Quark Structure of the X (4500), X (4700) and χc(4P,5P) States

We study some of the main properties (masses and open-flavor strong decay widths) of 4P and 5P charmonia. While there are two candidates for the χc0(4P,5P) states, the X(4500) and X(4700), the properties of the other members of the χc(4P,5P) multiplets are still completely unknown. With this in mind, we start to explore the charmonium interpretation for these mesons. Our second goal is to investigate if the apparent mismatch between the Quark Model (QM) predictions for χc0(4P,5P) states and the properties of the X(4500) and X(4700) mesons can be overcome by introducing threshold corrections in the QM formalism. According to our coupled-channel model results for the threshold mass shifts, the χc0(5P)→X(4700) assignment is unacceptable, while the χc0(4P)→X(4500) or X(4700) assignments cannot be completely ruled out.

Modelling the vertical motions of the Alboran Sea since the Messinian salinity crisis: Topographic reconstruction and glacial-isostatic sea-level effects

<p>The Messinian Salinity Crisis (MSC) was caused and terminated by changes in the Atlantic-Mediterranean connectivity in the western end of the Alboran Basin, a complex tectonic area affected by the Iberia-Africa collision and the presence of a subducted lithospheric slab beneath the Betic-Rif orogen.</p><p>The isostatic, tectonic and erosional effects on surface topography work on different spatial and temporal scales, and their relative contributions to the changes in connectivity and subsequent evaporite deposition and sea-level drop are difficult to constrain.</p><p>We perform 2D-planform flexural isostatic modeling using the Messinian Erosion Surface imaged in the Alboran Basin to reconstruct the topography and vertical motions of this region since the end of the MSC. The results constrain the original depth of the Messinian erosional features to test their consistency against the various models proposed for Mediterranean sea-level changes during the MSC. <br>We apply Glacial Isostatic Adjustment theory to quantify the time response of these vertical motions to the large MSC-related mass shifts (salinification, evaporite deposition and a kilometer-scale sea-level drop),  and their gravitational effects on sea-level in the Mediterranean. In particular, models for the Strait of Gibraltar allowus to identify the potential role of these effects as feedback mechanisms influencing the rates and duration of changes in the Atlantic-Mediterranean connectivity at the straits.  We will explore the possible implications of these for the timing of the closure of the last Atlantic-Mediterranean seaway.</p>

An integrated strategy reveals complex glycosylation of erythropoietin using top-down and bottom-up mass spectrometry

ABSTRACTThe characterization of glycoproteins, like erythropoietin, is challenging due to the structural micro- and macro-heterogeneity of the protein glycosylation. This study presents an in-depth strategy for glycosylation analysis of a first-generation erythropoietin (epoetin beta), including a developed top-down mass spectrometric workflow for N-glycan analysis, bottom-up mass spectrometric methods for site-specific N-glycosylation and a LC-MS approach for O-glycan identification. Permethylated N-glycans, peptides and enriched glycopeptides of erythropoietin were analyzed by nanoLC-MS/MS and de-N-glycosylated erythropoietin was measured by LC-MS, enabling the qualitative and quantitative analysis of glycosylation and different glycan modifications (e.g., phosphorylation and O-acetylation). Extending the coverage of our newly developed Python script to phosphorylated N-glycans enabled the identification of 140 N-glycan compositions (237 N-glycan structures) from erythropoietin. The site-specificity of N-glycans was revealed at glycopeptide level by pGlyco software using different proteases. In total, 215 N-glycan compositions were identified from N-glycan and glycopeptide analysis. Moreover, LC-MS analysis of de-N-glycosylated erythropoietin species identified two different O-glycan compositions, based on the mass shifts between non-O-glycosylated and O-glycosylated species. This integrated strategy allows the in-depth glycosylation analysis of a therapeutic glycoprotein to understand its pharmacological properties and improving the manufacturing processes.

