The inter‐ and intra‐operator variability in manual spot segmentation and its effect on spot quantitation in two‐dimensional electrophoresis analysis

Separation of complex mixtures of proteins by 2‐DE is a fundamental component of current proteomic technology. Quantitative analysis of the images generated by digitization of such gels is critical for identifying alterations in protein expression within a given biological system. Software packages are designed for this purpose. The accurate definition of protein spot boundaries, using a suitable method of image segmentation, is a key requirement for image analysis. It is often necessary for operators to intervene manually to correct mistakes in spot segmentation; therefore operator subjectivity and differences in ability can weaken the analysis. We estimated the error in spot quantification after manual spot segmentation, which was performed by different operators, using two different software packages. Our results clearly show that this operation was associated with significant inter‐ and intra‐variability and an overestimation of subsequent spot intensity, especially when spots were weak. For comparative studies, we suggest separately analysing spots which have been manually segmented by imposing a requirement for at least a threefold difference in spot intensity in addition to use of statistical tests.     

Delta2D and Proteomweaver: Performance evaluation of two different approaches for 2‐DE analysis

2‐DE is a fundamental technology used in proteomics research. However, despite its high capacity to simultaneously separate several proteins for subsequent identification and quantitative comparison studies, a drawback for this technique is its limited reproducibility, especially when comparing data from different laboratories. 2‐DE‐related variability can be broadly divided into two categories: experimental and post‐experimental. Experimental variability depends on physical and chemical parameters, whereas post‐experimental variability arises when gels are analyzed by different software packages, particularly when different workflows are followed. In this paper, we compared the analysis performance of two software packages, Delta2D and Proteomweaver, using both standard and experimental gel images. Using standard gel images, the false negative spot count was 50% lower, the false positive count was 77% lower, the true positive count was 19% higher and spot matching was 4% higher in Delta2D when compared to Proteomeweaver. Using experimental gel images, we found that the total amount of time taken to complete the analysis with Delta2D was 30% that of the time needed with Proteomweaver and required fewer user interventions. The differences between ease of use and workflow strategy of these programs is discussed.     

Static and Frequency‐Dependent Dipole–Dipole Polarizabilities of All Closed‐Shell Atoms up to Radium: A Four‐Component Relativistic DFT Study

We test the performance of four‐component relativistic density functional theory by calculating the static and frequency‐dependent electric dipole–dipole polarizabilities of all (ground‐state) closed‐shell atoms up to Ra. We consider 12 nonrelativistic functionals, including three asymptotically shape‐corrected functionals, by using two smooth interpolation schemes introduced by the Baerends group: the gradient‐regulated asymptotic connection (GRAC) procedure and the statistical averaging of (model) orbital potentials (SAOP). Basis sets of doubly augmented triple‐zeta quality are used. The results are compared to experimental data or to accurate ab initio results. The reference static electric dipole polarizability of palladium has been obtained by finite‐field calculations using the coupled‐cluster singles, doubles, and perturbative triples method within this work. The best overall performance is obtained using hybrid functionals and their GRAC shape‐corrected versions. The performance of SAOP is among the best for nonhybrid functionals for Group 18 atoms but its precision degrades when considering the full set of atoms. In general, we find that conclusions based on results obtained for the rare‐gas atoms are not necessarily representative of the complete set of atoms. GRAC cannot be used with effective core potentials since the asymptotic correction is switched on in the core region.     

