Bioactive components, antioxidant and antimicrobial activities of Paeonia rockii fruit during development.

In last ten years, much attention focused on tree peony fruit (TPF) for edible oil production despite other potential utilization. The present study identified and quantified 29 bioactive components by liquid chromatography-electrospray ionization-triple quadrupole-mass spectrometry (LC-ESI-QqQ-MS) targeted approach during the development of TPF. Trans-resveratrol, benzoic acid, luteolin, and methyl gallate were selected as predominant chemical markers between seeds and pods through principal component analysis (PCA) and orthogonal partial least square-discriminant analysis (OPLS-DA). Extremely high levels of paeoniflorin (1893 mg/100 g) and trans-resveratrol (1793 mg/100 g) were observed at stage 2 (S2) and S6 in seeds, respectively. Antioxidant activities determined by ABTS+•, DPPH•, and FRAP assays showed significant correlations with total phenolic content (TPC) and total flavonoid content (TFC). The strongest antibacterial effects of pod and seed against Staphylococcus aureus and Proteus vulgaris occurred at initial stages and maturation stages. TPF could be a potential source of bioactive compounds with functional properties.

Proof of concept for identifying cystic fibrosis from perspiration samples.

The gold standard for cystic fibrosis (CF) diagnosis is the determination of chloride concentration in sweat. Current testing methodology takes up to 3 h to complete and has recognized shortcomings on its diagnostic accuracy. We present an alternative method for the identification of CF by combining desorption electrospray ionization mass spectrometry and a machine-learning algorithm based on gradient boosted decision trees to analyze perspiration samples. This process takes as little as 2 min, and we determined its accuracy to be 98 ± 2% by cross-validation on analyzing 277 perspiration samples. With the introduction of statistical bootstrap, our method can provide a confidence estimate of our prediction, which helps diagnosis decision-making. We also identified important peaks by the feature selection algorithm and assigned the chemical structure of the metabolites by high-resolution and/or tandem mass spectrometry. We inspected the correlation between mild and severe CFTR gene mutation types and lipid profiles, suggesting a possible way to realize personalized medicine with this noninvasive, fast, and accurate method.

A graphical data processing pipeline for mass spectrometry imaging-based spatially resolved metabolomics on tumor heterogeneity.

Spatially resolved metabolomics is an excellent tool for elucidating in situ molecular events, but its use remains challenging due to the complexity of the endogenous metabolites in bio-tissue and tissue heterogeneity. In this study, a data processing pipeline for spatially resolved metabolomics analysis of tumor microregion heterogeneity was developed and built into a graphical interface with MSI software. Biological tissue sections were analysed by ambient air-flow assisted desorption electrospray ionization mass spectrometry imaging. Histology-driven and characterized ion images overlay combined with metabolic feature-based spatial segmentation were developed to accurately extract the metabolic profile from the tissue microregion of interest. In addition, appropriate data pretreatment methods were investigated to evaluate their ability to identify biological variations from the complicated spatially resolved metabolomics data. Diverse graphical metabolic feature extraction and various data pretreatment methods enable not only the achievement of the best multivariate statistical results in an intuitive and simple way but also the discovery of low-abundance but reliable biomarkers. The results from a papillary thyroid cancer tissue study demonstrated that this data processing pipeline is a powerful and easy-to-use tool for investigating the spatial molecular events in tumor microenvironments and to therefore thoroughly understand their metabolic heterogeneity.

ESI-LC-MS Method for Haptoglobin Fucosylation Analysis in Hepatocellular Carcinoma and Liver Cirrhosis.

A method for the detection of fucosylated glycans from haptoglobin in patient serum has been developed that provides enhanced sensitivity. The workflow involves isolation of the haptoglobin using an HPLC-based affinity column followed by glycan removal, extraction, and desialylation. The fucosylated glycans are then derivatized by Meladrazine, which significantly enhances the detection of the glycans in electrospray ionization. The separation of the derivatized glycans in a HILIC column shows that eight glycans from haptoglobin can be detected using less than 1 µL of a serum sample, with excellent reproducibility and quantitation, where without derivatization the glycans could not be detected. The ratio of the fucosylated peaks to their corresponding nonfucosylated forms shows that the fucosylated glycans are upregulated in the case of hepatocellular carcinoma (HCC) samples versus cirrhosis samples, where the relatively low abundance bifucosylated tetra-antennary form can be detected and may be a particularly good marker for HCC.

Improved intensity-based label-free quantification via proximity-based intensity normalization (PIN).

