Quantitation of Underivatized Free Amino Acids in Mammalian Cell Culture Media Using Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry

Metabolomics in Parkinson's disease

Parkinson's disease (PD) is a multifactorial neurodegenerative disorder in which environmental (lifestyle, dietary, infectious disease) factors as well as genetic make-up play a role. Metabolomics, an evolving research field combining biomarker discovery and pathogenetics, is particularly useful in studying complex pathophysiology in general and Parkinson's disease (PD) specifically. PD, the second most frequent neurodegenerative disorder, is characterized by the loss of dopaminergic neurons in the substantia nigra and the presence of intraneural inclusions of α-synuclein aggregates. Although considered a predominantly movement disorder, PD is also associated with number of non-motor features. Metabolomics has provided useful information regarding this neurodegenerative process with the aim of identifying a disease-specific fingerprint. Unfortunately, many disease variables such as clinical presentation, motor system involvement, disease stage and duration substantially affect biomarker relevance. As such, metabolomics provides a unique approach to studying this multifactorial neurodegenerative disorder.

Assessment of Reproducibility of Laser Electrospray Mass Spectrometry using Electrospray Deposition of Analyte

A nonresonant, femtosecond (fs) laser is employed to desorb samples of Victoria blue deposited on stainless steel or indium tin oxide (ITO) slides using either electrospray deposition (ESD) or dried droplet deposition. The use of ESD resulted in uniform films of Victoria blue whereas the dried droplet method resulted in the formation of a ring pattern of the dye. Laser electrospray mass spectrometry (LEMS) measurements of the ESD-prepared films on either substrate were similar and revealed lower average relative standard deviations for measurements within-film (20.9%) and between-films (8.7%) in comparison to dried droplet (75.5% and 40.2%, respectively). The mass spectral response for ESD samples on both substrates was linear (R² > 0.99), enabling quantitative measurements over the selected range of 7.0 × 10^-11 to 2.8 × 10^-9 mol, as opposed to the dried droplet samples where quantitation was not possible (R² = 0.56). The limit of detection was measured to be 210 fmol. Graphical Abstract ᅟ.

MALDI efficiency of metabolites quantitatively associated with their structural properties: a quantitative structure-property relationship (QSPR) approach

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) experiments require a suitable match of the matrix and target compounds to achieve a selective and sensitive analysis. However, it is still difficult to predict which metabolites are ionizable with a given matrix and which factors lead to an efficient ionization. In the present study, we extracted structural properties of metabolites that contribute to their ionization in MALDI-MS analyses exploiting our experimental data set. The MALDI-MS experiment was performed for 200 standard metabolites using 9-aminoacridine (9-AA) as the matrix. We then developed a prediction model for the ionization profiles (both the ionizability and ionization efficiency) of metabolites using a quantitative structure-property relationship (QSPR) approach. The classification model for the ionizability achieved a 91% accuracy, and the regression model for the ionization efficiency reached a rank correlation coefficient of 0.77. An analysis of the descriptors contributing to such model construction suggested that the proton affinity is a major determinant of the ionization, whereas some substructures hinder efficient ionization. This study will lead to the development of more rational and predictable MALDI-MS analyses.

Analytical approaches to metabolomics and applications to systems biology

Phenotypic expression of renal diseases encompasses a complex interaction between genetic, environmental, and local tissue factors. The level of complexity requires integrated understanding of perturbations in the network of genes, proteins, and metabolites. Metabolomics attempts to systematically identify and quantitate metabolites from biological samples. The small molecules represent the end result of complexity of biological processes in a given cell, tissue, or organ, and thus form attractive candidates to understand disease phenotypes. Metabolites represent a diverse group of low-molecular-weight structures including lipids, amino acids, peptides, nucleic acids, and organic acids, which makes comprehensive analysis a difficult analytical challenge. The recent rapid development of a variety of analytical platforms based on mass spectrometry and nuclear magnetic resonance have enabled separation, characterization, detection, and quantification of such chemically diverse structures. Continued development of bioinformatics and analytical strategies will accelerate widespread use and integration of metabolomics into systems biology. Here, we will discuss analytical and bioinformatic techniques and highlight recent studies that use metabolomics in understanding pathophysiology of disease processes.

Optimization of a modified aerospray deposition device for the preparation of samples for quantitative analysis by MALDI-TOFMS

A modified aerospray apparatus was used to prepare a thin layer sample of matrix and analyte for quantitative analysis by MALDI-TOFMS. The apparatus consists of a set of coaxial tubing; the liquid sample is forced by a syringe pump through the inner capillary and it is nebulized by a flow of gas through the outer capillary. The small droplets of sample exiting the device are deposited onto a rotating plate, which serves as the sample surface for a time-of-flight mass spectrometer. An optimization was carried out after initial experiments with the device resulted in poorer than expected reproducibility of analyte signal. A two-level plus center point factorial experiment was performed investigating several factors, including the inner capillary internal diameter, gas pressure, liquid flow, spray distance, and time. After optimization the within-sample reproducibility of the analyte signal improved 3-fold, while the sample-to-sample reproducibility improved 4.5-fold.

