A flexible data analysis tool for chemical genetic screens

High-throughput assays generate immense quantities of data that require sophisticated data analysis tools. We have created a freely available software tool, SLIMS (Small Laboratory Information Management System), for chemical genetics which facilitates the collection and analysis of large-scale chemical screening data. Compound structures, physical locations, and raw data can be loaded into SLIMS. Raw data from high-throughput assays are normalized using flexible analysis protocols, and systematic spatial errors are automatically identified and corrected. Various computational analyses are performed on tested compounds, and dilution-series data are processed using standard or user-defined algorithms. Finally, published literature associated with active compounds is automatically retrieved from Medline and processed to yield potential mechanisms of actions. SLIMS provides a framework for analyzing high-throughput assay data both as a laboratory information management system and as a platform for experimental analysis.     

Thermodynamic model for the analysis of calorimetric data of oligomeric proteins

The thermodynamic parameters for the process of protein unfolding can be obtained through differential scanning calorimetry. However, the unfolding process may not be a two-state one. Between the native and the unfolded state, there may be association or dissociation processes or the formation of an intermediate state. As a consequence of this, the precise interpretation of the calorimetric data should be done with a specific thermodynamic model. In this work, we present two general models for the unfolding process of an oligomeric protein: N n right harpoon over left harpoon nN right harpoon over left harpoon nD (model A) and N n right harpoon over left harpoon I n right harpoon over left harpoon nD (model B). In model A, the first step represents the dissociation of the oligomer into the monomeric native species, and the second step represents the denaturation process. In model B, the first step represents the conformational change of the oligomer, and the second step represents the dissociation of this species with the concomitant unfolding process. A canonical ensemble was employed to describe these systems, by considering that the total protein concentration remains constant. In the present work, we show and analyze the behavior of these systems in different conditions and how this analysis could help with the identification of the unfolding mechanism experimentally observed.     

ICP-atomic emission spectrometry as a tool for flexible single-element analysis of non-routine samples

Summary This paper deals with flexible single-element analysis using inductively coupled plasma-atomic emission spectrometry (ICP-AES). Some non-routine problems encountered in the daily practice of an analytical service group in a research laboratory of a large electronic industry were handled with ICP-AES and — when rational — also with wet-chemical techniques including atomic absorption spectrometry (AAS). The analyses covered micro and macro samples and involved the determination of trace constituents: Ni in a CrO₃-sulphuric acid etching liquid, Sn in 18% sulphuric acid, and B in TiO₂ powder; a minor constituent: Cr in Mg-ferrite; major constituents: Sm and Co in an Sm-Co alloy, Fe, Al and Si in a thin Fe-Al-Si layer, B and Li in LiBF₄, Si in thin Si₃N₄ layers, and Y and Eu in a thin Y₂O₃-Eu₂O₃ layer. The power of ICPAES as an analytical tool for solving a variety of nonroutine analytical problems with a relatively simple spectroscopic approach and little chemical treatment of the sample solutions became quite evident.

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ICP-AES als Verfahren für flexible Einzelelementanalysen von Nicht-Routine-Proben

Zusammenfassung Diese Arbeit betrifft die flexible Einzelelementanalyse mittels atomarer Emissionsspektrometrie unter Verwendung eines induktiv gekoppelten Hochfrequenzplasmas (ICP-AES). Es wurde mit ICP-AES und — soweit es vernünftig war — auch mit naß-chemischen Methoden einschließlich Atomabsorption (AAS) eine Reihe von Analysenproblemen bearbeitet, die nicht als Routine-Probleme zu bezeichnen sind, jedoch zum täglichen Aufgabenangebot einer analytischen Service-Gruppe in einem Forschungslabor eines großen Unternehmens der Elektronik-Industrie gehören. Die Analysen bezogen sich auf Mikround Makroproben und umfaßten die Bestimmung von Spuren: Ni in einer Chromoxid-Schwefelsäure-Ätzflüssigkeit, Sn in 18%-iger Schwefelsäure und B in TiO₂-Pulver; die Bestimmung einer Nebenkomponente: Cr in Mg-Ferrit; ferner die Bestimmung von Hauptkomponenten: Sm und Co in einer Sm-Co-Legierung, Fe, Al und Si in einer Fe-Al-Si-Dünnschicht, B und Li in LiBF₄, Si in Si₃N₄-Dünnschichten und Y und Eu in einer Y₂O₃-Eu₂O₃-Dünnschicht. Die Möglichkeit, mit ICP-AES eine Vielfalt von Analyseproblemen bei verhältnismäßig geringem spektroskopischem Arbeitsaufwand und nur wenigen chemischen Behandlungen der Probelösungen zu bewältigen, wurde eindeutig nachgewiesen.

