Stretched poly(dimethylsiloxane) gels as NMR alignment media for apolar and weakly polar organic solvents: an ideal tool for measuring RDCs at low molecular concentrations

The measurement of residual dipolar couplings (RDCs), meanwhile a standard method for obtaining structural information in biomolecular NMR, requires partial alignment of the sample. Special demands on alignment media so far limit the applicability of this approach to small molecules in organic solvents. Major limitations are the free scalability of alignment and the suppression of residual signals of the alignment medium to allow effective measurement of low-concentration samples. Here, we present stretched poly(dimethylsiloxane) (PDMS) cross-linked by beta-rays as an alignment medium with no visible impurities in 1H NMR spectra but a single signal at approximately 0.1 ppm that can easily be removed by slightly modified water suppression methods. Besides the free scalability, its applicability to the measurement of RDCs in small molecules at low concentration is demonstrated on a approximately 12 mM sample of spiroindene. The induced alignment tensor in this case can be predicted reasonably well by a simplified model on the basis of steric interactions only.     

Evaluation of different warping methods for the analysis of CE profiles of urinary nucleosides

Nowadays, numerous metabolite concentrations can readily be determined in a given biological sample by high-throughput analytical methods. However, such raw analytical data comprise noninformative components due to many disturbances normally occurring in the analyses of biological material. To eliminate those unwanted original analytical data components, advanced chemometric data preprocessing methods might be of help. Here, such methods are applied to electrophoretic nucleoside profiles in urine samples of cancer patients and healthy volunteers. In this study, three warping methods: dynamic time warping (DTW), correlation optimized warping (COW), and parametric time warping (PTW) were examined on two sets of electrophoretic data by means of quality of peaks alignment, time of preprocessing, and way of customization. The application of warping methods helped to limit shifting of peaks and enabled differentiation between whole electropherograms of healthy and cancer patients objectively by a principal component analysis (PCA). The evaluation of preprocessed data and raw data by PC analysis confirms differences between the applied warping tools and proves their suitability in metabonomic data interpretation.     

MassUntangler: a novel alignment tool for label-free liquid chromatography-mass spectrometry proteomic data

Liquid chromatography-mass spectrometry (LC-MS) has become an important analytical tool for quantitative proteomics and biomarker discovery. In the label-free differential LC-MS approach computational methods are required for an accurate alignment of peaks extrapolated from the experimental raw data accounting for retention time and m/z signals intensity, which are strongly affected by sample matrix and instrumental performance. A novel procedure "MassUntangler" for pairwise alignment has been developed, relying on a pattern-based matching algorithm integrated with filtering algorithms in a multi-step approach. The procedure has been optimized employing a two-step approach. Firstly, low-complexity LC-MS data derived from the enzymatic digestion of two standard proteins have been analyzed. Then, the algorithm's performance has been evaluated by comparing the results with other achieved using state-of-the-art alignment tools. In the second step, our algorithm has been used for the alignment of high-complexity LC-MS data consisting of peptides obtained by an Escherichia coli lysate available from a public repository previously used for the comparison of other alignment tools. MassUntangler gave excellent results in terms of precision scores (from 80% to 93%) and recall scores (from 68% to 89%), showing performances similar and even better than the previous developed tools. Considering the mass spectrometry sensitivity and accuracy, this approach allows the identification and quantification of peptides present in a biological sample at femtomole level with high confidence. The procedure's capability of aligning LC-MS data previously corrected for distortion in retention time has been studied through a hybrid approach, in which MassUntangler was interfaced with the OpenMS TOPP tool MapAligner. The hybrid aligner yielded better results, showing that an integration of different bioinformatic approaches for accurate label-free LC-MS data alignment should be used.     

A comparison of two algorithms for warping of analytical signals

The alignment of analytical signals is an important preprocessing step when further analysis (e.g. PCA) requires the same lengths of all of them. Two techniques for alignment of profiles, namely dynamic time warping (DTW) and correlation optimized warping (COW) were tested and compared. The attention was focused on chromatographic and spectroscopic profiles. Simulated and two sets of real data were studied in this study.     