LC-MS-based metabonomics analysis

Metabonomics aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples. It has shown particular promise in the areas of toxicology and drug development, functional genomics, systems biology, and clinical diagnosis. Comprehensive metabonomics investigations are primarily a challenge for analytical chemistry. High-performance liquid chromatography-mass spectrometry (HPLC-MS) is an established technology in drug metabolite analysis and is now expanding into endogenous metabolite research. Its main advantages include wide dynamic range, reproducible quantitative analysis, and the ability to analyze biofluids with extreme molecular complexity. The aims of developing HPLC-MS for metabonomics range from understanding basic biochemistry to biomarker discovery and the structural characterization of physiologically important metabolites. In this review, the strategy and application of HPLC-MS-based metabonomics are reviewed.

From exogenous to endogenous: the inevitable imprint of mass spectrometry in metabolomics

Mass spectrometry (MS) is an established technology in drug metabolite analysis and is now expanding into endogenous metabolite research. Its utility derives from its wide dynamic range, reproducible quantitative analysis, and the ability to analyze biofluids with extreme molecular complexity. The aims of developing mass spectrometry for metabolomics range from understanding basic biochemistry to biomarker discovery and the structural characterization of physiologically important metabolites. In this review, we will discuss the techniques involved in this exciting area and the current and future applications of this field.

Functionalized Magnetic Nanoparticles for Small-Molecule Isolation, Identification, and Quantification

Functionalized magnetic nanoparticles (MNPs) were synthesized to serve as laser desorption/ionization elements as well as solid-phase extraction probes for simultaneous enrichment and detection of small molecules in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. Two laser-absorbing matrices were each conjugated onto MNP to give MNP@matrix which provided high ionization efficiency and background-free detection in MS leading to unambiguous identification of target small molecules in a complex mixture. MNP@matrix was demonstrated to serve as a general matrix-free additive in MALDI-TOF MS analysis of structurally distinct small molecules. Also, MNP@matrix provides a simple, rapid, and reliable quantitative assay for small molecules by mass without either the use of an internal standard or an isotopic labeling tag. Furthermore, the affinity extraction of small molecules from complex biofluid was achieved by probe protein-conjugated MNP@matrix without laborious purification. We demonstrated that a nanoprobe-based assay is a cost-effective, rapid, and accurate platform for robotic screening of small molecules.

Metabolomic analysis of eukaryotic tissue and prokaryotes using negative mode MALDI time-of-flight mass spectrometry

Metabolites in islets of Langerhans and Escherichia coli strain DH5-alpha were analyzed using negative-mode, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). For analysis of anionic metabolites by MALDI, 9-aminoacridine as the matrix yielded a far superior signal in comparison to alpha-cyano-4-hydroxycinnamic acid, 2,5-dihydrobenzoic acid, 2,4,6,-trihydroxyacetophenone, and 3-hydroxypicolinic acid. Limits of detection for metabolite standards were as low as 15 nM for GDP, GTP, ADP, and ATP and as high as 1 muM for succinate in 1-muL samples. Analysis of islet extracts allowed detection of 44 metabolites, 29 of which were tentatively identified by matching molecular weight to compounds in METLIN and KEGG databases. Relative quantification was demonstrated by comparing the ratio of selected di- and triphosphorylated nucleotides for islets incubated with different concentrations of glucose. For islets at 3 mM glucose, concentration ratios of ATP/ADP, GTP/GDP, and UTP/UDP were 1.9 +/- 1.39, 1.12 +/- 0.50, and 0.79 +/- 0.35 respectively, and at 20 mM glucose stimulation, the ratios increased to 4.13 +/- 1.89, 5.62 +/-4.48, and 4.30 +/- 4.07 (n = 3). Analysis was also performed by placing individual, intact islets on a MALDI target plate with matrix and impinging the laser directly on the dried islet. Direct analysis of single islets allowed detection of 43 metabolites, 28 of which were database identifiable. A total of 43% of detected metabolites from direct islet analysis were different from those detected in islet extracts. The method was extended to prokaryotic cells by analysis of extracts from E. coli. Sixty metabolites were detected, 39 of which matched compounds in the MetaCyc database. A total of 27% of the metabolites detected from prokaryotes overlapped those found in islets. These results show that MALDI can be used for detection of metabolites in complex biological samples.