     

iMatch: a retention index tool for analysis of gas chromatography-mass spectrometry data

A method was developed to employ National Institute of Standards and Technology (NIST) 2008 retention index database information for molecular retention matching via constructing a set of empirical distribution functions (DFs) of the absolute retention index deviation to its mean value. The effects of different experimental parameters on the molecules' retention indices were first assessed. The column class, the column type, and the data type have significant effects on the retention index values acquired on capillary columns. However, the normal alkane retention index (I(norm)) with the ramp condition is similar to the linear retention index (I(T)), while the I(norm) with the isothermal condition is similar to the Kováts retention index (I). As for the I(norm) with the complex condition, these data should be treated as an additional group, because the mean I(norm) value of the polar column is significantly different from the I(T). Based on this analysis, nine DFs were generated from the grouped retention index data. The DF information was further implemented into a software program called iMatch. The performance of iMatch was evaluated using experimental data of a mixture of standards and metabolite extract of rat plasma with spiked-in standards. About 19% of the molecules identified by ChromaTOF were filtered out by iMatch from the identification list of electron ionization (EI) mass spectral matching, while all of the spiked-in standards were preserved. The analysis results demonstrate that using the retention index values, via constructing a set of DFs, can improve the spectral matching-based identifications by reducing a significant portion of false-positives.     

Application of chemometric analysis to complexity in isothermal calorimetric data

The interpretation of complexity in isothermal calorimetric data is demanding. The observed power signal is a composite of the powers arising from each of the individual events occurring (which can involve physical, as well as chemical, change). The challenge, therefore, lies in deconvoluting the observed data into their component parts. Here, we discuss the potential use of chemometric analysis, because it offers the significant advantage of being model-free, using principal component analysis to deconvolute data. Using model data, we discovered that the software required a minimum trivariate data matrix to be constructed. Two variables, power and time, were available from the raw data. Selection of a third variable was more problematic, but it was found that by running multiple experiments the small variation in the number of moles of compound in each experiment was sufficient to allow a successful analysis. In general we noted that it required a minimum 2n + 2 repeat experiments to allow analysis (where n is the number of reaction processes). The data outputted from the chemometric software were of the form intensity (arbitrary units) versus time, reflecting the fact that the software was written for analysis of spectroscopic data. We provide a mathematical treatment of the data that allows recovery of both reaction enthalpy and rate constants. The study demonstrates that chemometric analysis is a promising approach for the interpretation of complex calorimetric data.     

The VMFCI method: a flexible tool for solving the molecular vibration problem

The present article introduces a general variational scheme to find approximate solutions of the spectral problem for the molecular vibration Hamiltonian. It is called the "vibrational mean field configuration interaction" (VMFCI) method, and consists in performing vibrational configuration interactions (VCI) for selected modes in the mean field of the others. The same partition of modes can be iterated until self-consistency, generalizing the vibrational self-consistent field (VSCF) method. As in contracted-mode methods, a hierarchy of partitions can be built to ultimately contract all the modes together. So, the VMFCI method extends the traditional variational approaches and can be included in existing vibrational codes based on the latter approaches. The flexibility and efficiency of this new method are demonstrated on several molecules of atmospheric interest.     

Experimentally available kinetic codes as a tool for promising data extraction in thermal analysis

By the study of 3000 kinetic runs for all homogeneous two-step models under variation of activation and signal parameters, it has been stated that the generated Mechanistic Concentration Code (=MCC) is the best vehicle for data extraction in Thermal Analysis. It summarises the rate-controlling steps and their molecularities, independently of their activation data and (to 80–90%) of their method-specific signal parameters. Hence, an optimum evaluation needs the internal (best-fitted) reference step, the initial concentration of a reference reactant, and equal weight of theoretical and experimental results, reached using the same algorithms. Thus, the MCC of any series measured in general allows for a reliable model determination via the distribution into all two-step models, using the tools of probability and decision theory. A transfer of the strategy to heterogeneous reactions is discussed.

