Impact of intratumoral heterogeneity of breast cancer tissue on quantitative metabolomics using high-resolution magic angle spinning 1 H NMR spectroscopy.

High-resolution magic angle spinning (HR MAS) nuclear magnetic resonance (NMR) spectroscopy is increasingly being used to study metabolite levels in human breast cancer tissue, assessing, for instance, correlations with prognostic factors, survival outcome or therapeutic response. However, the impact of intratumoral heterogeneity on metabolite levels in breast tumor tissue has not been studied comprehensively. More specifically, when biopsy material is analyzed, it remains questionable whether one biopsy is representative of the entire tumor. Therefore, multi-core sampling (n = 6) of tumor tissue from three patients with breast cancer, followed by lipid (0.9- and 1.3-ppm signals) and metabolite quantification using HR MAS 1 H NMR, was performed, resulting in the quantification of 32 metabolites. The mean relative standard deviation across all metabolites for the six tumor cores sampled from each of the three tumors ranged from 0.48 to 0.74. This was considerably higher when compared with a morphologically more homogeneous tissue type, here represented by murine liver (0.16-0.20). Despite the seemingly high variability observed within the tumor tissue, a random forest classifier trained on the original sample set (training set) was, with one exception, able to correctly predict the tumor identity of an independent series of cores (test set) that were additionally sampled from the same three tumors and analyzed blindly. Moreover, significant differences between the tumors were identified using one-way analysis of variance (ANOVA), indicating that the intertumoral differences for many metabolites were larger than the intratumoral differences for these three tumors. That intertumoral differences, on average, were larger than intratumoral differences was further supported by the analysis of duplicate tissue cores from 15 additional breast tumors. In summary, despite the observed intratumoral variability, the results of the present study suggest that the analysis of one, or a few, replicates per tumor may be acceptable, and supports the feasibility of performing reliable analyses of patient tissue.

Studying the fragmentation mechanism of selected components present in crude oil by collision-induced dissociation mass spectrometry.

RATIONALE: Structural characterization of individual compounds in very complex mixtures is difficult to achieve. One important step in structural elucidation is understanding the mass spectrometric fragmentation mechanisms of the compounds present in such mixtures. Here, different individual compounds presumed to be present in a complex crude oil mixture have been synthesized and structurally characterized by tandem mass spectrometry (MS/MS) studies. METHODS: Model compounds with different aromatic cores and various substitutents were synthesized. Major effort has been put into producing isomerically pure compounds to better understand the fragmentation pattern. Each synthesized compound has been subjected to MSn studies using either a triple quadrupole or a linear ion trap mass spectrometer with electrospray or atmospheric pressure photoionization. The results are used to analyze individual compounds from a complex vacuum gas oil (VGO). RESULTS: The synthesized compounds and a chromatographically simplified vacuum gas oil were used for structural analysis. The major fragmentation mechanism is the benzylic cleavage of the aliphatic side chain. Each side chain can be separately removed from the aromatic core by using MSn methods. At the end of a series of fragmentations, the base aromatic core structure remains and can be chararcterized. CONCLUSIONS: By defining the fragmentation mechanism in complex oil samples it was possible to structurally characterize individual compounds present in a chromatographically simplified VGO. The compounds consist of an aromatic core with aliphatic side chains. Cleavage of all side chains can be achieved by MSn measurements, allowing characterization of the remaining core structure.

Metabolic profiling of ob/ob mouse fatty liver using HR-MAS 1H-NMR combined with gene expression analysis reveals alterations in betaine metabolism and the transsulfuration pathway.

