg/L, respectively. The molar absorptivity of the individual amino acid by the proposed reaction extends from 0.58×10⁴ to 2.86×10⁴M^-1cm^-1. The linearity equations for the proposed ninhydrin-molybdate for amino acid mixture is Abs=0.021×Conc (μM)-0.002. The applicability of the proposed method has been justified in food and biological samples in conjunction with Kjeldahl method.

Hyphenated MS-based targeted approaches in metabolomics

Review of targeted metabolomics, with a focus on the description of analytical methods.

Amino Acid Profiles of Serum and Urine in Search for Prostate Cancer Biomarkers: a Pilot Study

There is a great interest in searching for diagnostic biomarkers in prostate cancer patients. The aim of the pilot study was to evaluate free amino acid profiles in their serum and urine. The presented paper shows the first comprehensive analysis of a wide panel of amino acids in two different physiological fluids obtained from the same groups of prostate cancer patients (n = 49) and healthy men (n = 40). The potential of free amino acids, both proteinogenic and non-proteinogenic, as prostate cancer biomarkers and their utility in classification of study participants have been assessed. Several metabolites, which deserve special attention in the further metabolomic investigations on searching for prostate cancer markers, were indicated. Moreover, free amino acid profiles enabled to classify samples to one of the studied groups with high sensitivity and specificity. The presented research provides a strong evidence that ethanolamine, arginine and branched-chain amino acids metabolic pathways can be a valuable source of markers for prostate cancer. The altered concentrations of the above-mentioned metabolites suggest their role in pathogenesis of prostate cancer and they should be further evaluated as clinically useful markers of prostate cancer.

Development and validation of a CE-MS method for the targeted assessment of amino acids in urine

A CE-ESI-MS method was developed and validated for the separation and quantitative analysis of amino acids (AA) in urine. Experimental parameters related to the CE-MS interface, BGE, and mass spectrometer (MS) settings were optimized providing a good separation of 27 AA, including the isomers L-leucine, L-isoleucine, and L-alloisoleucine, in less than 30 min. The sheath liquid was composed by 0.50% formic acid in 60% (v,v) methanol-water delivered at a flow rate of 5 μL/min. The BGE consisted of 0.80 mol/L formic acid at pH 1.96 and 15% methanol. A pH stacking procedure was implemented to enhance sensitivity (a 12.5% NH4 OH solution was injected at 0.5 psi/9 s prior to samples injected at 0.6 psi/20 s). The proposed method was validated according to FDA and ICH protocols exhibiting acceptable parameters. Analytical curves presented coefficients of determination from 0.996 to 0.9997 (with large F statistics and low p-values). LODs and quantification ranged from 0.63 to 29 μmol/L and from 1.9 to 86 μmol/L, respectively. Practical repeatability was obtained for all AA with coefficients of variation better than 0.55% CV (migration time) and 1.7% CV (peak area ratios; methionine sulfone as internal standard). Recoveries of AA in spiked urine ranged from 92.0 to 123% with few exceptions. Moreover, a successful quantification of AA in pooled control and test urine samples, which compose a vesicoureteral reflux cohort, was achieved showing the potential applicability of the proposed method for targeted metabolomics studies using CE-ESI-MS with an Ion Trap as mass analyzer.

Capillary Electrophoresis in Metabolomics

Metabolomics is an analytical toolbox to describe (all) low-molecular-weight compounds in a biological system, as cells, tissues, urine, and feces, as well as in serum and plasma. To analyze such complex biological samples, high requirements on the analytical technique are needed due to the high variation in compound physico-chemistry (cholesterol derivatives, amino acids, fatty acids as SCFA, MCFA, or LCFA, or pathway-related metabolites belonging to each individual organism) and concentration dynamic range. All main separation techniques (LC-MS, GC-MS) are applied in routine to metabolomics hyphenated or not to mass spectrometry, and capillary electrophoresis is a powerful high-resolving technique but still underused in this field of complex samples. Metabolomics can be performed in the non-targeted way to gain an overview on metabolite profiles in biological samples. Targeted metabolomics is applied to analyze quantitatively pre-selected metabolites. This chapter reviews the use of capillary electrophoresis in the field of metabolomics and exemplifies solutions in metabolite profiling and analysis in urine and plasma.