Decay widths of $$^3 P_J$$ charmonium to $$DD,DD^*,D^*D^*$$ and corresponding mass shifts of $$^3 P_J$$ charmonium

In this work, we calculate the amplitudes of the processes $$c{{\bar{c}}}({^3P_J}) \rightarrow DD,DD^*, D^*D^* \rightarrow c\bar{c}({^3P_J})$$ c c ¯ ( 3 P J ) → D D , D D ∗ , D ∗ D ∗ → c c ¯ ( 3 P J ) in the leading order of the nonrelativistic expansion. The imaginary parts of the amplitudes are corresponding to the branch decay widths of the charmonium $$c{{\bar{c}}}({^3P_J}) \rightarrow DD,DD^*, D^*D^*$$ c c ¯ ( 3 P J ) → D D , D D ∗ , D ∗ D ∗ and the real parts are corresponding to the mass shifts of the charmonium $$c{{\bar{c}}}({^3P_J})$$ c c ¯ ( 3 P J ) due to these decay channels. After absorbing the polynomial contributions which are pure real, the ratios between the branch decay widths and the corresponding mass shifts are only dependent on the center-of-mass energy. We find the decay widths and the mass shifts of the $$^3P_2$$ 3 P 2 states are exact zero in the leading order. The ratios between the branch decay widths and the mass shifts for the $$^3P_0, {^3P_1}$$ 3 P 0 , 3 P 1 states are larger than 5 when the center-of-mass energy is above the $$DD,DD^*, D^*D^*$$ D D , D D ∗ , D ∗ D ∗ threshold. The dependence of the mass shifts on the center-of-mass energy is nontrivial especially when the center-of-mass energy is below the threshold. The analytic results can be extended to the b quark sector directly.

AA_stat enables extensive characterization of artefact and post-translational modifications in bottom-up proteomics

ABSTRACTWe report on AA_stat, a bioinformatic approach for panoramic profiling of artificial and post-translational modifications and their localization sites in large-scale proteomics data. Presented version of AA_stat provides validation of ultra-tolerant (open) search results followed by interpretation of the observed mass shifts and recommendation of the optimized sets of fixed and variable modifications for subsequent regular searches. Localization of modification sites is based on relative amino acid frequencies and analysis of tandem mass spectra. AA_stat determines groups of peptide identifications with mass shifts from the validated results of the open search and then scores each possible mass shift location by matching the MS/MS spectrum across the theoretical peptide isoforms. Here we demonstrate the utility of AA_stat for blind scanning of abundant and rare amino acid modifications of both artificial and biological origins and analyze advantages and limitations of open search strategies. AA_stat is implemented as an open-source command line tool available at https://github.com/SimpleNumber/aa_stat.

Using Biological Signals for Mass Recalibration of Mass Spectrometry Imaging Data

<p>Mass spectrometry imaging (MSI) is a powerful and convenient method to reveal the spatial chemical composition of different biological samples. The molecular annotation of the detected signals is only possible when high mass accuracy is maintained across the entire image and the <i>m/z</i> range. However, the heterogeneous molecular composition of biological samples could result in fluctuations in the detected <i>m/z</i>-values, called mass shift. Mass shifts impact the interpretability of the detected signals by decreasing the number of annotations and by affecting the spatial consistency and accuracy of ion images. The use of internal calibration is known to offer the best solution to avoid, or at least to reduce, mass shifts. The selection of internal calibrating signals for a global MSI acquisition is not trivial, prone to false positive detection of calibrating signals and therefore to poor recalibration. To fill this gap, this work describes an algorithm that recalibrates each spectrum individually by estimating its mass shift with the help of a list of internal calibrating ions generated automatically in a data-adaptive manner. The method exploits RANSAC (<i>Random Sample Consensus</i>) algorithm, to select, in a robust manner, the experimental signal corresponding to internal calibrating signals by filtering out calibration points with infrequent mass errors and by using the remaining points to estimate a linear model of the mass shifts. We applied the method to a zebrafish whole body section acquired at high mass resolution to demonstrate the impact of mass shift on data analysis and the capacity of our algorithm to recalibrate MSI data. We illustrate the broad applicability of the method by recalibrating 31 different public MSI datasets from METASPACE from various samples and types of MSI and show that our recalibration significantly increases the numbers of METASPACE annotations, especially the high-confident annotations at a low false discovery rate.</p>