Differential metabolomics using stable isotope labeling and two-dimensional gas chromatography with time-of-flight mass spectrometry

This work describes an approach to differential metabolomics that involves stable isotope labeling for relative quantification as part of sample analysis by two-dimensional gas chromatography/mass spectrometry (GCxGC/MS). The polar metabolome in control and experimental samples was extracted and differentially derivatized using isotopically light and heavy (D6) forms of the silylation reagent N-methyl-N-tert-butyldimethylsilyl)trifluoroacetamide (MTBSTFA). MTBSTFA derivatives are of much greater hydrolytic stability than the more common trimethylsilyl derivatives, thus diminishing the possibility of isotopomer scrambling during GC analysis. Subsequent to derivatization with MTBSTFA, differentially labeled samples were mixed and analyzed by GCxGC/MS. Metabolites were identified, and the isotope ratio of isotopomers was quantified. The method was tested using three classes of metabolites; amino acids, fatty acids, and organic acids. The relative concentration of isotopically labeled metabolites was determined by isotope ratio analysis. The accuracy and precision, respectively, in quantification of standard mixtures was 9.5 and 4.77% for the 16 amino acids, 9.7 and 2.83% for the mixture of 19 fatty acids, and 14 and 4.53% for the 20 organic acids. Suitability of the method for the examination of complex samples was demonstrated in analyses of the spiked blood serum samples. This differential isotope coding method proved to be an effective means to compare the concentration of metabolites between two samples simultaneously.     

Capillary electrophoresis-fourier transform ion cyclotron resonance mass spectrometry for the identification of cationic metabolites via a pH-mediated stacking-transient isotachophoretic method

Capillary electrophoresis-mass spectrometry (CE-MS) is still widely regarded as an emerging tool in the field of metabolomics and metabolite profiling. A major reason for this is a reported lack of sensitivity of CE-MS when compared to gas chromatography-mass spectrometry GC/MS and liquid chromatography-mass spectrometry. The problems caused by the lack of sensitivity are exacerbated when CE is coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), due to the relatively low data acquisition rate of FT-ICR MS. Here, we demonstrate the use of an online CE sample preconcentration method that uses a combination of pH-mediated stacking and transient isotachophoresis, coupled with FT-ICR MS to improve the overall detection of cationic metabolites in the bacterium Desulfovibrio vulgaris Hildenborough. This method showed a significant increase in signal-to-noise ratio when compared to CE normal sample stacking, while providing good separation efficiency, reproducibility, and linearity. Detection limits for selected amino acids were between 0.1 and 2 microM. Furthermore, FT-ICR MS detection consistently demonstrated good mass resolution and sub-ppm mass accuracy.     

Characterization of pyrogenic black carbon by desorption atmospheric pressure photoionization Fourier transform ion cyclotron resonance mass spectrometry

We present a new method for molecular characterization of intact biochar directly, without sample preparation or pretreatment, on the basis of desorption atmospheric pressure photoionization (DAPPI) coupled to Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. Conventional ionization methods (e.g., electrospray or atmospheric pressure photoionization) for characterization of natural organic matter have limited utility for the characterization of chars due to incomplete solubility in common solvents. Therefore, direct ionization techniques that do not require sample dissolution prior to analysis are ideal. Here, we apply DAPPI FTICR mass spectrometry to enable the first molecular characterization of uncharred parent oak biomass and after combustion (250 °C) or pyrolysis (400 °C). Parent oak is primarily composed of cellulose-, lignin-, and resin-like compounds. Oak combusted at 250 °C contains condensed aromatic compounds with low H/C and O/C ratios while retaining compounds with high H/C and O/C ratios. The bimodal distribution of aromatic and aliphatic compounds observed in the combusted oak sample is attributed to incomplete thermal degradation of lignin and hemicellulose. Pyrolyzed oak constituents exhibit lower H/C and O/C ratios: approximately three-quarters of the identified species are aromatic. DAPPI FTICR MS results agree with bulk elemental composition as well as functional group distributions determined by elemental analysis and solid state (13)C NMR spectroscopy. Complete molecular characterization of biomass upon thermal transformation may provide insight into the biogeochemical cycles of biochar and future renewable energy sources, particularly for samples currently limited by solubility, separation, and sample preparation.     