Metabolic perturbations resulting from excessive hepatic fat accumulation are poorly understood. Thus, in this study, leptin-deficient ob/ob mice, a mouse model of fatty liver disease, were used to investigate metabolic alterations in more detail. Metabolites were quantified in intact liver tissues of ob/ob (n = 8) and control (n = 8) mice using high-resolution magic angle spinning (HR-MAS) 1H-NMR. In addition, after demonstrating that HR-MAS 1H-NMR does not affect RNA integrity, transcriptional changes were measured by quantitative real-time PCR on RNA extracted from the same specimens after HR-MAS 1H-NMR measurements. Importantly, the gene expression changes obtained agreed with those observed by Affymetrix microarray analysis performed on RNA isolated directly from fresh-frozen tissue. In total, 40 metabolites could be assigned in the spectra and subsequently quantified. Quantification of lactate was also possible after applying a lactate-editing pulse sequence that suppresses the lipid signal, which superimposes the lactate methyl resonance at 1.3 ppm. Significant differences were detected for creatinine, glutamate, glycine, glycolate, trimethylamine-N-oxide, dimethylglycine, ADP, AMP, betaine, phenylalanine, and uridine. Furthermore, alterations in one-carbon metabolism, supported by both metabolic and transcriptional changes, were observed. These included reduced demethylation of betaine to dimethylglycine and the reduced expression of genes coding for transsulfuration pathway enzymes, which appears to preserve methionine levels, but may limit glutathione synthesis. Overall, the combined approach is advantageous as it identifies changes not only at the single gene or metabolite level but also deregulated pathways, thus providing critical insight into changes accompanying fatty liver disease. Graphical abstract A Evaluation of RNA integrity before and after HR-MAS 1H-NMR of intact mouse liver tissue. B Metabolite concentrations and gene expression levels assessed in ob/ob (steatotic) and ob/+ (control) mice using HR-MAS 1H-NMR and qRT-PCR, respectively.

Ionic liquids as stationary phases in gas chromatography--an LSER investigation of six commercial phases and some applications.

The separation properties of six novel stationary phases for gas chromatography, commercially available from Sigma-Aldrich (Supelco) and based on ionic liquids (ILs), were investigated. The linear solvation energy relationship model (LSER) was used to describe the molecular interactions between these stationary phases and 30 solutes. The solutes belong to different groups of compounds, like haloalkanes, alcohols, ketones, aromatics, aliphatics, and others. A good description of different interactions, as described by the LSER model, could be achieved. The calculated values of system constants for the ionic liquid phases were compared with constants of commonly used standard phases like a 5 % phenyl/95 % dimethyl siloxane and a polyethylene glycol phase. The solute descriptors are in good agreement with those found by previous authors who have used the LSER model for 44 different ionic liquids as stationary phase. The experiments were carried out at two temperatures to evaluate the influence on the phase parameters and separation characteristics. The interactions of different functional groups with the IL phases are discussed. These novel IL phases are a promising replacement of or an addition to common polar phases. Based on the evaluated phase properties, several possibilities for applications of these novel phases are shown.

Direct coupling of normal-phase high-performance liquid chromatography to atmospheric pressure laser ionization fourier transform ion cyclotron resonance mass spectrometry for the characterization of crude oil.

The high complexity of crude oil makes the use of chromatographic separation an important tool especially for sample simplification. The coupling of normal-phase high-performance liquid chromatography (HPLC) using a polar aminocyano column to a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer offers the best attributes of good separation prior to ultrahigh resolution mass spectrometry (MS) detection. Atmospheric pressure laser ionization (APLI) was used as an ionization technique to analyze the nitrogen-containing aromatic compounds in a deasphalted crude oil due to its unique selectivity toward aromatic compounds and also due to its sensitivity. Two main chromatographic peaks were observed during this separation indicating a class-based separation. Mass spectra obtained from fractions were collected along the entire retention time and compared with each other to assign the unique constituents. By coupling the HPLC system directly to the FTICR mass spectrometer, comparable ion and UV chromatograms were obtained, reflecting the scan-to-scan sensitivity of the coupling system. The results show that it is possible to calculate reconstructed class chromatograms (RCC), allowing differences in class composition to be traced along the retention time. As an example, radical and protonated nitrogen species generated by APLI were detected along the retention time which enabled a differentiation between basic and nonbasic species in the same polar peak, thus overcoming the limitation of chromatographic resolution. This report represents the first online LC-FTICR MS coupling in the field of crude oil analysis.

Atmospheric pressure chemical ionization Fourier transform ion cyclotron resonance mass spectrometry for complex thiophenic mixture analysis.