Letter: High-mass capabilities of positive-ion and negative-ion direct analysis in real time mass spectrometry

Of the ionic liquid 1-butyl-3-methylimidazolium (C(+)) tricyanomethide (A(-)) high-mass cluster ions of both positive ([C(n)A(n-1)](+)) and negative ([C(n-1)A(n)](-)) charge were generated and detected by direct analysis in real time (DART) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS). After optimization of the settings of the DART ionization source and of the mass analyzer ions of m/z values unprecedented in DART-MS were detected. Thus, the upper m/z limits of positive-ion and negative-ion DART- MS were substantially expanded. Negative-ion DART-MS delivered cluster ions up to [C(15)A(16)](-), m/z 3527 (nominal mass of monoisotopic ion), while positive-ion DART-MS even yielded ions up to [C(30)A(29)](+), m/z 6784. The identification of the cluster ions is supported by their accurate mass and exact mass differences corresponding to CA between adjacent cluster ion peaks.

Discovery of Anti-inflammatory Ingredients in Chinese Herbal Formula Kouyanqing Granule based on Relevance Analysis between Chemical Characters and Biological Effects

Kouyanqing Granule (KYQG) is a traditional Chinese herbal formula composed of Flos lonicerae (FL), Radix scrophulariae (RS), Radix ophiopogonis (RO), Radix asparagi (RA), and Radix et rhizoma glycyrrhizae (RG). In contrast with the typical method of separating and then biologicalily testing the components individually, this study was designed to establish an approach in order to define the core bioactive ingredients of the anti-inflammatory effects of KYQG based on the relevance analysis between chemical characters and biological effects. Eleven KYQG samples with different ingredients were prepared by changing the ratios of the 5 herbs. Thirty-eight ingredients in KYQG were identified using Ultra-fast liquid chromatography-Diode array detector-Quadrupole-Time-of-flight-Tandem mass spectrometry (UFLC-DAD-Q-TOF-MS/MS) technology. Human oral keratinocytes (HOK) were cultured for 24 hours with 5% of Cigarette smoke extract (CSE) to induce inflammation stress. Interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8), and tumour necrosis factor-α (TNF-α) were evaluated after treatment with the eleven KYQG samples. Grey relational analysis(GRA), Pearson’s correlations (PCC), and partial least-squares (PLS) were utilized to evaluate the contribution of each ingredient. The results indicated that KYQG significantly reduced interleukin-1β, interleukin-6, interleukin-8, and tumour necrosis factor-α levels, in which lysine, γ-aminobutyric acid, chelidonic acid, tyrosine, harpagide, neochlorogenic acid, chlorogenic acid, cryptochlorogenic acid, isoquercitrin, luteolin-7-o-glucoside, 3,4-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid, angoroside C, harpagoside, cinnamic acid, and ruscogenin play a vital role.

Assessment of the efficacy of anticancer drugs by amino acid metabolomics using fluorescence derivatization-HPLC

Metabolomic studies conducted for evaluating cancer pathogenesis and progression by monitoring the amino acids metabolic balance hold great promise for assessing current and future anticancer treatments. We performed a comprehensive quantification of 21 amino acids concentrations in cultured human colorectal adenocarcinoma cells treated with the anticancer drugs 5-fluorouracil, irinotecan, and cisplatin. A precolumn fluorescence derivatization-HPLC method involving 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate was used. Amino acid concentration data were analyzed by principal-component analysis and partial least-squares multivariate statistical methods to represent samples on two-dimensional graphs. The hierarchical cluster analysis and linear discriminant analysis were used to classify the samples on the score plots. Unlike the cluster analysis approach, the linear discrimination analysis classification successfully distinguished anticancer drug-treated samples from the untreated controls. Moreover, three candidate amino acids (serine, aspartic acid, and methionine) were identified from the loading plots as potential biomarkers. Our proposed method might be able to evaluate the effectiveness of anticancer therapy even in small laboratories or medical institutions.