Amino Acid analysis of peptides and proteins on the femtomole scale by gas chromatography/mass spectrometry

Amino acid analysis (AAA) is a useful aid in protein chemistry, but its routine application is limited by a modest limit of detection. Typically, 10 pmol of material is required, but even at this level the reproducibility can be poor. We have employed isotope dilution gas chromatography electron capture negative ionization mass spectrometry (GC/ECNI/MS) to provide accurate and reliable data on less than 100 fmol of material. Precision and accuracy are good, and all 20 non-hydrolyzed amino acids can be determined in this manner. The protein is hydrolyzed (HCl), and then a cocktail, composed of all 20 amino acids as stable isotope-labeled forms (i.e., (13)C and (2)H), is added. The mixture of protein-derived and stable isotope-labeled amino acids is then converted to volatile electron-capturing derivatives with a multistep approach employing heptafluorobutyric anhydride (HFBA), pentafluorobenzyl bromide (PFBBr), and N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA). These derivatives are then injected directly into the GC/MS system. Groups of selected ions, characteristic of each derivatized amino acid, are thereafter monitored at appropriate time intervals. The ratios of the ion current for the selected ions for the native amino acid and its labeled form are determined and converted to absolute amounts of the native amino acids in the protein hydrolyzate by reference to standard samples prepared at the time of the analysis.     

Acylic sugar derivatives for GC/MS analysis of 13C-enrichment during carbohydrate metabolism

Metabolic profiling with stable-isotope tracers in combination with gas chromatography/mass spectrometry (GC/MS) is a well-established technique for measuring substrate redistribution within metabolic pathways. This analysis relies on the ability to localize and quantify the fractional incorporation of 13C isotope into each carbon atom of precursor-derived metabolites. In this paper, several carbohydrate derivatization procedures (peracetylation, deuterioalditol acetates, and aldononitrile acetates) are evaluated for the positional isotopic information obtained by gas chromatography/electron impact mass spectrometry (GC/EI-MS). These derivatives have been compared for the quantitative evaluation of 13C distribution into isotopomers of 13C-labeled aldoses and ketoses, and the fragmentation pathways for 15 hexoses, pentoses, and amino sugars of biological origin have been assessed. In addition, a new type of carbohydrate derivative (dialkyldithioacetal acetates) has been developed for GC/MS that retains the charge on the anomeric carbon of the original monosaccharide. Electron impact ionization of these derivatives generates well-resolved base peaks arising from C1-C2 bond cleavage with charge retention at the C1 thiol groups. The dialkyldithioacetal acetates are uniquely well suited for measuring isotopic enrichment into the characteristic anomeric carbon of aldose sugars and will facilitate the global analysis of metabolic flux in carbohydrate pathways.     

Measuring complete isotopomer distribution of aspartate using gas chromatography/tandem mass spectrometry

We have developed a simple and accurate method for determining the complete positional isotopomer distribution of aspartate carbon atoms by gas chromatography/tandem mass spectrometry for (13)C-metabolic flux analysis. First, we screened tandem mass spectrometry (MS) spectra of the tert-butyldimethylsilyl (TBDMS) derivative of aspartate for daughter fragments with the necessary carbon atom fragmentations to fully resolve all 16 isotopomers of aspartate. Tandem MS scanning parameters were optimized for each daughter fragment, and the accuracy of tandem MS measurements were evaluated. We selected five accurate fragments that provided a redundant set of 47 labeling measurements to quantify the complete isotopomer distribution of aspartate by least-squares regression. The validity of the approach was demonstrated using six (13)C-labeled aspartate standards and natural aspartate.     