Self‐ and cross‐associations in two‐component mixed polymer gels

The gel properties of two‐component mixed polymer gels are investigated using a cascade model, which assumes that the gel network is formed via the self‐association of one of the two components and the cross‐association of the two components. The effects of the model parameters, such as the equilibrium constants and the functionalities for cross‐associations and self‐associations, on the composition dependence of the modulus and gel point curves are examined to elucidate the contribution of self‐associations to the gel network. The results show that the characteristics of self‐associations become pronounced when the equilibrium constant or the functionality for self‐associations is comparable to that for cross‐associations. The model is applied to analyze the critical gelling concentration data for xanthan/locust bean gum mixed gels, which shows significant self‐associations at high xanthan compositions. The resulting model curves agree well with the experimental data at all temperatures. The analysis of the temperature dependence of the best‐fit equilibrium constant yields values of enthalpy change that are consistent with previous findings. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 80–91, 2008     

High‐abundance protein depletion: Comparison of methods for human plasma biomarker discovery

Affinity depletion of abundant proteins from human plasma has become a routine sample preparation strategy in proteomics used prior to protein identification and quantitation. To date, there have been limited published studies comparing the performance of commercially available depletion products. We conducted a thorough evaluation of six depletion columns using 2‐DE combined with sophisticated image analysis software, examining the following criteria: (i) efficiency of high‐abundance protein depletion, (ii) non‐specific removal of other than the targeted proteins and (iii) total number of protein spots detected on the gels following depletion. From all the products investigated, the Seppro IgY system provided the best results. It displayed the greatest number of protein spots on the depleted plasma gels, minimal non‐specific binding and high efficiency of abundant protein removal. Nevertheless, the increase in the number of detected spots compared with the second best performing and cheaper multiple affinity removal column (MARC) was not shown to be statistically significant. The ProteoPrep spin column, considered to be the “deepest” depletion technique available at the time of conducting the study, surprisingly displayed significantly fewer spots on the flow‐through fraction gels compared with both the Seppro and the MARC. The spin column format and low plasma capacity were also found to be impractical for 2‐DE. To conclude, we succeeded in providing an overview of the depletion columns performances with regard to the three examined areas. Our study will serve as a reference to other scientists when deciding on the optimal product for their particular projects.     

A new specific metal ion chelated‐poly(N‐vinylimidazole) gel sorbents for albumin adsorption‐desorption

Poly(N‐vinylimidazole) (PVIm) hydrogels were prepared by γ‐irradiating binary mixtures of N‐vinylimidazole‐water in a ⁶⁰Co‐γ source having 4.5 kGy/h dose rate. These affinity gels having different swelling ratio of Cu(II)‐chelated, Co(II)‐chelated and plain PVIm in acetate buffer were used in the albumin adsorption studies. Bovine serum albumin (BSA) adsorption on these gels from aqueous solutions containing different amounts of BSA at different pH adjusted with acetate and phosphate buffer was investigated in batch reactors. The adsorption capacities of BSA on/in the gels were decreased dramatically by increasing the ionic strength (I) adjusting with NaCl. BSA adsorption capacities of the metal ion‐chelated gels were higher than the plain PVIm gel even if the swelling ratio of the metal ion‐chelated gels was very low comparing to the PVIm gel. The rigidity of the metal ion‐chelated gel is very high and it can be used for the column applications. More than 95% of BSA were desorbed in 3 h in the desorption medium containing KSCN for PVIm gel and EDTA for metal ion‐chelated gels. These results indicate that PVIm and metal ion‐chelated PVIm gels are very efficient to remove BSA and the different metal ion‐chelated PVIm gels show different affinity for BSA or biomolecules.     

Preparation of novel,high‐modulus,swollen‐ or jungle‐gym‐type polyimide gels end‐crosslinked with 1,3,5‐tris(4‐aminophenyl)benzene