RATIONALE: Polycyclic aromatic sulfur heterocycles (PASHs) are detrimental species for refining processes in petroleum industry. Current mass spectrometric methods that determine their composition are often preceded by derivatization and dopant addition approaches. Different ionization methods have different impact on the molecular assignment of complex PASHs. The analysis of such species under atmospheric pressure chemical ionization (APCI) is still considered limited due to uncontrolled ion generation with low- and high-mass PASHs. METHODS: The ionization behavior of a model mixture of five selected PASH standards was investigated using an APCI source with nitrogen as the reagent gas. A complex thiophenic fraction was separated from a vacuum gas oil (VGO) and injected using the same method. The samples were analyzed using Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS). RESULTS: PASH model analytes were successfully ionized and mainly [M + H](+) ions were produced. The same ionization pattern was observed for the real thiophenic sample. It was found that S1 class species were the major sulfur-containing species found in the VGO sample. These species indicated the presence of alkylated benzothiophenic (BT), dibenzothiophenic (DBT) and benzonaphthothiophenic (BNT) series that were detected by APCI-FTICR MS. CONCLUSIONS: This study provides an established APCI-FTICR MS method for the analysis of complex PASHs. PASHs were detected without using any derivatization and without fragmentation. The method can be used for the analysis of S-containing crude oil samples.

Capillary electrophoretic separation of polycyclic aromatic sulfur heterocycles.

Capillary electrophoresis (CE) was used to separate polycyclic aromatic sulfur heterocycles (PASHs), a class of compounds that occurs in fossil fuels and refined products of petroleum. An electric charge was introduced into the compounds through methylation or phenylation of the sulfur atom. Separations of standard PASHs that are expected to be present in industrially desulfurized fuels showed that CE possessed a higher resolution than reversed phase liquid chromatography. The CE method can separate all the monomethylbenzothiophenes; this is not achieved in capillary gas chromatography. A linear relationship was found between migration time and the calculated volume of the compounds. The PASHs in deeply desulfurized diesel were separated after preconcentration, and the electropherogram was compared with the chromatograms from GC and HPLC. Finally, derivatized PASHs are often enantiomeric and the enantiomers can be separated if a suitable cyclodextrin is added to the running buffer.

Characterization of supercomplex crude oil mixtures: what is really in there?

Through different windows: One major obstacle in energy research is the complexity and variety of compounds present in crude oil. A study of different ionization methods for mass spectrometry shows that the mass spectrum very strongly depends on which method is used.

A tiered analytical approach for target, non-target and suspect screening analysis of polar transformation products of polycyclic aromatic compounds.

Polycyclic aromatic compounds (PACs) possess toxicity towards humans, and their presence in the environment is unwanted. Polar transformation products (TPs) are more mobile, and can be considered emerging contaminants, as they represent a more bioavailable carrier of the same toxic properties. Acidic TPs has been proposed as an important class of polar TPs. This study presents a tiered analytical approach to investigate acidic and polar PAC TPs in environmental conditions. The tiered approach exploits target analysis for quantification of acids; suspect screening for tentative identification based on retention time and spectral matching using databases; and finally non-target analysis based on chromatography and data independent broadband MS to highlight potentially unknown analyte peaks. The approach includes a mixed-mode anion exchange solid phase extraction (MAX-SPE) to fractionate neutral and acidic compounds, and is applied to three cases: I) Photo-oxidation of six PACs generated suspected hydroxylated-, carbonylated- and carboxylated PACs but also proposed the presence of mono- and dicarboxylic acids, which have not been reported elsewhere. For a subset of four acids, conversion rates were determined. II) Recovery of spiked acids from diesel spilled harbor water was 80% by LC-MS, and diesel spill weathering was evaluated from the neutral fraction by GC-MS. III) By non-target analysis sulfonated PACs, presumable derived from photo-oxidation, were detected in run-off basins of an arctic landfarm, alongside hypothesized naturally occuring fatty acids. The tiered approach is a sensitive and versatile tool to extract information on PACs and their polar TPs from polluted environmental sites.

Fourier transform ion cyclotron resonance mass spectrometry in the speciation of high molecular weight sulfur heterocycles in vacuum gas oils of different boiling ranges.