Picogram quantitation of polycyclic aromatic hydrocarbons adsorbed on aerosol particles by two-step laser mass spectrometry

Polycyclic aromatic hydrocarbons (PAHs) are emitted into the atmosphere mostly by anthropogenic combustion sources. Because of their carcinogenic and mutagenic properties, PAHs are often analyzed in air quality measurements. Atmospheric concentrations of PAHs, typically in the nanograms-per-cubic-meter range, require significant effort for sample collection and processing when conventional methods such as gas chromatography/mass spectrometry (GC/MS) or liquid chromatography/mass spectrometry are used. In contrast, two-step laser mass spectrometry (L2MS) is highly sensitive and selective for PAHs and requires almost no sample preparation. Here, we present for the first time a method based on L2MS to quantify PAHs adsorbed on aerosol particles collected on a filter. Linear ranges for quantitation were determined for five different PAHs in the mass range of 178-276 Da (i.e., phenanthrene, pyrene, chrysene, benzo[e]pyrene, benzo[ghi]perylene) covering more than 2 orders of magnitude with detection limits between 50 and 300 pg of a single PAH on a whole filter sample. A quantitative comparison with GC/MS was performed using model aerosols consisting of benzo[e]pyrene adsorbed on inorganic salt aerosol particles. On average, 25% less benzo[e]pyrene was determined with GC/MS than with L2MS, with a variability between the two methods of +/-68%. The general lower amount measured with GC/MS is attributed to losses during the sample preparation for the GC/MS measurements.     

High sensitivity tracer detection using high-precision gas chromatography-combustion isotope ratio mass spectrometry and highly enriched [U-13C]-labeled precursors.

The use of highly enriched, uniformly labeled fatty acid ([U-13C]) with analysis by high-precision gas chromatography-combustion isotope ratio mass spectrometry (GCC-IRMS) has been evaluated as a metabolic tracer technique. 13C/12C ratios are routinely determined to precisions (SD) of less than 0.00001 (delta PDB less than 1/1000) for greater than 10 ng of fatty acid, and less than 0.001 (delta PDB less than 100/1000) for samples of 30 pg of fatty acid, the latter corresponding to a 100-fmol sample. Baseline fatty acid 13C/12C in human plasma fractions is shown to fluctuate not more than 0.000 04 (delta PDB 4/1000) over 10 h. 13C/12C enrichments greater than 0.001 (delta PDB 100/1000) are obtained in a fatty acid plasma fraction subsequent to a 10-mg dose of 42% 13C-labeled stearic acid to a 78-kg adult. Biokinetics are discerned over an 13C/12C enrichment range of less than 0.0002 (approximately 13/1000 in delta PDB units) in plasma. A means for correction of isotope ratio contamination due to carbon-containing derivatives is presented. High-precision GCC-IRMS used in concert with highly enriched tracers is shown to possess advantages versus organic GC/MS for stable isotopic tracer detection and is superior to radiotracer methods in terms of dose sizes and analysis efficiency.     

Determination of complex isotopomer patterns in isotopically labeled compounds by mass spectrometry

A classic problem in analytical chemistry has been determination of individual components in a mixture without availability of the pure individual components. Measurement of the distribution of isotopomers in a labeled compound or mixture of labeled compounds is an example of this problem that is commonly encountered when stable isotopically labeled metabolites are used to determine in vivo kinetics and metabolism. We present a method that uses the measured mass spectral data of the unlabeled material to represent any and all combinations of isotopomer variations of that material and to determine abundances of these isotopomers. Although examples of the method are presented for gas chromatography/mass spectrometry, the method is applicable to any type of mass spectrometry data. The method also accounts for errors induced by mass spectrometer ionization and resolution effects. To demonstrate this method, we determined the isotopomer distributions of samples of 13C-labeled leucine and glucose for both highly enriched isotopomers and labeled isotopomers present in low abundance against a natural isotopic abundance background. The method accurately and precisely determined isotopomer identity and abundance in the labeled materials without adding noise or error that was not inherent in the original mass spectral data. In examples shown here, isotopomer uncertainties were calculated with relative standard errors of <1% from good quality mass spectral data.     

Accurate assessment of amino acid mass isotopomer distributions for metabolic flux analysis

Metabolic flux analysis based on stable-isotope labeling experiments and analysis of mass isotopomer distributions (MID) of cellular metabolites is a tool of great significance for metabolic engineering and study of human disease. This method relies on accurate and precise measurements of mass isotopomers by gas chromatography/mass spectrometry. To improve flux estimates, we assessed potential errors in determining MID of tert-butyldimethylsilyl-derivatized amino acids, which were attributed to (i) the choice of integration algorithm, (ii) concentration effects, and (iii) overlapping fragments. We report 29 amino acid fragments that are useful for flux analysis and another 18 fragments that should be rejected, most importantly Val-302, Leu-200, Leu-302, Ile-302, Ser-302, and Asp-316. In addition, we provide a protocol to minimize errors for determining MID to less than 0.4 mol % for accepted fragments.     

