Phosphorylation site localization in peptides by MALDI MS/MS and the Mascot Delta Score

Owing to its broad biological significance, the large-scale analysis of protein phosphorylation is more and more getting into the focus of proteomic research. Thousands of phosphopeptides can nowadays be identified using state-of-the-art tandem mass spectrometers in conjunction with sequence database searching, but localizing the phosphate group to a particular amino acid in the peptide sequence is often still difficult. Using 180 individually synthesized phosphopeptides with precisely known phosphorylation sites (p-sites), we have assessed the merits of the Mascot Delta Score (MD score) for the assignment of phosphorylation sites from tandem mass spectra (MS/MS) generated on four different matrix-assisted laser desorption ionization (MALDI) mass spectrometers including tandem time-of-flight (TOF/TOF), quadrupole time-of-flight, and ion trap mass analyzers. The results show that phosphorylation site identification is generally possible with false localization rates of about 10%. However, a comparison to previous work also revealed that phosphorylation site determination by MALDI MS/MS is less accurate than by ESI-MS/MS particularly if several and/or adjacent possible phosphorylation acceptor sites exist in a peptide sequence. We are making the tandem MS spectra and phosphopeptide collection available to the community so that scientists may adapt the MD scores reported here to their analytical environment and so that informatics developers may integrate the MD score into proteomic data analysis pipelines.     

in situ FTIR Spectroscopic Characterization of Absorbed Species on Carbon Electrode,Part II: TCNE Anion Radical from Acetonitrile Solution

The reduction of tetracyanoethylene (TCNE) to its anion radicals on glassy carbon has been studied using in situ FTIR spectroscopy. In contrast to its adsorption behavior on a platinum electrode, TCNE was found to adsorb on a carbon surface not only as the dianion but also as the tricyanovinyl alcoholate (TVA) ion. A mechanism for the formation of the TVA ion involving the presence of surface functional groups on the carbon electrode is proposed.     

Photoisomerizable and Thermoresponsive N‐isopropylacrylamide–Surfmer Copolymer Hydrogels Prepared upon Electrostatic Self‐Assembly of an Azobenzene Bolaamphiphile

Photoreactive and thermoresponsive N‐isopropylacrylamide (NIPAM)–surfmer copolymer hydrogels containing 4,4′‐di(6‐sulfato‐hexyloxy)azobenzene (DSHA) dianions are described. The functional hydrogels are obtained in a two steps. First a micellar aqueous solution of (11‐(acryloyloxy)undecyl)trimethylammonium bromide (AUTMAB) and NIPAM is exposed to ⁶⁰Co‐gamma irradiation, and a thermoresponsive copolymer gel is obtained. Second, DSHA is included by shrinking the gel at 50 °C and subsequent reswelling in an aqueous solution of DSHA disodium salt at 20 °C. Reswelling is accompanied by electrostatic adsorption of DSHA dianions at the positively charged AUTMAB headgroups replacing the bromide ions. Gels containing trans‐DSHA are transparent yellow at room temperature (λ_max = 370 nm), while gels containing cis‐rich DSHA are orange (λ_max = 460 and 330 nm). Energy dispersive X‐ray measurements indicate that 41% of the bromide ions are exchanged if trans‐DSHA is used for adsorption, and only 7.5% if cis‐DSHA is used. The incorporation of DSHA lowers the lower critical solution temperature (LCST) from 34 to 32 °C. Below the LCST, DSHA can be switched from the trans‐ to the cis‐rich state and vice versa upon irradiation with UV (λ = 366 nm) or visible light (λ ≥ 450 nm). Above the LCST no photoreaction takes place.     

A Facile Route to Viologen Functional Macromolecules through Azide–Alkyne [3+2] Cycloaddition

Viologen end and side‐chain functional macromolecules are synthesized through a high‐yielding, copper‐mediated azide–alkyne [3+2] cycloaddition reaction. Specifically, poly(ethylene glycol) (PEG) and the C‐terminus of a model oligopeptide are quantitatively end‐coupled to a viologen moiety as confirmed by ¹H NMR, gel permeation chromatography (GPC), and mass spectrometry (MS). Side‐chain functionalization of a styrene backbone is also readily achieved forming a polyelectrolyte species and demonstrating the applicability of this method across a range of macromolecular species. It is found that viologen itself slows the reaction and that careful choice of counter ions, the specific chelating ligand for the copper‐mediated reaction, solvent, as well as the amount of copper also play major roles in the time to completion of the reaction and hence the yield. Macromolecules formed through this route bind effectively with supramolecular host molecule cucurbit[8]uril allowing for controlled solution‐phase self‐assembly, for example of a supramolecular star polymer.