Researchers are increasingly turning to label-free MS1 intensity-based quantification strategies within HPLC-ESI-MS/MS workflows to reveal biological variation at the molecule level. Unfortunately, HPLC-ESI-MS/MS workflows using these strategies produce results with poor repeatability and reproducibility, primarily due to systematic bias and complex variability. While current global normalization strategies can mitigate systematic bias, they fail when faced with complex variability stemming from transient stochastic events during HPLC-ESI-MS/MS analysis. To address these problems, we developed a novel local normalization method, proximity-based intensity normalization (PIN), based on the analysis of compositional data. We evaluated PIN against common normalization strategies. PIN outperforms them in dramatically reducing variance and in identifying 20% more proteins with statistically significant abundance differences that other strategies missed. Our results show the PIN enables the discovery of statistically significant biological variation that otherwise is falsely reported or missed.

[A plain method of prediction of visibility of peptides in mass spectrometry with electrospray ionization].

A new method for screening of essential peptides for protein detection and quantification analysis in the direct positive electrospray mass spectrometry has been proposed. Our method is based on the prediction of the normalized abundance of the mass spectrometric peaks using a linear regression model. This method has the following limitations: (i) selected peptides should be taken so that at pH 2.5 the tested peptides must be presented mainly as the 2+ and 3+ ions; (ii) only peptides having C-terminal lysine or arginine residues are considered. The amino acid composition of the peptide, the peptide concentration, the ratio of the polar surface of peptide to common surface and ratio of the polar volume to common volume are used as independent variables in equation. Several combinations of variables were considered and the best linear regression model had a determination coefficient in leave-one-out validation procedure equal 0.54. This model confidently discriminates peptides with high response ability and peptides with low response ability, and therefore it allows to select only the most promising peptides. This screening method, a plain and fast, can be successfully applied to reduce the list of observed peptides.

Confirmation of hormones in animal serum by liquid chromatography/tandem mass spectrometry according to European Commission Decision 2002/657.

A novel and rapid method was developed and validated for the confirmation of endogenous and synthetic hormones in animal serum using LC/MS/MS. Detection of 17 beta-estradiol and beta-testosterone below the respective European Union-recommended levels of 0.1 and 0.5 microg/L was achieved, as was a required performance level of 0.1 microg/L for 17 alpha-estradiol and 0.5 microg/L for 17 alpha-testosterone, medroxyprogesterone-17-acetate, and progesterone. The method was established with dilution of serum followed by ion-exchange SPE, LC separation and MS detection with electrospray ionization, selected reaction monitoring, and positivelnegative switching. Two characteristic transitions were monitored for each analyte. The method was applied to bovine, ovine, porcine, equine, and avian samples and validated according to European Commission Decision 2002/657/EC and accepted for ISO/IEC 17025:2005 accreditation. An extended calibration curve allows naturally occurring levels of endogenous hormones to be quantified. Recoveries ranged from 97.3% for 17 alpha-testosterone to 102.0% for 17 alpha-estradiol. The decision limit CCalpha ranged from 0.02 microg/L for 17 alpha- and beta-estradiol to 0.12 microg/L for progesterone. Detection capability CCbeta ranged from 0.03 microg/L for 17 a-estradiol to 0.20 microg/L for progesterone.

Quantification of global DNA methylation by capillary electrophoresis and mass spectrometry.

Two approaches for the evaluation of the relative degree of global DNA methylation through the quantification of 2' deoxynucleosides are described. Detection and quantification of 5-methyl 2'-deoxycytidine in genomic DNA is performed using both high-performance capillary electrophoresis (HPCE) with UV-Vis detection or liquid chromatography with electrospray ionization mass spectrometric detection (LC-ESI/MS). Treatment of genomic DNA with a ribonuclease and generation of nucleosides through enzymatic hydrolysis notably increases the specificity of both techniques. Both approaches have been demonstrated to be highly specific and sensitive, being useful for the rapid quantification of the degree of global DNA methylation and its exploitation for the analysis of poorly purified and/or concentrated DNA samples, such as tumor biopsies.

A sheathless poly(methyl methacrylate) chip-CE/MS interface fabricated using a wire-assisted epoxy-fixing method.