A comparison of microLC/electrospray ionization-MS and GC/MS for the measurement of stable isotope enrichment from a [2H2]-glucose metabolic probe in T-cell genomic DNA

Measurement of the proliferation of lymphocytes and other high-turnover cell populations in vivo can be accomplished through the incorporation of an isotopically labeled DNA precursor into actively dividing cells and the subsequent determination of the isotope enrichment in the isolated genomic DNA from selected cell populations. Two published gas chromatography/mass spectrometry (GC/MS) methods were successfully modified by our laboratory whereby a postinjection methylation reaction, rather than silylation or acetylation, was used to form a volatile derivative of deoxyadenosine (dA). We also developed a second robust microcapillary liquid chromatography-electrospray ionization (microLC-ESI)/MS method that is faster and more sensitive than the GC/MS method and does not require sample derivatization. Following administration of [6,6-(2)H(2)]-glucose to human immunodeficiency virus-infected patients, peripheral blood was drawn; cells were obtained by lymphapheresis and fractionated. DNA was isolated from the desired cell subtypes and enzymatically hydrolyzed to the free deoxyribonucleosides. The digest was analyzed using both capillary GC/MS and microLC/ESI-MS to measure the levels of the dA and [(2)H(2)]-dA or their reaction products. Sample enrichments were calculated by comparison to standard curves prepared from dA and [(2)H(2)]-dA. The microLC/ESI-MS method required fewer cells, less sample preparation, shorter analysis times, and a single calibration curve. Overall, the microLC/ESI-MS method is superior to the GC/MS method in terms of precision and accuracy, while providing a 4-fold increase in sensitivity (from 20 pmol at 0.2% [(2)H(2)]-dA enrichment to 5 pmol at 0.1% [(2)H(2)]-dA enrichment).     

Measuring deuterium enrichment of glucose hydrogen atoms by gas chromatography/mass spectrometry

We developed a simple and accurate method for determining deuterium enrichment of glucose hydrogen atoms by electron impact gas chromatography mass spectrometry (GC/MS). First, we prepared 18 derivatives of glucose and screened over 200 glucose fragments to evaluate the accuracy and precision of mass isotopomer data for each fragment. We identified three glucose derivatives that gave six analytically useful ions: (1) glucose aldonitrile pentapropionate (m/z 173 derived from C4-C5 bond cleavage; m/z 259 from C3-C4 cleavage; m/z 284 from C4-C5 cleavage; and m/z 370 from C5-C6 cleavage); (2) glucose 1,2,5,6-di-isopropylidene propionate (m/z 301, no cleavage of glucose carbon atoms); and (3) glucose methyloxime pentapropionate (m/z 145 from C2-C3 cleavage). Deuterium enrichment at each carbon position of glucose was determined by least-squares regression of mass isotopomer distributions. The validity of the approach was tested using labeled glucose standards and carefully prepared mixtures of standards. Our method determines deuterium enrichment of glucose hydrogen atoms with an accuracy of 0.3 mol %, or better, without the use of any calibration curves or correction factors. The analysis requires only 20 μL of plasma, which makes the method applicable for studying gluconeogenesis using deuterated water in cell culture and animal experiments.     

Quantification of deuterium isotopomers of tree-ring cellulose using nuclear magnetic resonance

Stable isotopes in tree rings are important tools for reconstruction of past climate. Deuterium (D) is of particular interest since it may contain climate signals and report on tree physiology. Measurements of the D/H ratio of tree-ring cellulose have proven difficult to interpret, presumably because the D/H ratio of the whole molecule blends the abundances of the seven D isotopomers of cellulose. Here we present a method to measure the abundance of the D isotopomers of tree-ring cellulose by nuclear magnetic resonance spectroscopy (NMR). The method transforms tree-ring cellulose into a glucose derivative that gives highly resolved, quantifiable deuterium NMR spectra. General guidelines for measurement of D isotopomers by NMR are described. The transformation was optimized for yield and did not alter the original D isotopomer abundances, thus, conserving the original signals recorded in wood cellulose. In the tree-ring samples tested, the abundances of D isotopomers varied by approximately +/-10% (2% standard error). This large variability can only be caused by biochemistry processes and shows that more information is present in D isotopomer abundances, compared to the D/H ratio. Therefore, measurements of the D isotopomer distribution of tree rings may be used to obtain information on long-term adaptations to environmental changes and past climate change.     

