Assessing a novel microfluidic interface for shotgun proteome analyses

Microfluidic interfaces coupled to ESI mass spectrometers hold great potential for proteomics as they have been shown to augment the overall sensitivity of measurements and require only a minimum of operator manipulations as compared to conventional nano-LC interfaces. Here, we evaluated a new type of HPLC-Chips holding larger enrichment columns (thus an increased sample loading capacity) for gel-free proteome studies. A tryptic digest of a human T-cell proteome was fractionated by strong cation exchange chromatography and selected fractions were analyzed by MS/MS on an IT mass spectrometer using both the new HPLC-Chip as well as a conventional nano-LC-MS/MS interface. Our results indicate that the HPLC-Chip is capable of handling very complex peptide mixtures and, in fact, leads to the identification of more peptides and proteins as compared to when a conventional interface was used. The HPLC-Chip preferentially produced doubly charged tryptic peptides. We further show that MS/MS spectra of doubly charged tryptic peptide ions are more readily identified by MASCOT as compared to those from triply charged precursors and thus argue that besides the improved chromatographic conditions provided by the HPLC-Chip, its peptide charging profile might be a secondary factor leading to an increased proteome coverage.     

Synthesis of water-soluble scaffolds for peptide cyclization, labeling, and ligation

The synthesis and applications of water-soluble scaffolds that conformationally constrain side chain unprotected linear peptides containing two cysteines are described. These scaffolds contain a functionality with orthogonal reactivity to be used for labeling and ligation. This is illustrated by the chemical ligation of two dissimilar constrained peptides via oxime ligation or strain-promoted azide-alkyne cycloaddition in aqueous media.     

Isolation and X-ray crystal structure of a stable calix[4]arene monohemiketal

The formation of a stable calix[4]arene monohemiketal is described. X-ray crystallographic data provide conclusive evidence for the presence of a stabilizing hydrogen bond. Supplementary Data. Lists of H-atom parameters and bond lengths and angles involving hydrogens have been deposited with the British Library Document Supply Centre as Supplementary Publication No. SUP 82159 (5 pp.).     

Molecular "chaperones" guide the spontaneous formation of a 15-component hydrogen-bonded assembly

Chaperones are small molecules that assist in the folding of naturally occurring peptides. There are no examples of small molecules acting as chaperones in the self-assembly of synthetic noncovalent assemblies. In this communication we describe an unprecedented example of the "chaperone effect" in the noncovalent synthesis of organic nanostructures. Tetrarosette assemblies 2(3).(BuCYA)(12) form quantitatively in CHCl(3) at room temperature upon mixing tetramelamine 2 with N-butylcyanurate (BuCYA) in the presence of 5,5-diethylbarbituric acid (DEB). Without the DEB units present, only oligomeric assemblies are formed that cannot rearrange to the tetrarosettes by themselves. The DEB units act as molecular "chaperones" by preorganizing the tetramelamine units for the spontaneous assembly of the tetrarosette structure.     

Solid-phase synthesis of heterocyclic aromates: applicability towards combinatorial chemistry; a review

Because of their biological activity, stability in vivo, the rigid spatial positioning of their substituents, and their synthetic challenges, heterocyclic aromates continue to be of interest to both academic and industrial medicinal chemists. Currently, many drug-like heterocyclic aromates are prepared via solid-phase organic chemistry methods. This review examines the applicability of those methods towards combinatorial chemistry with respect to the basic demands of such an approach: 1) synthesis, work-up and subsequent purification should be easily automated enabling the efficient simultaneous synthesis of large numbers of highly pure compounds in a minimum amount of time, 2) large diversity among the ligands to be synthesized, 3) high conversion rates of the individual reaction steps, and 4) the use of commercially available starting materials. Although many methods have been developed for the synthesis of heterocyclic aromates, very few of the available methods enable the synthesis of highly diverse heteroaromatic libraries.     

Multilevel component analysis of time-resolved metabolic fingerprinting data

Genomics-based technologies in systems biology have gained a lot of popularity in recent years. These technologies generate large amounts of data. To obtain information from this data, multivariate data analysis methods are required. Many of the datasets generated in genomics are multilevel datasets, in which the variation occurs on different levels simultaneously (e.g. variation between organisms and variation in time). We introduce multilevel component analysis (MCA) into the field of metabolic fingerprinting to separate these different types of variation. This is in contrast to the commonly used principal component analysis (PCA) that is not capable of doing this: in a PCA model the different types of variation in a multilevel dataset are confounded.

MCA generates different submodels for different types of variation. These submodels are lower-dimensional component models in which the variation is approximated. These models are easier to interpret than the original data. Multilevel simultaneous component analysis (MSCA) is a method within the class of MCA models with increased interpretability, due to the fact that the time-resolved variation of all individuals is expressed in the same subspace.

MSCA is applied on a time-resolved metabolomics dataset. This dataset contains ¹H NMR spectra of urine collected from 10 monkeys at 29 time-points during 2 months. The MSCA model contains a submodel describing the biorhythms in the urine composition and a submodel describing the variation between the animals. Using MSCA the largest biorhythms in the urine composition and the largest variation between the animals are identified.

Comparison of the MSCA model to a PCA model of this data shows that the MSCA model is better interpretable: the MSCA model gives a better view on the different types of variation in the data since they are not confounded.     

Learning to Teach: Prospective Teachers' Evaluation of Students' Written Responses on a 1992 NAEP Graphing Task

This article describes how prospective elementary teachers examined, analyzed, and evaluated four students' written responses on a graphing task for an end‐of‐course performance assessment in a mathematics methods course. Also, they described teaching strategies that built on what students know and do not know, as shown in the fourth‐grade students' work. This course assessment provided evidence of the prospective teachers' pedagogical content knowledge. Two themes emerged in the context of this final course project: the importance of process and correct answers and the usefulness of creating rubrics.