     

Comparison of multilayer formation between different cellulose nanofibrils and cationic polymers

The multilayer formation between polyelectrolytes of opposite charge offers possibility for creating new tailored materials. Exchanging one or both components for charged nanofibrillated cellulose (NFC) further increases the variety of achievable properties. We explored this by introducing unmodified, low charged NFC and high charged TEMPO-oxidized NFC. Systematic evaluation of the effect of both NFC charge and properties of cationic polyelectrolytes on the structure of the multilayers was performed. As the cationic component cationic NFC was compared with two different cationic polyelectrolytes, poly(dimethyldiallylammoniumchloride) and cationic starch. Quartz crystal microbalance with dissipation (QCM-D) was used to monitor the multilayer formation and AFM colloidal probe microscopy (CPM) was further applied to probe surface interactions in order to gain information about fundamental interactions and layer properties. Generally, the results verified the characteristic multilayer formation between NFC of different charge and how the properties of formed multilayers can be tuned. However, the strong nonelectrostatic affinity between cellulosic fibrils was observed. CPM measurements revealed monotonically repulsive forces, which were in good correspondence with the QCM-D observations. Significant increase in adhesive forces was detected between the swollen high charged NFC.     

Formation of Cocrystals between Alkali Triazine Tricarboxylates and Cyanuric Acid – Reactivity Considerations and Structural Characterization of the Adduct Phases M3[C3N3(CO2)3][C3N3O3H3]·H2O (M = K,Rb)

The reactivity of cyanuric acid towards alkali triazinetricarboxylates was investigated and the first triazine‐triazine adduct phases comprising alkali metal ions were synthesized and characterized by single‐crystal X‐ray diffraction and thermal analysis. An investigation of the reaction between the alkali triazine tricarboxylates M₃[C₃N₃(CO₂)₃] · xH₂O (M = Li, Na, K, Rb, Cs) and cyanuric acid showed that the degree of ion transfer from triazine tricarboxylate to cyanuric acid increases gradually from the lithium to the cesium salt reflecting an increasing basicity of the triazine tricarboxylates.The reaction of potassium and rubidium triazine tricarboxylate dihydrate with cyanuric yielded the novel co‐crystalsK₃[C₃N₃(CO₂)₃][C₃N₃O₃H₃] · H₂O ( 3a ) and Rb₃[C₃N₃(CO₂)₃][C₃N₃O₃H₃] · H₂O ( 3b ). In comparison to metal free triazine‐triazine adduct phases in these compounds the assembly of molecules in the crystal is mainly determined by Coulomb interactions and only to a certain degree by hydrogen bonds and dispersive interactions. In the crystal the s‐triazine units exhibit a layered structure with triazine tricarboxylate and isocyanuric acid being arranged in zigzag strands within the layers and stacked in columns perpendicular to the layers. Thermal analysis revealed a quite weak cohesion between triazine tricarboxylate and cyanuric acid upon heating.     

Evaluation of low-cost disposable polymeric materials for sorptive extraction of organic pollutants in water samples

The capabilities of four commercially available and low cost polymeric materials for the extraction of polar and non-polar contaminants (log K_ow = −0.07–6.88, from caffeine to octocrylene, respectively) from water samples was compared. Tested sorbents were polyethersulphone, polypropylene and Kevlar, compared to polydimethylsiloxane as reference material. Parameters that affect the extraction process such as pH and ionic strength of the sample, extraction time and desorption conditions were thoroughly investigated. A set of experimental partition coefficients (K_pw), at two different experimental conditions, was estimated for the best suited materials and compared with the theoretical octanol–water (K_ow) partition coefficients of the analytes. Polyethersulphone displayed the largest extraction yields for both polar and non-polar analytes, with higher K_pw and lower matrix effects than polydimethylsiloxane and polypropylene. Thus, a sorptive microextraction method, followed by large volume injection (LVI) gas chromatography–tandem mass spectrometry (GC–MS/MS), was proposed using the former sorbent (2 mg) for the simultaneous determination of model compounds in water samples. Good linearity (>0.99) was obtained for most of the analytes, except in the case of 4-nonylphenol (0.9466). Precision (n = 4) at 50 and 500 ng L⁻¹ levels was in the 2–24% and limits of detection (LODs) were in the 0.6–25 ng L⁻¹ range for all the analytes studied.     

Tetrakis(diisopropyl amide) substituted norbornadiene and quadricyclane are highly barium selective ligands

Tetrakis(diisopropyl amide) substituted norbornadiene and quadricyclane derivatives were investigated for their extraction and transport capabilities with alkaline earth metal cations. Both amides exhibited a remarkably high preference of Ba(2+) over any other alkali metal or alkaline earth cation. The binding geometries were determined by quantum chemical DFT calculations.