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Site-specific glycopeptide mapping for simultaneous glycan and peptide characterization by MS is difficult because of the heterogeneity and diversity of glycosylation in proteins and the lack of complete fragmentation information for either peptides or glycans with current fragmentation technologies. Indeed, multiple peptide and glycan combinations can readily match the same mass of glycopeptides even with mass errors less than 5 ppm providing considerably ambiguity and analysis of complex mixtures of glycopeptides becomes quite challenging in the case of large proteins. Here we report a novel strategy to reliably determine site-specific N-glycosylation mapping by combining collision-induced dissociation (CID)-only fragmentation with chromatographic retention times of glycopeptides. This approach leverages an experimental pipeline with parallel analysis of glyco- and deglycopeptides. As the test case we chose ABCA4, a large integral membrane protein with 16 predicted sites for N-glycosylation. Taking advantage of CID features such as high scan speed and high intensity of fragment ions together combined with the retention times of glycopeptides to conclusively identify the non-glycolytic peptide from which the glycopeptide was derived, we obtained virtually complete information about glycan compositions and peptide sequences, as well as the N-glycosylation site occupancy and relative abundances of each glycoform at specific sites for ABCA4. The challenges provided by this example provide guidance in analyzing complex relatively pure glycoproteins and potentially even more complex glycoprotein mixtures. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Ambiguity remains in the models explaining the photoinduced dynamics in pentacene thin films as observed in pump-probe experiments. One model advocates exciton fission as governing the evolution of the initially excited species, whereas the other advocates the formation of an excimeric species subsequent to excitation. On the basis of calculations by a combined quantum mechanics and molecular mechanics (QM/MM) method and general considerations regarding the excited states of pentacene we propose an alternative, where the initially excited species instead undergoes internal conversion to a doubly excited exciton. The conjecture is supported by the observed photophysical properties of pentacene from both static as well as time-resolved experiments. [ABSTRACT FROM AUTHOR]

There remain several ambiguities in the literature regarding the dominating sorption mechanisms involved in gas/particle partitioning, particularly for polar and ionizable compounds. The various hypothetical mechanisms would depend differently on relative humidity (RH) and the presence of various aerosol components. Thus, in order to resolve these ambiguities, here we measured the RH-dependency of gas/particle partitioning constants, Kip, for four diverse aerosol samples and a large set of chemicals covering apolar, polar, and ionizable organic compounds. In addition, we also removed the water-soluble components from two ambient particle samples to study how their presence influences sorption behavior. The measured Kip values collectively indicate that a dual-phase sorption mechanism is occurring, in which organic compounds partition into a RH-independent water-insoluble organic matter phase and additionally into a RH-dependent mixed-aqueous phase. All Kip values could be successfully fitted to a RH-dependent dual-phase sorption model. The trends in Kip data further support findings that the sorption behavior of ambient aerosol samples is different from raw mineral surfaces and soot. [ABSTRACT FROM AUTHOR]

In a wide variety of proteins, insolubility presents a challenge to structural biology, as X-ray crystallography and liquid-state NMR are unsuitable. Indeed, no general approach is available as of today for studying the three-dimensional structures of membrane proteins and protein fibrils. We here demonstrate, at the example of the microcrystalline model protein Crh, how high-resolution 3D structures can be derived from magic-angle spinning solid-state NMR distance restraints for fully labeled protein samples. First, we show that proton-mediated rare-spin correlation spectra, as well as carbon-13 spin diffusion experiments, provide enough short, medium, and long-range structural restraints to obtain high-resolution structures of this 2 × 10.4 kDa dimeric protein. Nevertheless, the large number of 13C/15N spins present in this protein, combined with solid-state NMR line widths of about 0.5-1 ppm, induces substantial ambiguities in resonance assignments, preventing 3D structure determination by using distance restraints uniquely assigned on the basis of their chemical shifts. In the second part, we thus demonstrate that an automated iterative assignment algorithm implemented in a dedicated solid-state NMR version of the program ARIA permits to resolve the majority of ambiguities and to calculate a de novo 3D structure from highly ambiguous solid-state NMR data, using a unique fully labeled protein sample. We present, using distance restraints obtained through the iterative assignment process, as well as dihedral angle restraints predicted from chemical shifts, the 3D structure of the fully labeled Crh dimer refined at a root-mean-square deviation of 1.33 Å. [ABSTRACT FROM AUTHOR]

