Multivariate analysis of extremely large ToFSIMS imaging datasets by a rapid PCA method

Principal component analysis (PCA) and other multivariate analysis methods have been used increasingly to analyse and understand depth profiles in X‐ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES) and secondary ion mass spectrometry (SIMS). These methods have proved equally useful in fundamental studies as in applied work where speed of interpretation is very valuable. Until now these methods have been difficult to apply to very large datasets such as spectra associated with 2D images or 3D depth‐profiles. Existing algorithms for computing PCA matrices have been either too slow or demanded more memory than is available on desktop PCs. This often forces analysts to ‘bin’ spectra on much more coarse a grid than they would like, perhaps even to unity mass bins even though much higher resolution is available, or select only part of an image for PCA analysis, even though PCA of the full data would be preferred. We apply the new ‘random vectors’ method of singular value decomposition proposed by Halko and co‐authors to time‐of‐flight (ToF)SIMS data for the first time. This increases the speed of calculation by a factor of several hundred, making PCA of these datasets practical on desktop PCs for the first time. For large images or 3D depth profiles we have implemented a version of this algorithm which minimises memory needs, so that even datasets too large to store in memory can be processed into PCA results on an ordinary PC with a few gigabytes of memory in a few hours. We present results from ToFSIMS imaging of a citrate crystal and a basalt rock sample, the largest of which is 134GB in file size corresponding to 67 111 mass values at each of 512 × 512 pixels. This was processed into 100 PCA components in six hours on a conventional Windows desktop PC. © 2015 The Authors. Surface and Interface Analysis published by John Wiley & Sons Ltd.     

Maleimide Glycidyl Ether: A Bifunctional Monomer for Orthogonal Cationic and Radical Polymerizations

A novel bifunctional monomer, namely maleimide glycidyl ether (MalGE), prepared in a four‐step reaction sequence is introduced. This monomer allows for selective (co)polymerization of the epoxide group via cationic ring‐opening polymerization, preserving the maleimide functionality. On the other hand, the maleimide functionality can be copolymerized via radical techniques, preserving the epoxide moiety. Cationic ring‐opening multibranching copolymerization of MalGE with glycidol was performed, and a MalGE content of up to 24 mol% could be incorporated into the hyperbranched polymer backbone (M_n = 1000–3000 g mol⁻¹). Preservation of the maleimide functionality during cationic copolymerization was verified via NMR spectroscopy. Subsequently, the maleimide moiety was radically crosslinked to generate hydrogels and additionally employed to perform Diels‐Alder (DA) “click” reactions with (functional) dienes after the polymerization process. Radical copolymerization of MalGE with styrene (M_n = 5000–9000 g mol⁻¹) enabled the synthesis of a styrene copolymer with epoxide functionalities that are useful for versatile crosslinking and grafting reactions.

     

Equalizer technology followed by DIGE‐based proteomics for detection of cellular proteins in artificial peritoneal dialysis effluents

Peritoneal dialysis effluent (PDE) represents a rich pool of potential biomarkers for monitoring disease and therapy. Until now, proteomic studies have been hindered by the plasma‐like composition of the PDE. Beads covered with a peptide library are a promising approach to remove high abundant proteins and concentrate the sample in one step. In this study, a novel approach for proteomic biomarker identification in PDEs consisting of a depletion and concentration step followed by 2D gel based protein quantification was established. To prove this experimental concept a model system of artificial PDEs was established by spiking unused peritoneal dialysis (PD) fluids with cellular proteins reflecting control conditions or cell stress. Using this procedure, we were able to reduce the amount of high abundant plasma proteins and concentrate low abundant proteins while preserving changes in abundance of proteins with cellular origin. The alterations in abundance of the investigated marker for cell stress, the heat shock proteins, showed similar abundance profiles in the artificial PDE as in pure cell culture samples. Our results demonstrate the efficacy of this system in detecting subtle changes in cellular protein expression triggered by unphysiological stress stimuli typical in PD, which could serve as biomarkers. Further studies using patients’ PDE will be necessary to prove the concept in clinical PD and to assess whether this technique is also informative regarding enriching low abundant plasma derived protein biomarker in the PDE.     