Amino acid analysis using chromatography-mass spectrometry: An inter platform comparison study

The analysis of amino acids has become a central task in many aspects. While amino acid analysis has traditionally mainly been carried out using either gas chromatography (GC) in combination with flame ionization detection or liquid chromatography (LC) with either post-column derivatization using ninhydrin or pre-column derivatization using o-phthalaldehyde, many of today's analysis platforms are based on chromatography in combination with mass spectrometry (MS). While derivatization is mandatory for the GC-based analysis of amino acids, several LC platforms have emerged, particularly in the dawn of targeted metabolite profiling using hydrophilic interaction liquid chromatography (HILIC) coupled to MS, allowing the analysis of underivatized amino acids. Among the numerous analytical platforms available for amino acid analysis today, we here compare three prominent approaches, being GC-MS and LC-MS after amino acid derivatization using chloroformate and HILIC-MS of underivatized amino acids. We compare and discuss practical issues as well as performance characteristics, e.g., the use of (13)C-labeled internal standards, of the different platforms and present data on their practical implementation in our laboratory. Finally, we compare the real-life applicability of all three platforms for a complex biological sample. While all three platforms are very-well suited for the analysis of complex biological samples they all show advantages and disadvantages for some analytes as discussed in detail in this manuscript.

Alkaline conditions in hydrophilic interaction liquid chromatography for intracellular metabolite quantification using tandem mass spectrometry

Modeling of metabolic networks as part of systems metabolic engineering requires reliable quantitative experimental data of intracellular concentrations. The hydrophilic interaction liquid chromatography-electrospray ionization-tandem mass spectrometry (HILIC-ESI-MS/MS) method was used for quantitative profiling of more than 50 hydrophilic key metabolites of cellular metabolism. Without prior derivatization, sugar phosphates, organic acids, nucleotides, and amino acids were measured under alkaline and acidic mobile phase conditions with pre-optimized multiple reaction monitoring (MRM) transitions. Irrespective of the polarity mode of the acquisition method used, alkaline conditions achieved the best quantification limits and linear dynamic ranges. Fully 90% of the analyzed metabolites presented detection limits better than 0.5pmol (on column), and 70% presented 1.5-fold higher signal intensities under alkaline mobile phase conditions. The quality of the method was further demonstrated by absolute quantification of selected metabolites in intracellular extracts of Escherichia coli. In addition, quantification bias caused by matrix effects was investigated by comparison of calibration strategies: standard-based external calibration, isotope dilution, and standard addition with internal standards. Here, we recommend the use of alkaline mobile phase with polymer-based zwitterionic hydrophilic interaction chromatography (ZIC-pHILIC) as the most sensitive scenario for absolute quantification for a broad range of metabolites.

Capillary electrophoresis-mass spectrometry

Capillary electrophoresis-mass spectrometry (CE-MS) has proven to be useful for metabolomics studies. Charged metabolites are first separated by CE based on charge and size and are subsequently selectively detected using MS. The major advantages of CE-MS are its high resolution and the fact that almost any charged species can be analyzed by two methods, both cationic and anionic. This technique can readily be applied to various types of biological samples originating from bacteria, plants, mammals, and body fluids. This chapter highlights detailed practical procedures for using this technology.

Direct determination of underivatized amino acids from Ginkgo biloba leaves by using hydrophilic interaction ultra high performance liquid chromatography coupled with triple quadrupole mass spectrometry

Ginkgo biloba leaf extract has been widely used in dietary supplements and more recently in some foods and beverages. In addition to the well-known flavonol glycosides and terpene lactones, G. biloba leaves are also rich in amino acids. To determine the content of free amino acids, a reliable method has been established by using hydrophilic interaction ultra-HPLC coupled with ESI-MS. 20 free amino acids were simultaneously determined without derivatization in 12 min. The proposed method was fully validated in terms of linearity, sensitivity, repeatability, as well as recovery. Furthermore, the principal component analysis was applied to different G. biloba leaves collected in November (after fruit harvest season), which revealed that the samples from different production areas exhibited regional disparity in different clusters in accordance with their various hydrophilic interaction chromatograms coupled with mass profiles. The established approach could be helpful for evaluation of the potential values as dietary supplements and the quality control of G. biloba leaves, which might also be utilized for the investigation of other medicinal herbs containing amino acids.

