Intra-batch effect correction in liquid chromatography-mass spectrometry using quality control samples and support vector regression (QC-SVRC)

Intra-batch effects in liquid chromatography-mass spectrometry are corrected using quality control samples and support vector regression.

Determination of Peroxide-Based Explosives Using Liquid Chromatography with On-Line Infrared Detection

A nondestructive analytical method for peroxide-based explosives determination in solid samples is described. Reversed-phase high-performance liquid chromatography in combination with on-line Fourier transform infrared (FT-IR) detection is used for the analysis of triacetonetriperoxide (TATP) and hexamethylenetriperoxide diamine (HMTD). In contrast to other liquid chromatographic methods with optical detection, no derivatization or decomposition of the peroxides is required. The peroxides are identified and quantified via their characteristic absorption spectra in the mid-infrared range of the electromagnetic spectrum. The detection limit of 0.5 mmol L-1 for HMTD and 1 mmol L-1 for TATP allows the identification of the explosives in complex matrixes.

Urinary Lipid Peroxidation Byproducts: Are They Relevant for Predicting Neonatal Morbidity in Preterm Infants?

Preterm infants have an immature antioxidant system; however, they frequently require supplemental oxygen. Oxygen-free radicals cause both pulmonary and systemic inflammation, and they are associated with increased morbidity and mortality. Consequently, screening of metabolite profiles representing the amount of lipid peroxidation is considered of great relevance for the evaluation of in vivo oxidative stress and derived inflammation and damage. Ranges for total relative contents of isoprostanes (IsoPs), isofurans (IsoFs), neuroprostanes (NeuroPs), and neurofurans (NeuroFs) within targeted SpO2 ranges were determined in urine samples of 254 preterm infants<32 weeks of gestation within the frame of two randomized, controlled, and blinded clinical trials employing ultra-performance liquid chromatography-tandem mass spectrometry. A total of 536 serial urine samples collected during the first 4 weeks after birth in recruited infants who did not develop free radical associated conditions were analyzed. A reference range for lipid peroxidation byproducts, including isoprostanes, isofurans, neuroprostanes, and neurofurans, was calculated and possible correlations with neonatal conditions were investigated. Urinary elimination of isofurans in the first 4 days after birth correlated with later development of bronchopulmonary dysplasia. Our observations lead to the hypothesis that early urinary determination of lipid peroxidation byproducts, especially isofurans, is relevant to predict development of chronic lung conditions.

Analysis of lipid peroxidation biomarkers in extremely low gestational age neonate urines by UPLC-MS/MS

Extremely low gestational age neonates (ELGAN) frequently require the use of oxygen supply in the delivery room leading to systemic inflammation and oxidative stress that are responsible for increased morbidity and mortality. The objective of this study was to establish reference ranges of a set of representative isoprostanes and prostaglandins, which are stable biomarkers of lipid peroxidation often correlated with oxidative stress-related disorders. First, a quantitative ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was developed and validated. The proposed analytical method was tailored for its application in the field of neonatology, enabling multi-analyte detection in non-invasive, small-volume urine samples. Then, the lipid peroxidation product concentrations in a total of 536 urine samples collected within the framework of two clinical trials including extremely low gestational age neonates (ELGAN) were analyzed. The access to a substantially large number of samples from this very vulnerable population provided the chance to establish reference ranges of the studied biomarkers. Up to the present, and for this population, this is the biggest reference data set reported in literature. Results obtained should assist researchers and pediatricians in interpreting test results in future studies involving isoprostanes and prostaglandins, and could help assessing morbidities and evaluate effectiveness of treatment strategies (e.g., different resuscitation conditions) in the neonatal field.

Automated sample preparation and analysis using a sequential-injection–capillary electrophoresis (SI–CE) interface