A novel preparation approach for high‐performance polyimide gels that are swollen or have a jungle‐gym‐type structure is proposed. A new rigid and symmetric trifunctional amine, 1,3,5‐tris(4‐aminophenyl)benzene (TAPB), was synthesized as a crosslinker. Three different kinds of amic acid oligomers derived from pyromellitic dianhydride (PMDA), 4,4′‐oxydiphthalic anhydride (ODPA), p‐phenylenediamine (PDA), and 4,4′‐oxydianiline (ODA) were end‐crosslinked with TAPB at a high temperature to make polyimide networks with different structures. Transparent polyimide gels were obtained from the ODPA–ODA/TAPB series with high compression moduli of about 1 MPa at their equilibrium swollen states in N‐methylpyrrolidone. Microscopic phase separation occurred during the gelation–imidization process when polyimide networks were generated from PMDA–PDA/TAPB and PMDA–ODA/TAPB. After these opaque polyimide networks were dried, a jungle‐gym‐like structure was obtained for the PMDA–PDA/TAPB and PMDA–ODA/TAPB series; that is, there was a high void content inside the networks (up to 70%) and little volume shrinkage. These polyimide networks did not expand but absorbed the solvent and showed moduli as high as those of solids. Therefore, using the highly rigid crosslinker TAPB combined with the flexible monomers ODPA and ODA and the rigid monomers PMDA and PDA, we prepared swollen, high‐performance polyimide gels and jungle‐gym‐type polyimide networks, respectively. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2501–2512, 2002     

Development of C3‐Symmetric Tris‐Urea Low‐Molecular‐Weight Gelators

This article describes recent developments in C₃‐symmetric tris‐urea low‐molecular‐weight gelators and their applications. The C₃‐symmetric tris‐ureas are excellent frameworks to form supramolecular polymers through noncovalent interactions. In organic solvents, hydrophobic tris‐ureas form supramolecular gels. Amphiphilic tris‐ureas form supramolecular gels in aqueous media. Functional supramolecular gels were prepared by introducing appropriate functional groups into the outer sphere of tris‐ureas. Supramolecular hydrogels obtained from amphiphilic tris‐ureas were used in the electrophoresis of proteins. These electrophoreses results showed several unique characteristics compared to typical electrophoreses results obtained using polyacrylamide matrices.

     

Local Hartree–Fock orbitals using a three‐level optimization strategy for the energy

Using the three‐level energy optimization procedure combined with a refined version of the least‐change strategy for the orbitals—where an explicit localization is performed at the valence basis level—it is shown how to more efficiently determine a set of local Hartree–Fock orbitals. Further, a core–valence separation of the least‐change occupied orbital space is introduced. Numerical results comparing valence basis localized orbitals and canonical molecular orbitals as starting guesses for the full basis localization are presented. The results show that the localization of the occupied orbitals may be performed at a small computational cost if valence basis localized orbitals are used as a starting guess. For the unoccupied space, about half the number of iterations are required if valence localized orbitals are used as a starting guess compared to a canonical set of unoccupied Hartree–Fock orbitals. Different local minima may be obtained when different starting guesses are used. However, the different minima all correspond to orbitals with approximately the same locality. © 2013 Wiley Periodicals, Inc.     

Assessing the suitability of capillary electrophoresis‐mass spectrometry for biomarker discovery in plasma‐based metabolomics

The actual utility of capillary electrophoresis‐mass spectrometry (CE‐MS) for biomarker discovery using metabolomics still needs to be assessed. Therefore, a simulated comparative metabolic profiling study for biomarker discovery by CE‐MS was performed, using pooled human plasma samples with spiked biomarkers. Two studies have been carried out in this work. Focus of study I was on comparing two sets of plasma samples, in which one set (class I) was spiked with five isotope‐labeled compounds, whereas another set (class II) was spiked with six different isotope‐labeled compounds. In study II, focus was also on comparing two sets of plasma samples, however, the isotope‐labeled compounds were spiked to both class I and class II samples but with concentrations which differ by a factor two between both classes (with one compound absent in each class). The aim was to determine whether CEMS‐based metabolomics could reveal the spiked biomarkers as the main classifiers, applying two different data analysis software tools (MetaboAnalyst and Matlab). Unsupervised analysis of the recorded metabolic profiles revealed a clear distinction between class I and class II plasma samples in both studies. This classification was mainly attributed to the spiked isotope‐labeled compounds, thereby emphasizing the utility of CE‐MS for biomarker discovery.     