Screening of Nerve Agent Degradation Products by MALDI-TOFMS

A novel method for the rapid screening of degradation products derived from nerve agents by matrix-assisted laser desorption ionization time-of-flight mass spectrometry is described. Five standard products were selected as model compounds, including isopropyl methylphosphonic acid (IMPA), pinacolyl methylphosphonic acid (PMPA), ethyl methylphosphonic acid (EMPA), isobutyl methylphosphonic acid (i-BuMPA), and cyclohexyl methylphosphonic acid (CHMPA), which are degradation products of Sarin (GB), Soman (GD), VX, Russian VX (RVX), and GF, respectively. For comparison, CHCA (alpha-cyano-4-hydroxycinnamic acid) and DCCA (7-(diethylamino)coumarin-3-carboxylic acid) were used as the MALDI-matrix when the third harmonic generation (355 nm) of a Nd:YAG laser and a hydrogen Raman laser (multifrequency laser) were used, respectively. The method permitted the five nerve agent degradation products to be screened rapidly and successfully, suggesting that it has the potential for use as a routine monitoring tool.

Comparison of flow injection analysis electrospray mass spectrometry and tandem mass spectrometry and electrospray high-field asymmetric waveform ion mobility mass spectrometry and tandem mass spectrometry for the determination of underivatized amino acids

Twenty proteinogenic amino acids (AAs) were determined without derivatization using flow injection analysis followed by electrospray ionization mass spectrometry and tandem mass spectrometry (ESI-MS and ESI-MS/MS) and electrospray ionization high-field asymmetric waveform ion mobility mass spectrometry and tandem mass spectrometry (ESI-FAIMS-MS and ESI-FAIMS-MS/MS), in positive and negative ionization modes. Three separate sets of ESI-FAIMS conditions were used for the separation and detection of the 20 AAs. Typically ESI-FAIMS-MS showed somewhat improved sensitivity and significantly better signal-to-noise ratios than ESI-MS mainly due to the elimination of background noise. However, the difference between ESI-FAIMS-MS and ESI-MS/MS was significantly less. ESI-FAIMS was able to partially or completely resolve all the isobaric amino acid overlaps such as leucine, isoleucine and hydroxyproline or lysine and glutamine. Detection limits for the amino acids in ESI-FAIMS-MS mode ranged from 2 ng/mL for proline to 200 ng/mL for aspartic acid. Overall, ESI-FAIMS-MS is the preferred method for the quantitative analysis of AAs in a hydrolyzed yeast matrix.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based amino acid analysis

Amino acid analysis has been an integral part of analytical biochemistry for more than 50 years. However, its experimental design, which includes derivatization of amino acids followed by some kind of chromatographic separation, has not changed over the years. We have developed a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-based method for the quantitative analysis of amino acids. This method does not require any amino acid modification, derivatization, or chromatographic separation. The data acquisition time is decreased to several seconds for a single sample. No significant ion suppression effects were observed with the developed sample deposition technique, and the method was found to be reproducible. Linear responses between the amino acid concentration and the peak intensities ratio of corresponding amino acid to internal standard were observed for all amino acids analyzed in the range of concentrations from 20 to 300 microM, and correlation coefficients were between 0.983 (for arginine) and 0.999 (for phenylalanine). Limits of quantitation were between 0.03 microM (for arginine) and 3.7 microM (for histidine and homocysteine). This method was applicable to the mixtures of free amino acids as well as to HCl hydrolysates of proteins. Furthermore, we have shown that this method can be applied to other biologically important low-molecular weight compounds such as glucose.

Quantitation of Lysergic Acid Diethylamide in Urine Using Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Ion Trap Mass Spectrometry

A quantitative method was developed for analysis of lysergic acid diethylamide (LSD) in urine using atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry (AP MALDI-ITMS). Following solid-phase extraction of LSD from urine samples, extracts were analyzed by AP MALDI-ITMS. The identity of LSD was confirmed by fragmentation of the [M + H](+) ion using tandem mass spectrometry. The quantification of LSD was achieved using stable-isotope-labeled LSD (LSD-d(3)) as the internal standard. The [M + H](+) ion fragmented to produce a dominant fragment ion, which was used for a selected reaction monitoring (SRM) method for quantitative analysis of LSD. SRM was compared with selected ion monitoring and produced a wider linear range and lower limit of quantification. For SRM analysis of samples of LSD spiked in urine, the calibration curve was linear in the range of 1-100 ng/mL with a coefficient of determination, r(2), of 0.9917. This assay was used to determine LSD in urine samples and the AP MALDI-MS results were comparable to the HPLC/ ESI-MS results.

Qualitative and quantitative analysis of low molecular weight compounds by ultraviolet matrix-assisted laser desorption/ionization mass spectrometry using ionic liquid matrices

A major problem hampering the use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for quantitative measurements is the inhomogeneous distribution of analytes and matrices in solid sample preparations. The use of ionic liquids as matrices for the qualitative and quantitative analysis of low molecular weight compounds like amino acids, sugars and vitamins was investigated. The ionic liquid matrices are composed of equimolar combinations of classical MALDI matrices (sinapinic acid, alpha-cyano-4-hydroxycinnamic acid or 2,5-dihydroxybenzoic acid) with organic bases. These matrix systems allow a homogenous sample preparation with a thin ionic liquid layer having negligible vapour pressure. This leads to a facilitated qualitative and quantitative measurement of the analytes compared with classical solid matrices.