Detection and determination of antimalarial drugs and their metabolites in body fluids

This review of methods for determining antimalarial drugs in biological fluids has focused on the various analytical techniques for the assay of chloroquine, quinine, amodiaquine, mefloquine, proguanil, pyrimethamine, sulphadoxine, primaquine and some of their metabolites. The methods for determining antimalarials and their metabolites in biological samples have changed rapidly during the last eight to ten years with the increased use of chromatographic techniques. Chloroquine is still the most used antimalarial drug, and various methods of different complexity exist for the determination of chloroquine and its metabolites in biological fluids. The pharmacokinetics of chloroquine and other antimalarials have been updated using these new methods. The various analytical techniques have been discussed, from simple colorimetric methods of intermediate selectivity and sensitivity to highly sophisticated, selective and sensitive chromatographic methods applied in a modern analytical laboratory. Knowledge concerning the method for a particular study is determined by the type of application and the facilities, equipment and personnel available. Often is it useful to apply various methods when conducting a clinical study in malaria-endemic areas. Field-adapted methods for the analysis of urine samples can be applied at the study site for screening, and corresponding blood samples can be preserved for subsequent analysis in the laboratory. Selecting samples for laboratory analysis is based on clinical, parasitological and field-assay data. The wide array of methods available for chloroquine permit carefully tailored approaches to acquire the necessary analytical information in clinical field studies concerning the use of this drug. The development of additional field-adapted and field-interfaced methods for other commonly used antimalarials will provide similar flexibility in field studies of these drugs.     

A closer look at analytical signals

Analytical chemistry will be considered here as the measurement science of chemistry that generates, treats, and evaluates signals which contain information about the composition and structure of samples. Analytical information is always obtained from signals. Characteristics and peculiarities of analytical signals will be considered from a very general point of view. A mathematical model of the influencing of signals will be given from which essential performance characteristics of analytical methods can be derived, e.g. sensitivity, cross-sensitivity, specificity, selectivity, and ruggedness (robustness).     

Material- und Signalfluß

An industrial production process is considered to be divided into a working process and an information process. Starting point for the information process is the sampling of a material flow. The meaning of “representative” samples as well as questions of continuous and non-continuous sampling methods are discussed. The signals coming out of analysis are arranged in a special way according to statistical methods. Thereafter the information content is calculated by using rules of the information theory. The transmission of the information content within a certain time results in an information flux. The information flux actually required by the working process is compared to the information flux provided by analysis; and both are put into an equilibrium followed by considerations on “necessary and sufficient” analytical actions. It is the aim of analytical information processes to reduce the entropy of the working process to a minimum.     

Variable alignment of high resolution data by cluster analysis

High resolution time-of-flight secondary ion mass spectrometry (HR TOF-SIMS) is a powerful surface analytical method. For complex samples, this technique may yield intricate spectra that are difficult to interpret visually. Chemometric methods are useful for data analysis. However, these methods require that spectra are represented in a matrix format. Variances in mass measurements caused by calibration or instrumental effects may present difficulties in properly aligning mass spectral peaks into the correct columns of the data matrix. Cluster analysis of resolution elements is proposed as an alternative approach to construct the data matrix. An automated method for optimizing the data alignment is presented and evaluated for standard steel samples.     

Target selection for alignment of chromatographic signals obtained using monochannel detectors

The alignment of instrumental signals, such as chromatograms, is regarded as an important step before applying multivariate chemometric techniques for data analysis. Nowadays, many alignment techniques are available and they differ in achieving their goal. They can correct peak shifts in a set of chromatograms with differing degrees of success. Almost all alignment techniques, with few exceptions [e.g., W. Yu, B. Wu, N. Lin, K. Stone, K. Williams, H. Zhao, Comput. Biol. Chem. 30 (2006) 27], require a careful choice of the target profile. The selection of a target signal is not an easy task and some difficulties related to this selection are discussed in this paper. An analysis of several simulated sets of chromatographic signals showed that the target selection can be a crucial step if the aligned signals are then used as input to unsupervised approaches, such as, e.g., principal component analysis and to supervised methods like discriminant partial least squares. Different proposals for target selection known-to-date are reviewed. As demonstrated in our study the target profile with the highest correlation coefficient among all the signals studied gave the most satisfactory results.     

Peak alignment of NMR signals by means of a genetic algorithm

Nuclear magnetic resonance (NMR) analysis of complex samples, such as biofluid samples is accompanied by variations in peak position and peak shape not directly related to the sample. This is due to variations in the background matrix of the sample and to instrumental instabilities. These variations complicate and limit the interpretation and analysis of NMR data by multivariate methods. Alignment of the NMR signals may circumvent these limitations and is an important preprocessing step prior to multivariate analysis. Previous aligning methods reduce the spectral resolution, are very computer-intensive for this kind of data (65k data points in one spectrum), or rely on peak detection. The method presented in this work requires neither data reduction nor preprocessing, e.g. peak detection. The alignment is achieved by taking each segment of the spectrum individually, shifting it sidewise, and linearly interpolating it to stretch or shrink until the best correlation with a corresponding reference spectrum segment is obtained. The segments are automatically picked out with a routine, which avoids cutting in a peak, and the optimization process is accomplished by means of a genetic algorithm (GA). The peak alignment routine is applied to NMR metabonomic data.¹     

Automated alignment of one-dimensional chromatographic fingerprints

A general framework for the automatic alignment of one-dimensional chromatographic signals is presented in this article. The alignment of signals was achieved by explicitly modeling the warping function. Its shape was estimated using a linear combination of several B-spline functions. The coefficients of the spline functions were found in the course of an optimization procedure to maximize the Pearson's correlation coefficient between a target chromatogram and aligned chromatogram(s). The computational requirements of the method are discussed with respect to the correlation optimized warping method, frequently used for the alignment of chromatographic signals. As illustrated with two sets of one-dimensional chromatographic fingerprints, the automatic alignment approach performs well even when non-linear peak shifts need to be corrected. It can be applied in an on-the-fly manner since the alignment of signals is rapid.     