Volatile compounds profiling by using proton transfer reaction‐time of flight‐mass spectrometry (PTR‐ToF‐MS). The case study of dark chocolates organoleptic differences

Direct‐injection mass spectrometry (DIMS) techniques have evolved into powerful methods to analyse volatile organic compounds (VOCs) without the need of chromatographic separation. Combined to chemometrics, they have been used in many domains to solve sample categorization issues based on volatilome determination. In this paper, different DIMS methods that have largely outperformed conventional electronic noses (e‐noses) in classification tasks are briefly reviewed, with an emphasis on food‐related applications. A particular attention is paid to proton transfer reaction mass spectrometry (PTR‐MS), and many results obtained using the powerful PTR‐time of flight‐MS (PTR‐ToF‐MS) instrument are reviewed. Data analysis and feature selection issues are also summarized and discussed. As a case study, a challenging problem of classification of dark chocolates that has been previously assessed by sensory evaluation in four distinct categories is presented. The VOC profiles of a set of 206 chocolate samples classified in the four sensory categories were analysed by PTR‐ToF‐MS. A supervised multivariate data analysis based on partial least squares regression‐discriminant analysis allowed the construction of a classification model that showed excellent prediction capability: 97% of a test set of 62 samples were correctly predicted in the sensory categories. Tentative identification of ions aided characterisation of chocolate classes. Variable selection using dedicated methods pinpointed some volatile compounds important for the discrimination of the chocolates. Among them, the CovSel method was used for the first time on PTR‐MS data resulting in a selection of 10 features that allowed a good prediction to be achieved. Finally, challenges and future needs in the field are discussed.     

Synthesis of organic‐inorganic hybrid gels by means of thiol‐ene and azide‐alkene reactions

Organic–inorganic hybrid gels have been synthesized from a multi‐vinyl functional cyclic siloxane, 1,3,5,7‐tetravinyltetramethylcyclotetrasiloxane (TVMCTS), or a cubic silsesquioxane, octavinyloctasilasesquioxane (PVOSS), and α,ω‐dithiol compounds, 1,6‐hexanedithiol (HDT), 1,10‐decanedithiol (DDT), using thiol‐ene reaction in toluene. The network structure of the resulting gels, mesh size and mesh size distribution, was quantitatively characterized by means of a scanning microscopic light scattering (SMILS). The gels obtained from TVMCTS‐HDT formed homogeneous network structure with 1.5–1.6 nm mesh. Relaxation peaks derived from large clusters and/or micro gels were detected in the SMILS analysis of the TVMCTS‐DDT, PVOSS‐HDT, and PVOSS‐DDT gels besides those from the small meshes. The organic–inorganic hybrid gels were also synthesized from TVMCTS, PVOSS with α,ω‐diazide compounds, 1,6‐hexanediazide (HDA), 1,10‐decanediazide (DDA), using azide‐alkene reaction in toluene. All the gels obtained with the azide‐alkene reaction formed the homogeneous network structure. Enthalpy relaxation at the glass transition of the dried samples was detected by differential scanning calorimetry to study the network uniformity of the original gels. The gels synthesized by the azide‐alkene reaction showed larger enthalpy than the gels synthesized by the thiol‐ene reaction, indicating homogeneous network structure in the former gels. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2229–2238     

The Rearrangement of 2,2‐Diphenyl‐1‐[(E)‐2‐phenylethenyl]cyclopropane to 3,4,4‐Triphenylcyclopent‐1‐ene: a DFT Analysis