Decoding the components of dynamics in three‐domain proteins

In this study, we examine the feasibility and limitations of describing the motional behavior of three‐domain proteins in which the domains are linearly connected. In addition to attempting the determination of the internal and overall reorientational correlation times, we investigate the existence of correlations in the motions between the three domains. Since in linearly arranged three‐domain proteins, there are typically no experimental data that can directly report on motional correlation between the first and the third domain, we address this question by dynamics simulations. Two limiting cases occur: (1) for weak repulsive potentials and (2) when strong repulsive potentials are applied between sequential domains. The motions of the terminal domains become correlated in the case of strong interdomain repulsive potentials when these potentials do not allow the angle between the sequential domains to be smaller than about 60°. Using the model‐free (MF) and extended MF formalisms of Lipari and Szabo, we find that the motional behavior can be separated into two components; the first component represents the concerted overall motion of the three domains, and the second describes the independent component of the motion of each individual domain. We find that this division of the motional behavior of the protein is maintained only when their timescales are distinct and can be made when the angles between sequential domains remain between 60° and 160°. In this work, we identify and quantify interdomain motional correlations. © 2013 Wiley Periodicals, Inc.     

THM PyGC–MS of wood fragment and vegetable fibre forensic samples

Wood fragments and vegetable fibres were investigated using thermally assisted hydrolysis and methylation with pyrolysis gas chromatography–mass spectrometry (THM PyGC–MS). Multiple ion chromatography was used to decrease the interference from cellulosic peaks, and to obtain greater resolution between the lignin peaks. Forty-four wood samples were analysed using THM PyGC–MS. The wood fragments were able to be differentiated into angiosperms (hardwoods) and gymnosperms (softwoods) using principle component analysis (PCA), hierarchical cluster analysis (HCA), and the ratio of syringyl to guaiacyl lignin fragments (S/G ratio). PCA and HCA also differentiated several Monterey pine samples from the rest of the gymnosperms, primarily by the presence of β-pinene, an extractive compound. Other gymnosperm species and the individual angiosperm species were unable to be differentiated. A pilot study investigating the use of THM PyGC–MS for the analysis of vegetable fibres in forensic science found that the fibre types tended to group into two clusters, with one containing cotton, hemp and linen; and the other consisting of hessian, sisal, jute and coir. The seagrass sample was able to be differentiated from both groups. These groups were well separated using PCA, HCA and by the ratio of cinnamyl phenolic derivatives to guaiacyl lignin derivatives (C/G ratio). Some grouping of each fibre type was evident within each cluster, however the separation between the clusters was insufficient to differentiate them using these statistical techniques. THM PyGC–MS of vegetable fibres showed some potential for future use in forensic science.     

A luminescent rhenium(I) complex of 2,7-dimethyl-1,8-naphthyridine: synthesis,spectroscopy and X-ray crystal structure

2,7-Dimethyl-1,8-naphthyridine (L¹) reacts with pentacarbonylchlororhenium in toluene or chloroform to give the target complex fac-{ReCl(CO)₃(L¹)}. X-ray crystallographic data were obtained for fac-{ReCl(CO)₃(L¹)}. The structural and ¹H NMR data suggest that the ligand coordinates to the rhenium in a bidentate fashion in both solid and solution states. The complex was also found to be luminescent in both solution and solid states. The fluxionality of the ligand in solution causes ligand-centred emission to be observed in solution, whereas only ³MLCT emission was observed in the solid state. Although the complex was air-stable, the lability of L¹ was studied in ¹H NMR experiments where CD₃OD induced complete ligand dissociation over the course of 24 h, and also in reaction of fac-{ReCl(CO)₃(L¹)} with one equivalent of 2,2′-bipyridine in chloroform which resulted in quantitative ligand exchange. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Catalyst free,base free microwave irradiated synthesis of aryl nitrites from potassium aryltrifluoroborates and bismuth nitrate

A mixture of bismuth nitrate pentahydrate and potassium aryltrifluoroborate in toluene under microwave heating at 120 °C for 20 min provides an interesting and mild reaction protocol for the synthesis of aryl nitrite. The conversion to aryl nitrites from aryltrifluoroborates without transition metal catalyst and base in high yields is remarkable.     

Synthesis of sugar oxime ether surfactants

A straightforward synthesis of a novel class of sugar surfactants is described. The key step is the chemoselective condensation of a hydrophobic alkoxyamine with the resident aldehyde/ketone moiety on a hydrophilic sugar. Neither protection/deprotection of the sugars nor extensive product purification is required. The method allows for the facile adjustment of hydrophobic and hydrophilic domains of the sugar oxime ether surfactant and uses inexpensive, readily accessible, and renewable materials.