The analysis of sulfur aromatics in vacuum gas oils (VGO) distilled from an Iranian light crude oil is discussed. The VGOs were fractionated into three boiling ranges, 390-460, 460-520, and 520-550 degrees C, and were analyzed using liquid chromatographic separation on a Pd(II)-bonded stationary phase followed by identification with electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). It was possible to detect a large number of thiophenes, including a substantial number of isomers, in the three VGO fractions. Separation on the palladium phase and inclusion of sulfur-selective derivatization makes electrospray ionization of these nonpolar compounds possible. An elemental composition can be assigned to a large number of S(1) compounds without ambiguity in the presence of abundant hydrocarbons. With an increase in boiling temperature, an increase in the size of the aromatic system and the number of side chain carbon atoms was observed. In addition, the masses of higher magnitude shifted toward larger aromatic systems with an increase in boiling range. A comparison of FT-ICR MS and comprehensive gas chromatography is also given.

Qualitative analysis of phenols and alcohols in complex samples after derivatization to esters of ferrocene carboxylic acid by gas chromatography with mass spectrometric detection.

Phenols and alcohols in complex petrochemical samples are derivatized to esters of ferrocene carboxylic acid in a rapid and simple reaction. These esters show several characteristic ions of high intensity in gas chromatography coupled with electron impact ionization mass spectrometry (GC-EI-MS) which can be used for the identification of the analyte. A differentiation between alcohols and phenols is possible due to the McLafferty rearrangement shown only by the alcohol esters. Selective ion monitoring of m/z 213 yields a phenol-selective chromatogram and m/z 230 an alcohol-selective chromatogram. For all iron containing fragments, the isotopic pattern of iron can be observed which enhances the reliability of the peak identification. The ferrocene esters of 11 alcohols, 20 alkylphenols (including octyl- and nonylphenol), phenylphenol, naphthol and hydroxyphenanthrene, several chloro- and all mononitrophenols were synthesized as well as the esters of pentadeutero- and two fluorinated phenols. Their fragmentation pattern under EI ionization is studied and a GC-ion trap-MS system was optimized for simultaneous use of the full scan mode and an MS/MS experiment in the same run. This provides for a very high selectivity in the detection of the esters and makes available the complete mass spectra without any additional measurements. The benefits of the simple and rapid derivatization procedure in combination with this powerful detection method are demonstrated for selected petrochemical samples. Several alkylphenols could be successfully identified in such samples and molecular information about unknown phenolic components could be easily obtained.

Speciation of alkylated dibenzothiophenes through correlation of structure and gas chromatographic retention indexes.

The gas chromatographic (GC) speciation of polycyclic aromatic sulfur heterocycles (PASH) in deeply desulfurized fuels is difficult without recourse to authentic standard compounds. Here we investigate the GC retention indexes for 30 alkylated dibenzothiophenes on two methylphenylsiloxane stationary phases of different selectivity (5% and 50% phenyl groups) with a view to avoid the synthesis of all congeners. The influence of the substitution pattern on the retention indexes is discussed. With the measured data it is possible to carry out a multiple linear regression (MLR) to calculate parameters for predicting the retention indexes of unknown polymethylated isomers based only on their structural features. Nine trimethyldibenzothiophene in a synthesis product are identified through their retention indexes. The retention indexes for a total of 43 alkyldibenzothiophenes are listed.

beta-Cyclodextrin as a stationary phase for the group separation of polycyclic aromatic compounds in normal-phase liquid chromatography.

The separation of highly alkylated polycyclic aromatic compounds according to the size of their aromatic system is investigated using the polycyclic aromatic sulfur heterocycles in vacuum gas oil. A large number of reference compounds containing several parent ring systems and different alkylation patterns were first investigated to characterize the retention of polycyclic aromatic compounds likely to occur in high-boiling petroleum samples. A beta-cyclodextrin phase, Merck ChiraDex, was found to be more suitable than chemically bonded aminopropanosilane and tetrachlorophthalimide in normal-phase HPLC with respect to a combination of selectivity towards the number of aromatic double bonds and degree of influence of the alkyl groups of the aromatic compounds. Finally the preseparated polycyclic aromatic sulfur heterocycles from a vacuum gas oil were fractionated according to the number of condensed aromatic rings on the ChiraDex phase and were characterized by Fourier transform ion cyclotron resonance mass spectrometry.

Simple and sensitive determination of o-phenylphenol in citrus fruits using gas chromatography with atomic emission or mass spectrometric detection.