A fully automated sequential-injection-capillary electrophoresis (SI-CE) system was developed using commercially available components as the syringe pump, the selection and injection valves and the high voltage power supply. The interface connecting the SI with the CE unit consisted of two T-pieces, where the capillary was inserted in one T-piece and a Pt electrode in the other (grounded) T-piece. By pressurising the whole system using a syringe pump, hydrodynamic injection was feasible. For characterisation, the system was applied to a mixture of adenosine and adenosine monophosphate at different concentrations. The calibration curve obtained gave a detection limit of 0.5 microg g(-1) (correlation coefficient of 0.997). The reproducibility of the injection was also assessed, resulting in a RSD value (5 injections) of 5.4%. The total time of analysis, from injection, conditioning and separation to cleaning the capillary again was 15 minutes. In another application, employing the full power of the automated SIA-CE system, myoglobin was mixed directly using the flow system with different concentrations of sodium dodecyl sulfate (SDS), a known denaturing agent. The different conformations obtained in this way were analysed with the CE system and a distinct shift in migration time and decreasing of the native peak of myoglobin (Mb) could be observed. The protein samples prepared were also analysed with off-line infrared spectroscopy (IR), confirming these results.

On-line gel permeation chromatography-attenuated total reflectance-Fourier transform infrared determination of lecithin and soybean oil in dietary supplements

Gel permeation chromatography (GPC) with attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectrometry detection has been proposed for the simultaneous determination of lecithin and soybean oil in dietary supplements. The method involves the extraction of analytes with dichloromethane in an ultrasound water bath and the injection of 2 ml of centrifuged and filtered extracts into the system integrated by two Envirogel GPC columns (19 mm x150 mm, 19 mm x 300 mm) coupled on-line. Dichloromethane was used as mobile phase. A method has been developed to select the most appropriated wavenumber to be used for the determination of each considered compound from the calculation of a factor which maximizes the analyte signal minimizing the interferent contributions, being selected the detection wavenumbers of 1034 and 1138 cm(-1) for lecithin and soybean oil, respectively in the first order derivative ATR-FTIR spectra. The method provides limits of detection of 2 and 4 mg ml(-1) for lecithin and soybean oil and repeatability values, measured as relative standard deviation, of 2.5% and 3.4% being extended the linear range till 100 mg ml(-1) for lecithin and up to 50 mg ml(-1) for soybean oil. Accurate results were found for 10 synthetic samples and 7 commercial dietary supplement preparations.

Determination of acrylamide in foods by pressurized fluid extraction and liquid chromatography-tandem mass spectrometry used for a survey of Spanish cereal-based foods

An automated and rapid method for the determination of acrylamide in different food products is presented. The method involves pressurized fluid extraction (PFE) of foods with acetonitrile and precipitation with Carrez reagents. The final extract is analysed by liquid chromatography coupled to electrospray ionization tandem mass spectrometry (ESI-MS-MS). The main parameters affecting the performance of ESI-MS-MS and PFE were optimized using a design of experiments approach. The limit of quantification of the method was 5 microg kg(-1), and recoveries from incurred samples ranged between 93 and 101%. The accuracy was evaluated using the reference test materials FAPAS T3002, T3005 and T3011. Using the optimized method, 62 food samples of potato chips, snacks, biscuits, breakfast cereals and crisp bread sampled from Valencia, Spain, supermarkets were surveyed for acrylamide levels. The levels were similar to those reported in the European Union and USA.

A rapid method for the differentiation of yeast cells grown under carbon and nitrogen-limited conditions by means of partial least squares discriminant analysis employing infrared micro-spectroscopic data of entire yeast cells

This paper shows the ease of application and usefulness of mid-IR measurements for the investigation of orthogonal cell states on the example of the analysis of Pichia pastoris cells. A rapid method for the discrimination of entire yeast cells grown under carbon and nitrogen-limited conditions based on the direct acquisition of mid-IR spectra and partial least squares discriminant analysis (PLS-DA) is described. The obtained PLS-DA model was extensively validated employing two different validation strategies: (i) statistical validation employing a method based on permutation testing and (ii) external validation splitting the available data into two independent sub-sets. The Variable Importance in Projection scores of the PLS-DA model provided deeper insight into the differences between the two investigated states. Hence, we demonstrate the feasibility of a method which uses IR spectra from intact cells that may be employed in a second step as an in-line tool in process development and process control along Quality by Design principles.