A computational study on the rearrangement of 2,2‐diphenyl‐1‐[(E)‐2‐phenylethenyl]cyclopropane ( 1 ) is presented, using density functional theory (DFT), (U)B3LYP with the 6‐31G* basis set (DFT1) and (U)M05‐2X with the 6‐311+G** basis set (DFT2). In agreement with a biradical character of the transition structure (TS) or intermediate, the potential‐energy hypersurface is lowered by the influence of three conjugated Ph groups. Surprisingly, two conformations of the geminal diphenyl group (different twist angles) induce two different minimum‐energy pathways for the rearrangement. Independent of the functional used, the first hypersurface harbors true biradical intermediates, whereas the second energy surface is a flat, slightly ascending slope from the starting material to the TS. The functional (U)M05‐2X with the basis set 6‐311+G** provides realistic energies which seem to be close to experiment. The activation energy for racemization of enantiomers of 1 is lower than that of rearrangement by 2.5 kcal mol^?1, in agreement with experiment.     

Complete determination of plant tissues based only on auto‐fluorescence and the advanced image analysis – study of needles and stamens

Proper determination of tissues is one of the challenging problems in modern medicine and histology. Currently, interpretation of the results mainly depends on the experience of a histologist, leading to high percentage of results misinterpretation. Bearing in mind potential application, we proposed the set of procedures that allow us to obtain precise, mathematically determined parameters for tissue discrimination. First, the method was tested on simulated set of images and compared with several other algorithms. As the set of experimentally obtained input data, auto‐fluorescence images of needle cross sections (Picea omorika) and stamens of common centaury (Centaurium erythraea) were used. Determination of cell types is based on inherent features of plant cells – auto‐fluorescence. As each cell type consists of various fluorescent components in different quantities for each type of tissue, its integral emission spectrum can be used as the fingerprint for identification. Cross sections were imaged using four sets of filters for detection of fluorescence (both excitation and emission). Such filter set is standard equipment for most fluorescence microscopes. One additional image was transmission image using the same optics. By applying ℓ₀‐norm‐constrained nonnegative matrix factorization in a space induced by explicit feature maps, it is possible to identify up to 11 tissues in needles and five in stamens (actual number of tissues). In comparison to other image analysis methods, the greatest advantage is the fact that the number of extracted components significantly exceeds the number of initial images while most other techniques can extract only as much components as the number of initial images. Copyright © 2015 John Wiley & Sons, Ltd.     

Interlaboratory study comparing analyses of simulated angle‐resolved X‐ray photoelectron spectroscopy data

An interlaboratory study has been conducted to determine the following: (i) the similarities and differences of film thicknesses and composition profiles obtained from analyses of simulated angle‐resolved X‐ray photoelectron spectroscopy (ARXPS) data by different analysts using different algorithms for data analysis, and (ii) the effects of two assumptions commonly made in data‐analysis algorithms for ARXPS on derived film thicknesses and composition profiles. The analyzed data were generated by the National Institute of Standards and Technology Database for the Simulation of Electron Spectra for Surface Analysis, (SESSA) which provides a simple way to study the influence of the aforementioned effects on compositional depth profile reconstruction. Sets of simulated ARXPS data were produced for thin films of SiO₂, SiON, HfO₂, and HfON of varying thicknesses on a Si substrate. For some HfON films, the N concentration varied with depth. Eleven groups participated in the round robin study. The majority (eight) employed a commercial ARXPS instrument in which the angular distribution is measured for a fixed sample geometry, in contrast to conventional ARXPS in which the sample is tilted for angular variation. The average deviations between the reported average depth, film thickness, and amount of material typically varied between 20% and 30% but were considerably larger, between 30% and 80%, for some cases. The average errors were generally larger for simulations that included elastic scattering and the finite analyzer‐acceptance angle (realistic conditions) than those for simulations that neglected elastic scattering and the finite analyzer‐acceptance angle (simplified conditions). The retrieved N depth profiles were quantitatively different from the true depth profiles and showed substantial variability among the group of members who used the same instrument and analysis software. Copyright © 2014 John Wiley & Sons, Ltd.     