Creatinine determination in urine samples by batchwise kinetic procedure and flow injection analysis using the Jaffé reaction: chemometric study

The classical Jaffé reaction for the determination of creatinine in urine samples is tested. A comparative study of the main analytical characteristics focussed to minimize the bias error and improve the precision, for the batchwise and flow injection (FI) methods is realized. Also, the effect of the albumin concentration in the determination of creatinine has been studied. Different analytical signals were studied. Absorbance increments at different times permit to estimate the creatinine concentration free from bias error in urine by the batchwise method using the calibration graph obtained with creatinine standards and no measurement of the blank solution is needed. The lineal interval was 0.92–50 mg l⁻¹ and seven samples can be processed per hour by an operator. No previous treatment of the urine sample is necessary. The FI method provides also good results. The lineal interval was 30–100 mg l⁻¹ and the sample rate was around 20 samples per hour. If increased albumin levels are detected in the urine, standard addition method or the calibration graphs with standards in presence of albumin are needed in order to obtain accurate results when FI method is employed. The obtained accuracy of the both methods allows its application as diagnostic tool to establish the urinary creatinine levels.     

Creatinine determination in urine samples by batchwise kinetic procedure and flow injection analysis using the Jaffé reaction: chemometric study

The classical Jaffé reaction for the determination of creatinine in urine samples is tested. A comparative study of the main analytical characteristics focussed to minimize the bias error and improve the precision, for the batchwise and flow injection (FI) methods is realized. Also, the effect of the albumin concentration in the determination of creatinine has been studied. Different analytical signals were studied. Absorbance increments at different times permit to estimate the creatinine concentration free from bias error in urine by the batchwise method using the calibration graph obtained with creatinine standards and no measurement of the blank solution is needed. The lineal interval was 0.92-50 mg l(-1) and seven samples can be processed per hour by an operator. No previous treatment of the urine sample is necessary. The FI method provides also good results. The lineal interval was 30-100 mg l(-1) and the sample rate was around 20 samples per hour. If increased albumin levels are detected in the urine, standard addition method or the calibration graphs with standards in presence of albumin are needed in order to obtain accurate results when FI method is employed. The obtained accuracy of the both methods allows its application as diagnostic tool to establish the urinary creatinine levels.     

Coupled stochastic resonance to improve chromatography determinations

Traditional bistable stochastic resonance has been demonstrated as an effective tool to detect the weak signal in a strong noise background. To achieve a better signal-to-noise ratio for the output signal, a coupled stochastic resonance was developed by nonlinearly coupling two double-well potential systems. The response characteristics of coupled stochastic resonance subjected to analytical signals have been investigated and compared with those of bistable stochastic resonance. The improvement of chromatographic determination with the proposed coupled stochastic resonance was validated by both simulated signals and chromatographic signals. The weak signals from both simulated data and plasma samples with different concentrations were all amplified significantly and the quantitative relationship between different concentrations and responses was kept well. It is reasonable to believe that coupled stochastic resonance could play an important role in applications where quantitative determination of low-concentration samples is crucial.     

Software tool for coupling chromatographic total ion current dependencies of GC/MSD and MCC/IMS

More than 90,000 ion mobility spectrometer (IMS) are in use worldwide, mostly without coupling to chromatographic columns for pre-separation of the neutrals entering the ionization region of the IMS. Related to new application fields e.g. breath analysis or determination of volatile metabolites of cell cultures and bacteria/fungi an effective way for pre-separation is needed strongly. The acceptance of IMS within the analytical world will be enhanced by supplying automatic procedures for peak finding, referencing and database-related identification of the signals within IMS-Chromatograms. Some papers are available concerning the internal loop of relation of IMS signals between different instruments, alignment for automatic interpretation with respect of reference analytes used and interpolation within the different members of classes of analytes in case that some missed e.g. within a homologous row of chemicals. With respect to inter comparison of recent findings using MCC/IMS and GC/MS experiments effective alignment procedures are developed. In the present paper we describe a software tool making the visualization of the total ion current (TIC) from chromatograms of GC/MSD possible in direct relation to the corresponding IMS-Chromatogram of MCC/IMS. Thus, parallel measurements of e.g. samples of human breath using MCC/IMS and thermodesorption (TD)-GC/MSD become comparable directly. On the other hand, the direct identification and relation of so far unknown peaks found in IMS-Chromatograms will be supported using the TIC results of GC/MSD.     