Using a wire-assisted epoxy-fixing method, a sheathless CE/MS interface on a poly-(methyl methacrylate) (PMMA) CE chip has been developed. The sheathless chip-CE/MS interface utilized a tapered fused-silica tip and the electrical connection was achieved through a layered coating of conductive rubber. The wire-assisted method provided facile alignment of channels between the PMMA CE chip and an external capillary sprayer without the need for micromachining. Because the wire was in the channel during fixing, the risk of channel blockage by the epoxy was avoided. This chip CE device has minimal dead volume because the interstitial spaces were filled by a fast-fixing epoxy resin. The performance of the chip-CE-ESI-MS device was demonstrated with the analysis of peptide mixtures.

High-accuracy peak picking of proteomics data using wavelet techniques.

A new peak picking algorithm for the analysis of mass spectrometric (MS) data is presented. It is independent of the underlying machine or ionization method, and is able to resolve highly convoluted and asymmetric signals. The method uses the multiscale nature of spectrometric data by first detecting the mass peaks in the wavelet-transformed signal before a given asymmetric peak function is fitted to the raw data. In an optional third stage, the resulting fit can be further improved using techniques from nonlinear optimization. In contrast to currently established techniques (e.g. SNAP, Apex) our algorithm is able to separate overlapping peaks of multiply charged peptides in ESI-MS data of low resolution. Its improved accuracy with respect to peak positions makes it a valuable preprocessing method for MS-based identification and quantification experiments. The method has been validated on a number of different annotated test cases, where it compares favorably in both runtime and accuracy with currently established techniques. An implementation of the algorithm is freely available in our open source framework OpenMS.

Heuristic charge assignment for deconvolution of electrospray ionization mass spectra.

We propose a new algorithm for deconvolution of electrospray ionization mass spectra based on direct assignment of charge to the measured signal at each mass-to-charge ratio (m/z). We investigate two heuristics for charge assignment: the entropy-based heuristic is adapted from a deconvolution algorithm by Reinhold and Reinhold;10 the multiplicative-correlation heuristic is adapted from the multiplicative-correlation deconvolution algorithm of Hagen and Monnig.6 The entropy-based heuristic is insensitive to overestimates of z(max), the maximum ion charge. We test the deconvolution algorithm on two single-component samples: the measured spectrum of human beta-endorphin has two prominent and one very weak line whereas myoglobin has a well-developed quasi-gaussian envelope of 17 peaks. In both cases, the deconvolution algorithm gives a clean deconvoluted spectrum with one dominant peak and very few artefacts. The relative heights of the peaks due to the parent molecules in the deconvoluted spectrum of a mixture of two peptides, which are expected to ionize with equal efficiency, give an accurate measure of their relative concentration in the sample.

A robust approach for the analysis of peptides in the low femtomole range by capillary electrophoresis-tandem mass spectrometry.

A capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) approach has been developed for routine application in proteomic studies. Robustness of the coupling is achieved by using a standard coaxial sheath-flow sprayer. Thereby, greater stability than nanoelectrospray ionization-mass spectrometry coupling of sheathless capillary electrophoresis or nanoliquid chromatography (nano-LC) is achieved, resulting in stable operation for several weeks and unattended overnight sequences. The applied sheath flow is reduced to 1-2 microL/min in order to increase sensitivity. Standard peptides and those of digests of standard proteins and gel-separated proteins can be detected in the low femtomole range (full scan and MS/MS). Detection limits are found to be as low as 500 amol. Low femtomole amounts are required for unequivocal identification by MS/MS experiments in the ion trap and subsequent database search. By applying a simple pH-mediated stacking the concentration sensitivity can be lowered to some tens of fmol/microL (nM), depending on capillary size. This sensitivity is close to published values for sheathless CE-MS and nano-LC-MS, respectively (a comparison to reference values is presented). Moreover, with capillaries of about 50 cm in length separations in less than 10 min are possible resulting in a throughput of up to four analyses per hour. This is a factor of 4-12 times faster than nano-LC separation, being the state-of-the-art techniques for proteomic studies.

Automated deconvolution and deisotoping of electrospray mass spectra.

Electrospray ionization (ESI) of peptides and proteins produces a series of multiply charged ions with a mass/charge (m/z) ratio between 500 and 2000. The resulting mass spectra are crowded by these multiple charge values for each molecular mass and an isotopic cluster for each nominal m/z value. Here, we report a new algorithm simultaneously to deconvolute and deisotope ESI mass spectra from complex peptide samples based on their mass-dependent isotopic mean pattern. All signals corresponding to one peptide in the sample were reduced to one singly charged monoisotopic peak, thereby significantly reducing the number of signals, increasing the signal intensity and improving the signal-to-noise ratio. The mass list produced could be used directly for database searching. The developed algorithm also simplified interpretation of fragment ion spectra of multiply charged parent ions.