Comparison of ethanol-soluble proteins from different rye (Secale cereale) varieties by two-dimensional electrophoresis

The major storage proteins from six rye varieties, grown under the same conditions in 1997 and 1998 in Rønhave, Denmark, were analyzed by two‐dimensional (2‐D) polyacrylamide gel electrophoresis. The proteins were extracted from ground rye kernels with 70% ethanol and separated by 2‐D electrophoresis. The gels were scanned, compared using ImageMaster® software and the data sets were analyzed by principal component analysis (PCA) using THE UNSCRAMBLER software. Afterwards MATLAB was used to make a cluster analysis of the varieties based on PCA. The analysis of the gels showed, that the protein patterns (number of different proteins and their isoelectric points and molecular weights) from the six rye varieties were different. Based on the presence of unique cultivar‐specific spots it was possible to differentiate between all six varieties if the two harvest years were investigated separately. When the results were combined from the two years five varieties could be differentiated. The results from the PCA confirmed the finding of the unique spots and cluster analysis was made in order to illustrate the results. The combination of the results from 2‐D electrophoresis and other grain characteristics showed that one protein spot was located close to the parameters bread volume and bread height.     

Exploratory data analysis groupware for qualitative and quantitative electrophoretic gel analysis over the Internet-WebGel

Many scientists use quantitative measurements to compare the presence and amount, of various proteins and nucleotides among series of one- and two-dimensional (1-D and 2-D) electrophoretic gels. These gels are often scanned into digital image files. Gel spots are then quantified using stand-alone analysis software. However, as more research collaborations take place over the Internet, it has become useful to share intermediate quantitative data between researchers. This allows research group members to investigate their data and share their work in progress. We developed a World Wide Web group-accessible software system, WebGel, for interactively exploring qualitative and quantitative differences between electrophoretic gels. Such Internet databases are useful for publishing quantitative data and allow other researchers to explore the data with respect to their own research. Because intermediate results of one user may be shared with their collaborators using WebGel, this form of active data-sharing constitutes a groupware method for enhancing collaborative research. Quantitative and image gel data from a stand-alone gel image processing system are copied to a database accessible on the WebGel Web server. These data are then available for analysis by the WebGel database program residing on that server. Visualization is critical for better understanding of the data. WebGel helps organize labeled gel images into montages of corresponding spots as seen in these different gels. Various views of multiple gel images, including sets of spots, normalization spots, labeled spots, segmented gels, etc. may also be displayed. These displays are active and may be used for performing database operations directly on individual protein spots by simply clicking on them. Corresponding regions between sets of gels may be visually analyzed using Flicker-comparison (Electrophoresis 1997, 18, 122-140) as one of the WebGel methods for qualitative analysis. Quantitative exploratory data analysis can be performed by comparing protein concentration values between corresponding spots for multiple samples run in separate gels. These data are then used to generate reports on statistical differences between sets of gels (e.g., between different disease states such as benign or metastatic cancers, etc.). Using combined visual and quantitative methods, WebGel can help bridge the analysis of dissimilar gels which are difficult to analyze with stand-alone systems and can serve as a collaborative Internet tool in a groupware setting.     

Automated mass spectrometry imaging with a matrix-assisted laser desorption ionization time-of-flight instrument

The automated use of a matrix-assisted laser desorption ionization (MALDI) mass spectrometer (MS) is described for image analysis of samples through implementation of new software for instrument control, data acquisition, and data analysis. The software permits automated acquisition of MS MALDI spectra to form an ordered data array and contains display features to provide images at one or more mass-to-charge ratio values. The technique can be used to scan tissue samples, blotted samples, gels, or other sample surfaces where the image analysis of that sample is required. The program achieves a time of typically 1 s per image point, permitting an analysis made up of large numbers of points with high spatial resolution up to 850 dpi. The features of the software are demonstrated in this paper with samples of printed images, where visible images can be compared to those obtained by mass spectrometry. Quantitative aspects are introduced by analyzing a series of sample spots containing different amounts of several proteins.