Hyphenation of gas chromatography to microcoil 1H nuclear magnetic resonance spectroscopy

Whereas the hyphenation of gas chromatography (GC) with mass spectrometry is of great importance, little is known about the coupling to nuclear magnetic resonance spectroscopy (NMR). The investigation of this technique is an attractive proposition because of the valuable information given by NMR on molecular structure. The experiments shown here are to our knowledge the first hyphenating capillary GC to microcoil NMR. In contrast to liquids, gases have rarely been investigated by NMR, mainly due to the experimental difficulties in handling gases and the low signal-to-noise-ratio (SNR) of the NMR signal obtained at atmospheric pressure. With advances in NMR sensitivity (higher magnetic fields and solenoidal microprobes), this limitation can be largely overcome. In this paper, we describe the use of a custom-built solenoidal NMR microprobe with an active volume of 2 microL for the NMR detection of several compounds at 400 MHz, first in a mixture, and then with full coupling to capillary GC to identify them separately. The injected amounts of each analyte in the hyphenated experiments are in the range of 15-50 micromol, resulting in reasonable SNR for sample masses of 1-2 microg.     

A structural mass spectrometry strategy for the relative quantitation of ligands on mixed monolayer-protected gold nanoparticles

It is becoming increasingly common to use gold nanoparticles (AuNPs) protected by a heterogeneous mixture of thiolate ligands, but many ligand mixtures on AuNPs cannot be properly characterized due to the inherent limitations of commonly used spectroscopic techniques. Using ion mobility-mass spectrometry (IM-MS), we have developed a strategy that allows measurement of the relative quantity of ligands on AuNP surfaces. This strategy is used for the characterization of three samples of mixed-ligand AuNPs: tiopronin:glutathione (av diameter 2.5 nm), octanethiol:decanethiol (av diameter 3.6 nm), and tiopronin:11-mercaptoundecyl(poly ethylene glycol) (av diameter 2.5 nm). For validation purposes, the results obtained for tiopronin:glutathione AuNPs were compared to parallel measurements using nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) without ion mobility separation. Relative quantitation measurements for NMR and IM-MS were in excellent agreement, with an average difference of less than 1% relative abundance. IM-MS and MS without ion mobility separation were not comparable, due to a lack of ion signals for MS. The other two mixed-ligand AuNPs provide examples of measurements that cannot be performed using NMR spectroscopy.     

High-throughput global peptide proteomic analysis by combining stable isotope amino acid labeling and data-dependent multiplexed-MS/MS

In this work, we describe the application of a stable isotope amino acid (lysine) labeling in conjunction with data-dependent multiplexed tandem mass spectrometry (MS/MS) to facilitate the characterization and identification of peptides from proteomic (global protein) digests. Lysine auxotrophic yeast was grown in the presence of 13C-labeled or unlabeled lysine and combined after harvesting in equal proportions. Endoproteinase LysC digestion of the cytosolic fraction produced a global proteomic sample, consisting of heavy/light labeled peptide pairs. Then data-dependent multiplexed-MS/MS was applied to simultaneously select and dissociate only labeled peptide ion pairs. The approach allows differentiation between N-terminal (e.g., b-type ions) and C-terminal fragment ions (e.g., y-type ions) in resulting tandem mass spectra, as well as the capability of differentiation between near-isobaric glutamine and lysine residues. We also describe the utility of peptide composition and fragment information to support peptide identifications and examine the potential application of lysine labeling for differential quantitative protein analysis.     

Determination of lysergic acid diethylamide (LSD), iso-LSD, and N-demethyl-LSD in body fluids by gas chromatography/tandem mass spectrometry.