Model fitting to small-angle scattering patterns from a series of dilute sodium- and cesium alkyl sulfate micellar solutions results in two significantly different sets of best-fit parameters for each solution. One of the sets defines nearly monodisperse prolate ellipsoids; the other defines slightly, but significantly, polydisperse oblate ellipsoids. In the prolate and oblate minimum locations, the mean form and structure factors as well as the mean core volumes are equal within the experimental error such that the axial ratios are approximately the reciprocals of each other. The experimental finding is numerically generalized:  it is demonstrated that, in a Qrange, the upper limit of which depends on the axial ratio, the squared mean and the mean square of the scattering amplitude from homogeneous ellipsoids with equatorial radii and axial ratios, respectively (r,) and (r23,1/), are indistinguishable in practice. In dilute solutions without added salt, neither the best-fit values of the model parameters nor the available thermodynamic models provide direct evidence for the conformation, although the prolate ellipsoidal shape is indirectly supported by experiment. The elongated conformation of ionic micelles in dense and/or salinated systems seems realistic. [ABSTRACT FROM AUTHOR]

A large fraction of observed fragment ion intensity remains unidentified in top-down proteomics. The elucidation of these unknown fragment ions could enable researchers to identify additional proteoforms and reduce proteoform ambiguity in their analyses. Internal fragment ions have received considerable attention as a major source of these unidentified fragment ions. Internal fragments are product ions that contain neither protein terminus, in contrast with terminal ions that contain a single terminus. There are many more possible internal fragments than terminal fragments, and the resulting computational complexity has historically limited the application of internal fragment ions to low-complexity samples containing only one or a few proteins of interest. We implemented internal fragment ion functionality in MetaMorpheus to allow the proteome-wide annotation of internal fragment ions. MetaMorpheus first uses terminal fragment ions to identify putative proteoforms and then employs internal fragment ions to disambiguate similar proteoforms. In the analysis of mammalian cell lysates, we found that MetaMorpheus could disambiguate over half of its previously ambiguous proteoforms while also providing up to a 7% increase in proteoform-spectrum matches identified at a 1% false discovery rate.

The article discusses the ambiguities in chemical kinetics rates and rate constants. Reaction rate laws and rate constants are determined by following the temporal changes in the concentration or pressures of reactants or products. With respect to different physical rates, to define reaction rates and rate constants unambiguously, it is required to adopt a convention. The reaction rates and rate constants constitute conventional quantities. The investigators have concluded that only two of texts have all aspects of the problem was essentially correct, after examining general chemistry texts widely used in the instruction of science and pre-medical students.

Glycopeptides identified by tandem mass spectrometry rely on the identification of the peptide backbone sequence and the attached glycan(s) by the incomplete fragmentation of both moieties. This may lead to ambiguous identifications where multiple structures could explain the same spectrum equally well due to missing information in the mass spectrum or incorrect precursor mass determination. To date, approaches to solving these problems have been limited, and few inroads have been made to address these issues. We present a technique to address some of these challenges and demonstrate it on previously published data sets. We use a linear modeling approach to learn the influence of the glycan composition on the retention time of a glycopeptide and use these models to validate glycopeptides within the same experiment, detecting over 400 incorrect cases during the MS/MS search and correcting 75 cases that could not be identified based on mass alone. We make this technique available as a command line executable program, written in Python and C, freely available at https://github.com/mobiusklein/glycresoft in source form, with precompiled binaries for Windows.

The article focuses on a report regarding the language-related confusion that students have in understanding the concept of the word neutral. It states that the report summarizes the results of interviews on 20 lower- and upper-division chemistry students. It mentions that results of the interview suggest that the word neutral was unconsciously being conveyed as unreactive or at equilibrium. It adds that some students even mix the scientific meanings of neutral, which are uncharged and neither acidic nor basic. It concludes that understanding the colloquial and scientific meanings of a word presents a roadblock to the students' understanding of some concepts in science and the responsibility now lies with the instructors to clarify this ambiguity to students.