In this work, a simple and sensitive method for the analysis of the pesticide o-phenylphenol (OPP) on citrus fruits was developed. OPP is extracted with dichloromethane by ultrasonication and derivatized with ferrocenecarboxylic acid chloride. Using ferrocene as a label, residues of OPP are determined by gas chromatography with atomic emission detection in the iron selective mode or with mass spectrometric detection. Sample cleanup is simple and rapid and merely involves a removal of excess reagent on an alumina minicolumn. The method detection limit is 2 ng of OPP/g of fruit, and recoveries from lemon samples fortified at levels of 35 and 140 ng/g are 101 and 106%, respectively. The citrus fruits analyzed (oranges, grapefruits, lemons) contained between 60 ng/g and 0.37 microg/g OPP (RSD = 8-13%), and the results were in good agreement with results obtained when OPP was analyzed using an established HPLC-FLD method. Several alcohols could also be identified in the fruit peel.

Overview of Polycyclic Aromatic Compounds (PAC).

The chemical group of polycyclic aromatic compounds (PAC), including the better-known subgroup of polycyclic aromatic hydrocarbons (PAH) and the heterocyclic aromatic compounds (NSO-PAC, heterocycles), comprise several thousand individual compounds. It is hard to find a comprehensive overview in the literature of these PACs that includes a substantial amount of relevant properties. Here an attempt is made to summarize the most studied but also some less well-known PACs. In addition to basic data such as recommended names, abbreviations, CAS numbers, molecular formulas, chemical structures, and exact mono-isotopic molecular weights, physico-chemical properties taken from the literature like boiling points, vapor pressures, water solubilities, Henry's Law constants, n-octanol-water partition coefficients (log KOW), and pKa are summarized. Selected toxicological data are listed indicating carcinogenic and mutagenic activity or effects on different organisms. PAC nomenclature is a complex topic, so suggestions for practical use are made. Regarding available data, estimated (instead of measured) values should be used with caution because considerable deviations from experimentally determined values can occur. For an enhanced understanding of the behavior of single PACs in comparison with each other, some of the properties mentioned above are plotted vs. the number of rings or the degree of alkylation. Also, some physico-chemical data are correlated with different functional groups as substituents of the PAHs. This article reveals that rather little is known about the less common PACs, e.g., higher molecular weight compounds, alkylated or otherwise substituted aromatics, for instance, keto-, oxo-, amino-, nitro-, cyano-PAHs, or some heterocyclic aromatic compounds, including their derivatives. It mirrors the limited state of knowledge about the variety of PACs that do not belong to the 16 EPA PAHs.

Time to Say Goodbye to the 16 EPA PAHs? Toward an Up-to-Date Use of PACs for Environmental Purposes.

The 16 EPA PAHs have played an exceptionally large role above all in environmental and analytical sciences in the last 40 years, but now there are good reasons to question their utility in many circumstances even though their use is so established and comfortable. Here we review the reasons why the list has been so successful and why sometimes it is seen as less relevant. Three groups of polycyclic aromatic compounds (PAC) are missing: larger and highly relevant PAHs, alkylated PACs, and compounds containing heteroatoms. Attempts to improve the situation for certain matrixes are known and here: (1) an updated list of PAHs (including the 16 EPA PAHs) for the evaluation of the toxicity in the environment (40 EnvPAHs); (2) a list of 23 NSO-heterocyclic compounds and 6 heterocyclic metabolites; and (3) lists of 10 oxy-PAHs and 10 nitro-PAHs are proposed for practical use in the future. A discussion in the scientific community about these lists is invited. Although the state of knowledge has improved dramatically since the introduction of the 16 EPA PAHs in the 1970s, this summary also shows that more research is needed about the toxicity, occurrence in the environment and chemical analysis, particularly of alkylated PAHs, higher molecular weight PAHs and substituted PACs such as amino-PAHs, cyano-PAHs, etc.. We also suggest that a long overdue discussion of an update of regulatory environmental PAH analysis is initiated.

Changes of the metal composition in German white wines through the winemaking process. A study of 63 elements by inductively coupled plasma-mass spectrometry.