Procedures for detection and quantitation of lysergic acid diethylamide (LSD), iso-LSD, and N-demethyl-LSD by capillary chromatography/tandem mass spectrometry (GC/MS/MS) are presented. Several methods for derivatization, sample introduction, and ionization, in combination with mass spectrometry/mass spectrometry (MS/MS), have been evaluated for overall ionization efficiency and product-ion sensitivity and specificity. Fragmentation pathways derived from low-energy collision-induced dissociation (CID) spectra of protonated LSD, and the protonated trimethylsllyl derivatives of LSD (LSD-TMS) and deuterium-labeled analogs of LSD, have been proposed. Principal dissociations primarily involve the amide and piperidine-ring moieties in which losses of CH3 radical, CH3NH2, CH3NCH2, diethylamine, diethylformamide, and N,N-diethylpropenamide from MH+ are observed. Positive-ion ammonia chemical ionization and subsequent MS/MS analysis of the protonated molecules (MH+) of the trimethylsilyl (TMS) derivatives of LSD, iso-LSD, and N-demethyl-LSD provide a high degree of specificity for identification of these compounds in urine or blood at low-pg/mL concentrations. Negative-ion chemical ionization and GC/MS/MS analysis of the molecular anion (M-) of the trifluoroacetyl (TFA) derivative is well suited for trace-level identification of N-demethyl-LSD, a metabolite of LSD.     

Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry

Measuring dynamics of proteins abundance in cells in response to stimuli such as growth factors or drugs requires analysis of more than one time point. Proteomic approaches have traditionally been used to measure only one state at a time because quantitation is difficult, especially when mass spectrometry is used as a readout. Isotopically labeled reagents have recently been introduced that allow comparison of two or three different states by mass spectrometry. Here, we evaluate the reproducibility of an experiment that measures three states simultaneously through stable isotope labeling of cells with amino acids in cell culture (SILAC) using light, medium, and heavy versions of amino acids. The major goal of this study was to assess the reproducibility of such experiments in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS). Our results show that it is possible to obtain reproducible quantitative data to study protein dynamics based on our analysis of more than 220 peptide sets derived from 20 proteins from 3 different LC-MS/MS runs.     

Method for estimating the isotopic distributions of metabolically labeled proteins by MALDI-TOFMS: application to NMR samples

We have developed an efficient method of estimating metabolic incorporation of heavy isotopes into proteins, including those where a single amino acid carries the label. The protein is digested with trypsin, and the resulting peptide mixture is examined directly by MALDI-TOF mass spectrometry. Peptides are chosen for analysis if they contain one or more labeled atoms and also exhibit clearly separated mass spectra. The known atomic composition of the peptide is then used to simulate ion distributions for various proportions of heavy isotope incorporation, to obtain the best match to the observed ion distribution. We demonstrate the method by comparing simulated and observed mass spectra of tryptic peptides of Escherichia coli citrate synthase labeled with 15N in several ways and show that the method is particularly applicable when only one amino acid is isotopically labeled.     

Assessment of compatibility between extraction methods for NMR- and LC/MS-based metabolomics

Because of the wide range of chemically and structurally diverse metabolites, efforts to survey the complete metabolome rely on the implementation of multiplatform approaches based on nuclear magnetic resonance (NMR) and mass spectrometry (MS). Sample preparation disparities between NMR and MS, however, may limit the analysis of the same samples by both platforms. Specifically, deuterated solvents used in NMR strategies can complicate LC/MS analysis as a result of potential mass shifts, whereas acidic solutions typically used in LC/MS methods to enhance ionization of metabolites can severely affect reproducibility of NMR measurements. These intrinsically different sample preparation requirements result in the application of different procedures for metabolite extraction, which involve additional sample and unwanted variability. To address this issue, we investigated 12 extraction protocols in liver tissue involving different aqueous/organic solvents and temperatures that may satisfy the requirements for both NMR and LC/MS simultaneously. We found that deuterium exchange did not affect LC/MS results, enabling the measurement of metabolites by NMR and, subsequently, the direct analysis of the same samples by using LC/MS with no need for solvent exchange. Moreover, our results show that the choice of solvents rather than the temperature determined the extraction efficiencies of metabolites, a combination of methanol/chloroform/water and methanol/water being the extraction methods that best complement NMR and LC/MS analysis for metabolomic studies.