Metabolomic Analysis of Gastric Cancer Progression within the Correa's Cascade Using Ultraperformance Liquid Chromatography-Mass Spectrometry

Gastric cancer (GC) is among the most common cancers worldwide. Gastric carcinogenesis is a multistep and multifactorial process beginning with chronic gastritis induced by Helicobacter pylori (H. pylori) infection. This process is often described via a sequence of events known as Correas's cascade, a stepwise progression from nonactive gastritis, chronic active gastritis, precursor lesions of gastric cancer (atrophy, intestinal metaplasia, and dysplasia), and finally adenocarcinoma. Our aim was to identify a plasma metabolic pattern characteristic of GC through disease progression within the Correa's cascade. This study involved the analysis of plasma samples collected from 143 patients classified in four groups: patients with nonactive gastritis and no H. pylori infection, H. pylori infected patients with chronic active gastritis, infected or noninfected patients with precursor lesions of gastric cancer, and GC. Independent partial least-squares-discriminant binary models of UPLC-ESI(+)-TOFMS metabolic profiles, implemented in a decision-directed acyclic graph, allowed the identification of tryptophan and kynurenine as discriminant metabolites that could be attributed to indoleamine-2,3-dioxygenase upregulation in cancer patients leading to tryptophan depletion and kynurenine metabolites generation. Furthermore, phenylacetylglutamine was also classified as a discriminant metabolite. Our data suggest the use of tryptophan, kynurenine, and phenylacetylglutamine as potential GC biomarkers.

Detection of batch effects in liquid chromatography-mass spectrometry metabolomic data using guided principal component analysis

Metabolomics based on liquid chromatography-mass spectrometry (LC-MS) is a powerful tool for studying dynamic responses of biological systems to different physiological or pathological conditions. Differences in the instrumental response within and between batches introduce unwanted and uncontrolled data variation that should be removed to extract useful information. This work exploits a recently developed method for the identification of batch effects in high throughput genomic data based on the calculation of a δ statistic through principal component analysis (PCA) and guided PCA. Its applicability to LC-MS metabolomic data was tested on two real examples. The first example involved the repeated analysis of 42 plasma samples and 6 blanks in three independent batches, and the second data set involved the analysis of 101 plasma and 18 blank samples in a single batch with a total runtime of 50h. The first and second data set were used to evaluate between and within-batch effects using the δ statistic, respectively. Results obtained showed the usefulness of using the δ statistic together with other approaches such as summary statistics of peak intensity distributions, PCA scores plots or the monitoring of IS peak intensities, to detect and identify instrumental instabilities in LC-MS.

Integrative Metabolomic and Transcriptomic Analysis for the Study of Bladder Cancer

Metabolism reprogramming is considered a hallmark of cancer. The study of bladder cancer (BC) metabolism could be the key to developing new strategies for diagnosis and therapy. This work aimed to identify tissue and urinary metabolic signatures as biomarkers of BC and get further insight into BC tumor biology through the study of gene-metabolite networks and the integration of metabolomics and transcriptomics data. BC and control tissue samples (n = 44) from the same patients were analyzed by High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance and microarrays techniques. Besides, urinary profiling study (n = 35) was performed in the same patients to identify a metabolomic profile, linked with BC tissue hallmarks, as a potential non-invasive approach for BC diagnosis. The metabolic profile allowed for the classification of BC tissue samples with a sensitivity and specificity of 100%. The most discriminant metabolites for BC tissue samples reflected alterations in amino acids, glutathione, and taurine metabolic pathways. Transcriptomic data supported metabolomic results and revealed a predominant downregulation of metabolic genes belonging to phosphorylative oxidation, tricarboxylic acid cycle, and amino acid metabolism. The urinary profiling study showed a relation with taurine and other amino acids perturbed pathways observed in BC tissue samples, and classified BC from non-tumor urine samples with good sensitivities (91%) and specificities (77%). This urinary profile could be used as a non-invasive tool for BC diagnosis and follow-up.

Monitoring of system conditioning after blank injections in untargeted UPLC-MS metabolomic analysis

Ultra-performance liquid chromatography – mass spectrometry (UPLC-MS) is widely used for untargeted metabolomics in biomedical research. To optimize the quality and precision of UPLC-MS metabolomic analysis, evaluation of blank samples for the elimination of background features is required. Although blanks are usually run either at the beginning or at the end of a sequence of samples, a systematic analysis of their effect of the instrument performance has not been properly documented. Using the analysis of two common bio-fluids (plasma and urine), we describe how the injection of blank samples within a sequence of samples may affect both the chromatographic and MS detection performance depending on several factors, including the sample matrix and the physicochemical properties of the metabolites of interest. The analysis of blanks and post-blank conditioning samples using t-tests, PCA and guided-PCA provides useful information for the elimination of background UPLC-MS features, the identification of column carry over and the selection of the number of samples required to achieve a stable performance.

