A new approach to untargeted integration of high resolution liquid chromatography–mass spectrometry data

Because of its high sensitivity and specificity, hyphenated mass spectrometry has become the predominant method to detect and quantify metabolites present in bio-samples relevant for all sorts of life science studies being executed. In contrast to targeted methods that are dedicated to specific features, global profiling acquisition methods allow new unspecific metabolites to be analyzed. The challenge with these so-called untargeted methods is the proper and automated extraction and integration of features that could be of relevance. We propose a new algorithm that enables untargeted integration of samples that are measured with high resolution liquid chromatography–mass spectrometry (LC–MS). In contrast to other approaches limited user interaction is needed allowing also less experienced users to integrate their data. The large amount of single features that are found within a sample is combined to a smaller list of, compound-related, grouped feature-sets representative for that sample. These feature-sets allow for easier interpretation and identification and as important, easier matching over samples. We show that the automatic obtained integration results for a set of known target metabolites match those generated with vendor software but that at least 10 times more feature-sets are extracted as well. We demonstrate our approach using high resolution LC–MS data acquired for 128 samples on a lipidomics platform. The data was also processed in a targeted manner (with a combination of automatic and manual integration) using vendor software for a set of 174 targets. As our untargeted extraction procedure is run per sample and per mass trace the implementation of it is scalable. Because of the generic approach, we envision that this data extraction lipids method will be used in a targeted as well as untargeted analysis of many different kinds of TOF-MS data, even CE- and GC–MS data or MRM. The Matlab package is available for download on request and efforts are directed toward a user-friendly Windows executable.     

Evaluation of the Chromatographic Performance of Conventional, Polar-Endcapped and Calixarene-Bonded Stationary Phases for the Separation of Water-Soluble Vitamins

The performance of four different reversed-phase columns which included a conventional C₁₈ phase, a C₁₈ polar-endcapped phase, an ether-linked phenyl polar-endcapped phase and a calixarene-bonded phase has been systematically compared for the separation of mixture of some water-soluble vitamins containing basic, neutral and acidic compounds of different polarities, as well as different functional groups at three pH levels and different proportions of buffer/methanol. The characteristics of water-soluble vitamins make this combination of compounds very useful as a test mixture to check column performance with real samples. Due to the physical and chemical differences between these compounds, the type of chosen column has a significant influence on the chromatographic behavior. Results of this comparison show that the C₁₈ polar-endcapped phase was the most suitable for the separation of this group of vitamins. The presence of a polar group as an endcapping agent does not seem to influence the overall hydrophobic nature of the polar-endcapped stationary phases. At the same time, these phases displayed enhanced hydrogen bonding and silanol activity.     

CdS and Cd carboxylate nanoclusters dispersed in polymer matrix produced by a freeze drying method

Cadmium sulfide (CdS) nanoclusters were prepared by a freeze drying method from two types of cadmium carboxylates. One was cadmium methacrylates that were part of poly(methyl methacrylate) (PMMA) ionomer. The other was cadmium acetates that were dispersed in PMMA. X-ray diffraction was mainly used to study the formation and the size of nanoclusters. The size of CdS made from the ionomer was 0.9 nm, whereas that from the composite of cadmium acetate and PMMA was 2 nm. This was consistent with the size difference of the precursors of CdS: i.e., Cd carboxylate nanoclusters (ionic aggregates) were smaller in the ionomer than in the PMMA mixture, because ionic groups in the ionomer were constrained due to their connectivity to backbone chains and thus forming smaller ionic aggregates. Once stabilized, however, CdS nanocluster sizes were unchanged despite thermal treatments at up to 220 °C for 24 h for both systems. Structural transformations from a freeze dried cadmium carboxylate powder, to a CdS-containing powder, and to a heat-treated CdS-containing sample are speculated for both types of systems.     

Halogenation of 2-Hydroxynicotinic Acid

A convenient method to prepare 5-halo-2-hydroxy-nicotinic acid is described.     

A Synthesis of (S)-3-(Phenylmethyl)morpholine from (S)-Phenylalanol.

A preparation of (S)-3-(phenylmethyl)morpholine from (S)-phenylalanol is described.     

Decarboxylation of α-Amino Acids Containing Two and Three Stereogenic Centers: A Simple One-Step Procedure to Prepare two Optically Active β-Amino Alcohols and a Bicyclic Pyrrolidine Derivative

The decarboxylation of L-threonine (2S,3R)-1, L-hydroxyproline (2S,4R)-2 and D-2-azabicyclo[3.3.0]octan-3-carboxylic acid (1R,3R,5R)-5 yield in a simple one-step procedure the corresponding optically active β-amino alcohols (R)-3 and (R)-4 and the bicyclic pyrrolidine derivative (1R,5R)-6 in 72–82% yield and >99% ee.     

Small changes—Huge influences: NMR chemical shifts of Ni(II) complexes with polar substrates

Neutral Ni(II) complexes have been shown to be highly valuable as robust and versatile catalysts in olefin polymerization. But they show reduced reactivity when the polar monomers methyl acrylate and vinyl acetate are incorporated. To get further insight into this behavior, NMR chemical shift calculations were performed on the system [(N,O) Ni (H) (PMe3)] 1 (N,O = ‐N,O‐{2,6‐(3,5‐(F3C)2C6H3)2C6H3) NC(H)‐3,5‐I2‐2‐O‐C6H2}). The chemical shifts show reasonable agreement with experiment but are also extremely influenced by geometrical features of the complex as well as the inserted substrate. The first prominent feature, the low‐field shift of the C_carbonyl in the incorporated monomer, can only be reproduced when it is in close proximity to the Ni and in this way hinders the attack of a new monomer. Second, the almost 100 ppm difference in the chemical shift of the carbon of the two substrates directly bound to Ni can be reasoned by the different directionality of polarization as disclosed by natural bond orbital (NBO) analysis. © 2013 Wiley Periodicals, Inc.     

Efficient One‐Pot Four‐Component Synthesis and X‐ray Crystallographic Structure of 2‐Pyridone Derivatives

A series of 3‐cyano‐2‐pyridone derivatives were synthesized by one‐pot four‐component condensation reaction involving a benzaldehyde derivative, alkyl cyanoacetate, acyclic or cyclic ketones, and ammonium acetate in reflux condition. The X‐ray structure of the products 5a and 5d confirm symmetric dimers via hydrogen bonding interactions between individual pyridine molecules showing, in addition, also π–π stacking interactions.     

Convenient preparations of racemic and enantiopure methyl 6-oxopipecolate

Short, convenient syntheses of racemic and enantiopure methyl 6-oxopipecolate are described, starting from either pipecolic acid or (S)-lysine respectively. The sequence for the latter compound relies upon improved methodology for the oxidation of C-6 of lysine.     

Mild,Efficient, and Regioselective Monobromination of Arylamines and Phenols Using [BBIm]Br3 as a New Reagent

We report here an efficient method for the synthesis and characterization of the room-temperature ionic liquid 1,3-di-n-butylimidazolium tribromide ([BBIm]Br₃) (2) and its application as an efficient reagent and solvent for regioselective bromination of arylamines and phenols under mild conditions. The bromination was carried out in the absence of organic solvents, and in most cases, the only extraction solvent needed was water. The spent 1,3-di-n-butylimidazolium bromide (1) was easily recycled.