Interlaboratory study of identification and quantitation of multiresidue pyrethroids in agricultural products by gas chromatography-mass spectrometry

This paper deals with the different GC-MS analytical conditions adopted by four laboratories in an attempt to confirm the accuracy of the GC-electron-capture detection (ECD) analytical results during the international collaborative study for the establishment of the AOAC Official Method 998. 01. What is especially noted is that two laboratories have conducted comparative analysis of the respective 12 blind samples with both methods of GC-ECD and GC-MS, and the analytical results of the two methods turn out to be basically identical. This fully demonstrates that GC-MS is not only an effective confirmation tool in the analysis of the pyrethroid residues but also of sufficient sensitivity regarding the maximum residue limit of determination prescribed by FAO/WHO. Moreover, its selectivity is better than GC-ECD.     

免疫算法: 一种新的多组分重叠色谱信号的解析方法

色谱及其联用技术的快速发展使其成为复杂样品分析的重要手段,但在复杂样品分析中仍难以避免多组分色谱信号的重叠。化学计量学利用数学方法对复杂重叠信号进行解析,为复杂样品的色谱分析提供了新的手段。本文对免疫算法研究的近期进展进行了总结,并以具体的实例介绍了其在多组分重叠色谱信号解析方面的应用。     

两种轻烃分析方法(“PTV切割反吹”和“顶空”)的对比研究

 建立了“程序升温蒸发进样器 (PTV)切割反吹”和“顶空”两种有关原油中轻烃的分析方法 ,色谱柱的使用寿命长、分析周期短 ,原油中 < ,将原油直接注入汽化室所得的分析数据较可靠 ,并对引起误差的原因进行了探讨。指出用这两种方法所获得的数据是不能合在一起作地化研究的 ) % 5 2 1%～ ( 19个地化参数的相对误差范围约为± 10个油样用两种分析方法所得 6个油区的 ,还报道了采自我国 ,并有良好的重复性。。     

Pattern recognition in capillary electrophoresis data using dynamic programming in the wavelet domain

A novel approach for CE data analysis based on pattern recognition techniques in the wavelet domain is presented. Low-resolution, denoised electropherograms are obtained by applying several preprocessing algorithms including denoising, baseline correction, and detection of the region of interest in the wavelet domain. The resultant signals are mapped into character sequences using first derivative information and multilevel peak height quantization. Next, a local alignment algorithm is applied on the coded sequences for peak pattern recognition. We also propose 2-D and 3-D representations of the found patterns for fast visual evaluation of the variability of chemical substances concentration in the analyzed samples. The proposed approach is tested on the analysis of intracerebral microdialysate data obtained by CE and LIF detection, achieving a correct detection rate of about 85% with a processing time of less than 0.3 s per 25,000-point electropherogram. Using a local alignment algorithm on low-resolution denoised electropherograms might have a great impact on high-throughput CE since the proposed methodology will substitute automatic fast pattern recognition analysis for slow, human based time-consuming visual pattern recognition methods.     

Identity confirmation of anthocyanins in berries by LC–DAD–IM-QTOFMS

Rugged analytical methods for the screening and identity confirmation of anthocyanins require a dedicated sample preparation, chromatographic setup, and the reliable generation of multiple identification points to confirm identity against the wide range of phenolic compounds typically present in food, beverage, and plant material samples. To this end, combinations of spectroscopic and mass spectrometric detection are frequently employed for this application to provide higher confidence in the absence of authentic standards. In the present work, low-field drift tube ion mobility (DTIM) separation is evaluated for this task using a LC–DAD–DTIM–QTOFMS method. DTIM-MS allows accurate determination of collision cross sections (^DTCCS) for all analysed compounds as well as a precise alignment tool for reconciling fragment and precursor ions in data independent acquisition mode. The presented approach thereby allows for an anthocyanin screening method taking true advantage of all dimensions of the analytical platform: relative retention (RPLC), UV/VIS absorption spectrum, accurate mass, ^DTCCS_N2, and confirmed high-resolution fragment ions. From the analysis of authentic standards and several berry samples primarily from the Vaccinium genus, Level 1 confirmation data for six anthocyanins from the cyanidin family, and Level 2 confirmation for a further 29 anthocyanins confirmed in berry samples is provided. The method and accompanying dataset provided as part of this work provides a means to develop anthocyanin screening methods using the ion mobility dimension as an additional alignment and filtering parameter in data independent analysis acquisition across any LC–IM–MS platform.