Detoxification of aldehydes by histidine-containing dipeptides: from chemistry to clinical implications

Aldehydes are generated by oxidized lipids and carbohydrates at increased levels under conditions of metabolic imbalance and oxidative stress during atherosclerosis, myocardial and cerebral ischemia, diabetes, neurodegenerative diseases and trauma. In most tissues, aldehydes are detoxified by oxidoreductases that catalyze the oxidation or the reduction of aldehydes or enzymatic and nonenzymatic conjugation with low molecular weight thiols and amines, such as glutathione and histidine dipeptides. Histidine dipeptides are present in micromolar to millimolar range in the tissues of vertebrates, where they are involved in a variety of physiological functions such as pH buffering, metal chelation, oxidant and aldehyde scavenging. Histidine dipeptides such as carnosine form Michael adducts with lipid-derived unsaturated aldehydes, and react with carbohydrate-derived oxo- and hydroxy-aldehydes forming products of unknown structure. Although these peptides react with electrophilic molecules at lower rate than glutathione, they can protect glutathione from modification by oxidant and they may be important for aldehyde quenching in glutathione-depleted cells or extracellular space where glutathione is scarce. Consistent with in vitro findings, treatment with carnosine has been shown to diminish ischemic injury, improve glucose control, ameliorate the development of complications in animal models of diabetes and obesity, promote wound healing and decrease atherosclerosis. The protective effects of carnosine have been linked to its anti-oxidant properties, its ability to promote glycolysis, detoxify reactive aldehydes and enhance histamine levels. Thus, treatment with carnosine and related histidine dipeptides may be a promising strategy for the prevention and treatment of diseases associated with high carbonyl load.

Capillary electrophoresis mass spectrometry with sheathless electrospray ionization for high sensitivity analysis of underivatized amino acids

A high durability sheathless electrospray ionization interface of CE-MS is applied for the sensitive analysis of underivatized amino acids. The sheathless interface was realized using an ionophore membrane-packed electro-conduction channel. The interface functioned well with a volatile alkaline background electrolyte (BGE) and uncoated fused-silica capillaries for CE-MS analysis of underivatized amino acids. High electroosmotic flow with alkaline BGE facilitated high separation efficiency (>100,000 theoretical plates) and short analysis time (<15 min). Both the short-term stability and long-term durability are particularly suited for routine applications. Using electrokinetic injection and the multiple reaction monitoring (MRM) mode with a triple-quadrupole analyzer, high sensitivity was achieved, which yielded detection limits of 0.05-0.81 μM. For the quantitation of underivatized amino acids, quantification precisions (RSDs) for intra- and inter-day analyses were less than 3%. Recoveries from serum were 96.3-101.8% for isotope dilution mass spectrometry (IDMS). When compared with HPLC-IDMS for human serum samples, highly agreeable (96.9-102.0%) results were obtained with the proposed CE-IDMS method.

Quantification of citrulline by parallel fragmentation monitoring--a novel method using graphitized carbon nanoparticles and MALDI-TOF/TOF mass spectrometry

BACKGROUND

Selected reaction monitoring (SRM) is a reliable mass spectrometry (MS)-based technique for quantification of small molecules. However, it is not applicable to matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem MS (MALDI-TOF/TOF MS) instruments. This work presents a novel comparable MALDI-TOF/TOF MS technique, "Parallel Fragmentation Monitoring" (PFM), for high-throughput quantification of citrulline.

METHOD

Calibrator/sample solutions were spiked with internal standard that was a stable isotopic analog with 1 mass unit heavier than citrulline. Both citrulline and internal standard were isolated and fragmented in parallel by MALDI-TOF/TOF MS in the presence of graphitized carbon nanoparticles as matrix. The ratio of the peak intensities of the selected fragment of citrulline to that of internal standard was used to calibrate/calculate the concentrations of citrulline in samples.

RESULTS

Linear calibration curves were obtained in the range of 10-250 μmol/l citrulline with correlation coefficients ≥0.997. Stored calibration curve and batch-specific calibration curve produced highly similar measurement values. Within- and between-day CVs were 3.1-8.7% and 3.5-10.6%, respectively, illustrating the reliability and robustness of PFM.

CONCLUSION

Using citrulline for proof-of-concept, we have developed the PFM technique with tremendous potential for high-throughput quantification of amino acids and other small molecules.