Elemental patterns are often used for the classification or identification of the origin of wines. A prerequisite is that the concentration of the elements is not strongly influenced by the addition of different substances such as yeast and fining products during the winemaking process. Inductively coupled plasma-mass spectrometry (ICP-MS) has been used in this study to determine in total 63 elements (including some nonmetals and the rare earth elements) in five German white wines from five regions of origin. The whole winemaking process was studied, from the must to the ready wine. Microwave acid digestion was used for sample preparation, and indium was added as internal standard for a semiquantitative analysis. Two winemaking processes were compared: with the addition of clarifying agents (bentonites) before and after the fermentation. The concentration of only a few elements such as Li, B, Mg, Ca, Rb, Cs, and Pb seems to be constant throughout the whole winemaking process (changes of <+/-50%) and are independent of the time of addition of the bentonites. When bentonites are added before fermentation, the concentration of other elements, such as V, Co, and Fe, remains constant. If bentonites are added after fermentation, the concentration of some other elements such as Sr, Zn, and Mn is nearly unaffected. These elements are therefore robust elements for origin studies in German white wines.

Classification of German white wines with certified brand of origin by multielement quantitation and pattern recognition techniques.

A procedure is proposed for the determination of the authenticity of white wines from four German wine-growing regions (Baden, Rheingau, Rheinhessen, and Pfalz) based on their content of some major, trace, and ultratrace elements. One hundred and twenty-seven white wine samples possessing a certificate of origin, all of the 2000 vintage, were analyzed. The concentrations of 13 elements (Li, B, Mg, Ca, V, Mn, Co, Fe, Zn, Rb, Sr, Cs, and Pb) were determined in wine diluted 1:20 by sector field inductively coupled plasma mass spectrometry (SF-ICP-MS). Indium was routinely used as internal standard. Supervised pattern recognition techniques such as discriminant analysis and classification trees were applied for the interpretation of the data. A quadratic discriminant analysis (QDA) allowed the four regions to be discriminated with 83% accuracy when using only eight variables (Li, B, Mg, Fe, Zn, Sr, Cs, and Pb), and the prediction ability for classifying new samples was 76%. By use of a second method, a decision tree, the classification of samples coming from the four regions could be performed with an accuracy of 84% when only four elements were used: Li (very low in samples from Baden), Zn (abnormally low in the samples from the Rheingau), and Mg and Sr (both important for the differentiation between Pfalz and Rheinhessen samples). For this method, the prediction ability was only 74% in the identification of unknown samples. The robustness of the QDA model was not good enough, and therefore the tree is better recommended for the classification of new wine samples from these areas of German wine production.

Weathering trend characterization of medium-molecular weight polycyclic aromatic disulfur heterocycles by Fourier transform ion cyclotron resonance mass spectrometry.

Different weathering factors act to change petroleum composition once it is spilled into the environment. n-Alkanes, biomarkers, low-molecular weight polyaromatic hydrocarbons and sulfur heterocycles compositional changing in the environment have been extensively studied by different researchers and many parameters have been used for oil source identification and monitoring of weathering and biological degradation processes. In this work, we studied the fate of medium-molecular weight polycyclic aromatic disulfur heterocycles (PAS2Hs), up to ca. 900Da, of artificially weathered Flotta North Sea crude oil by ultra high-resolution Fourier transform ion cyclotron resonance mass spectrometry. It was found that PAS2Hs in studied crude oil having double bond equivalents (DBE) from 5 to 8 with a mass range from ca 316 to 582Da were less influenced even after six months artificial weathering experiment. However, compounds having DBEs 12, 11 and 10 were depleted after two, four and six months weathering, respectively. In addition, DBE 9 series was more susceptible to weathering than those of DBE 7 and 8.

Argentation chromatography for the separation of polycyclic aromatic compounds according to ring number.

Crude oils are the most complex mixtures known and every speciation method relies on a simplification of their complexity. Argentation chromatography is shown to be superior to traditional liquid chromatographic ways of separating aromatic compounds based on the number of aromatic carbon atoms. A silver(I) mercaptopropano silica gel allows an efficient group separation of polycyclic aromatic compounds to be achieved. The usefulness of this phase is demonstrated for SRM 1582 Wilmington crude oil and a diesel fuel. Furthermore, the phase can also be used for semi-preparative purposes to collect fractions for further analysis with high resolution mass spectrometry. Orbitrap mass spectra are obtained here for the polycyclic aromatic sulfur heterocycles and it is demonstrated that they can contain one to five naphtheno rings.