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Zusammenfassung Durch die Untersuchung von über 3000 kinetischen Abläufen für alle homogenkinetischen Zweistufen-Modelle wurde festgestellt, da\ der Mechanistische Konzentrations-Code (= MCC) ein optimaler Datenträger in der Thermischen Analyse ist: Er beschreibt die geschwindigkeitsbestimmenden Schritte und ihre Molekularität, unab- hängig von deren Aktivierungsdaten und, zu 80–90%, von ihren methodenspezifischen Signalparametern. Ein optimales Auswerteverfahren benötigt einen internen (optimal angepa\ten) Referenzschritt, die Startkonzentration eines Referenz-Reaktanten und Gleichberechtigung theoretischer und experimenteller Befunde, erreicht, durch Verwendung derselben Algorithmen. Allgemein ermöglicht der MCC aus einer Reihe von Experimenten dann eine Modellbestimmung über eine Verteilung, die durch entscheidungstheoretische Kriterien die Wahrscheinlichkeiten aller Zweistufenmodelle auflistet.Eine übertragung des Verfahrens auf heterogene Prozesse wird diskutiert.

     

Micellar electrokinetic capillary chromatography and data alignment analysis: a new tool in urine profiling

The complex nature of biofluids demands efficient, sensitive and high-resolution analytical methodologies to examine how the 'metabolic fingerprint' changes during disease. This paper describes how sulphated beta-cyclodextrin-modified micellar electrokinetic capillary chromatography (SbetaCD-MECC) has been combined with data alignment analysis and may prove a useful new tool in urine profiling, allowing for separation of over 80 urinary analytes in under 25 min. The optimised and validated SbetaCD-MECC methodology combined with data alignment analysis provides rapid identification of 'mismatches' between urine profiles which are not easily detected with the naked eye as well as a 'similarity score' which indicates the total sum of differences between one profile and another. The combination of SbetaCD-MECC with data alignment software should prove a useful alternative tool in metabonomic studies for rapid comparison of urine profiles.     

Application of a simple calorimetric data analysis on the binding study of cyanide ions by Jack bean urease

<正>Cyanide ion was studied as an effector of Jack bean urease(JBU) at 300 K in 30 mmol/LTris buffer,pH 7 by isothermal titration calorimetry(ITC).The simple novel model was used for CN~- + JBU interaction over the whole range of CN~- concentrations.The binding parameters recovered from the simple novel model were attributed to the cyanide ion interaction.It was found that cyanide ion acted as a noncooperative inhibitor of JBU,and there is a set of 12 identical and independent binding sites for CN~- ions.The dissociation equilibrium constant is 750μmol/L.The molar enthalpy of binding is△H= -13.6 kJ mol~(-1).The technique used provided an accurate and quick assessment of the effectiveness of the compounds to inhibit Jack bean urease.     

Application of a simple calorimetric data analysis on the binding study of calcium ions by human growth hormone

A simple graphical linear method was introduced for isothermal titration calorimetric data analysis in the protein-ligand interaction. The number of binding sites, the dissociation binding constant and the molar enthalpy of binding site can be obtained by using this new isothermal titration calorimetric data analysis method. The method was applied to the study of the interaction of human growth hormone (hGH) with divalent calcium ion at 27°C in NaCl solution, 50 mM. hGH has a set of three identical and independent binding sites for Ca ²⁺ . The intrinsic dissociation equilibrium constant and the molar enthalpy of binding are 52 μMand -17.4, respectively. Results obtained by this new calorimetric data analysis are in good agreement with results obtained using our previous method.     

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.     

Comparison of calorimetric and IR-spectroscopic data for alcohols and alcoholic solutions

The heats of solution of alcohols in hexane can be considered as the energy necessary to break hydrogen bonds (H-bond). The amount of non H-bonded OH groups estimated from caloric data, are in good agreement with IR-spectroscopic data. Comparison of calorimetric and IR-spectroscopically determined H-bond energies permit the separation of intermolecular van der Waals effects from H-bond interactions. This separation shows that van der Waals interactions of alcohols or water should not be underestimated.     