Assessment of oxidative damage to proteins and DNA in urine of newborn infants by a validated UPLC-MS/MS approach

The assessment of oxidative stress is highly relevant in clinical Perinatology as it is associated to adverse outcomes in newborn infants. This study summarizes results from the validation of an Ultra Performance Liquid Chromatography–tandem Mass Spectrometry (UPLC-MS/MS) method for the simultaneous quantification of the urinary concentrations of a set of endogenous biomarkers, capable to provide a valid snapshot of the oxidative stress status applicable in human clinical trials, especially in the field of Perinatology. The set of analytes included are phenylalanine (Phe), para-tyrosine (p-Tyr), ortho-tyrosine (o-Tyr), meta-tyrosine (m-Tyr), 3-NO₂-tyrosine (3NO₂-Tyr), 3-Cl-tyrosine (3Cl-Tyr), 2′-deoxyguanosine (2dG) and 8-hydroxy-2′-deoxyguanosine (8OHdG). Following the FDA-based guidelines, appropriate levels of accuracy and precision, as well as adequate levels of sensitivity with limits of detection (LODs) in the low nanomolar (nmol/L) range were confirmed after method validation. The validity of the proposed UPLC-MS/MS method was assessed by analysing urine samples from a clinical trial in extremely low birth weight (ELBW) infants randomized to be resuscitated with two different initial inspiratory fractions of oxygen.

Determination of caffeine in tea samples by Fourier transform infrared spectrometry

A sustainable and environmentally friendly procedure has been developed for the FTIR determination of caffeine in tea leaf samples. The method is based on the extraction with ammonia and CHCl3 and direct determination of caffeine on the chloroform extracts using peak height absorbance measurements at 1658.5 cm(-1) and external calibration. The method provides a sensitivity of 0.2142 absorbance units mg(-1) mL and a limit of detection of 1 mg L(-1), corresponding to 0.002% m/m caffeine in tea leaves. As compared with a reference procedure, based on UV absorbance measurement at 276 nm after low pressure column chromatography, the developed procedure reduces the consume of CHCl3 by a factor of 10, that of NH4OH by a factor of 20 and avoids the use of diethyl ether and Celite. The time required to do the analysis of a sample is 15 minutes as compared with the 6 hours for the reference one.

Comparing Targeted vs. Untargeted MS2 Data-Dependent Acquisition for Peak Annotation in LC-MS Metabolomics

One of the most widely used strategies for metabolite annotation in untargeted LCMS is based on the analysis of MSⁿ spectra acquired using data-dependent acquisition (DDA), where precursor ions are sequentially selected from MS scans based on user-selected criteria. However, the number of MSⁿ spectra that can be acquired during a chromatogram is limited and a trade-off between analytical speed, sensitivity and coverage must be ensured. In this research, we compare four different strategies for automated MS² DDA, which can be easily implemented in the frame of standard QA/QC workflows for untargeted LC–MS. These strategies consist of (i) DDA in the MS working range; (ii) iterated DDA split into several m/z intervals; (iii) dynamic iterated DDA of (pre)selected potentially informative features; and (iv) dynamic iterated DDA of (pre)annotated metabolic features using a reference database. Their performance was assessed using the analysis of human milk samples as model example by comparing the percentage of LC–MS features selected as the precursor ion for MS², the number, and class of annotated features, the speed and confidence of feature annotation, and the number of LC runs required.

Current Practice in Untargeted Human Milk Metabolomics

Human milk (HM) is considered the gold standard for infant nutrition. HM contains macro- and micronutrients, as well as a range of bioactive compounds (hormones, growth factors, cell debris, etc.). The analysis of the complex and dynamic composition of HM has been a permanent challenge for researchers. The use of novel, cutting-edge techniques involving different metabolomics platforms has permitted to expand knowledge on the variable composition of HM. This review aims to present the state-of-the-art in untargeted metabolomic studies of HM, with emphasis on sampling, extraction and analysis steps. Workflows available from the literature have been critically revised and compared, including a comprehensive assessment of the achievable metabolome coverage. Based on the scientific evidence available, recommendations for future untargeted HM metabolomics studies are included.