Multivariate curve resolution applied to in situ X-ray absorption spectroscopy data: An efficient tool for data processing and analysis

Large datasets containing many spectra commonly associated with in situ or operando experiments call for new data treatment strategies as conventional scan by scan data analysis methods have become a time-consuming bottleneck. Several convenient automated data processing procedures like least square fitting of reference spectra exist but are based on assumptions. Here we present the application of multivariate curve resolution (MCR) as a blind-source separation method to efficiently process a large data set of an in situ X-ray absorption spectroscopy experiment where the sample undergoes a periodic concentration perturbation. MCR was applied to data from a reversible reduction–oxidation reaction of a rhenium promoted cobalt Fischer–Tropsch synthesis catalyst. The MCR algorithm was capable of extracting in a highly automated manner the component spectra with a different kinetic evolution together with their respective concentration profiles without the use of reference spectra. The modulative nature of our experiments allows for averaging of a number of identical periods and hence an increase in the signal to noise ratio (S/N) which is efficiently exploited by MCR. The practical and added value of the approach in extracting information from large and complex datasets, typical for in situ and operando studies, is highlighted.     

Liquid chromatography: a tool for the analysis of metal species

An overview is presented of classic and more recent applications of liquid chromatography for the analysis of metal species. The different approaches involving ion-exchange, ion-pair, and chelation separation mechanisms are discussed as well as the new philosophy of simply removing interferents before specific detections of metal ions (alkali and alakaline earths, rare earths, heavy and transition metals). New more selective materials enabling difficult separations and studies on multimodal or hyphenated techniques for metal speciation (e.g. arsenic and chromium) are considered.     

Overpressured layer chromatography (OPLC)--a flexible tool of analysis and isolation

This review briefly summarizes the overpressured layer chromatography (OPLC) technique and its progress from the beginning until today. Some theoretical aspects, important technical and methodological solutions, as well as analytical separations and isolations are demonstrated covering the last 30 years. The infusion and transfusion OPLC operations, as well as their combination, and their off-line and on-line processes, and off-line and on-line hyphenations for detection and structure elucidation are presented. The combination of OPLC separation with biological detection by direct bioautography and BioArena as an important solution touches the potential of analysis and isolation based on biological activity.     

Reactive chemical hedges: a search tool for comprehensive retrieval of chemical safety data

A step-by-step procedure has been developed for compiling search hedges and has been applied to the topic of reactive chemicals. Special problems encountered in compiling the reactive chemical hedges are presented, including improvements in processing efficiency and recall performance achieved by trimming the hedge with a controlled vocabulary. A reactive chemical value index has been developed and used to rank six chemical databases according to their safety content. From these rankings, new on-line sources have been identified for reactive chemical information.     

Local covariance order diffusion-ordered spectroscopy: a powerful tool for mixture analysis

Diffusion-ordered spectroscopy (DOSY) is an important tool in NMR mixture analysis that has found use in most areas of chemistry, including organic synthesis, drug discovery, and supramolecular chemistry. Typically the aim is to disentangle the overlaid, and often overlapped, NMR spectra of individual mixture components and/or to obtain size and interaction information from their respective diffusion coefficients. The most common processing method, high-resolution DOSY, breaks down where component spectra overlap; here multivariate methods can be very effective, but only for small numbers (2-5) of components. In this study, we present a hybrid method, local covariance order DOSY (LOCODOSY), that breaks a spectral data set into suitable windows and analyzes each individually before combining the results. This approach uses a multivariate algorithm (e.g., SCORE or DECRA) to resolve only a small number of components in any given window. Because a small spectral region should contain signals from only a few components, even when the spectrum as a whole contains many more, the total number of resolvable chemical components rises dramatically. It is demonstrated here that complete resolution of component spectra can be achieved for mixtures that are much more complex than could previously be analyzed with DOSY. Thus, LOCODOSY is a powerful, flexible tool for processing NMR diffusion data of complex mixtures.     

Development of a calorimetric sensor for medical application

A calorimetric sensor has been developed to measure the calorific dissipation through a determined area of the human body surface. An experimental laboratory prototype with a capturing surface of 36 cm² has been built, and a functioning model suggesting an operational method that allows to determine the calorific power going through the sensor has been proposed.