Top-Down Mass Analysis of Protein Tyrosine Nitration: Comparison of Electron Capture Dissociation with “Slow-Heating” Tandem Mass Spectrometry Methods

Tyrosine nitration in proteins is an important post-translational modification (PTM) linked to various pathological conditions. When multiple potential sites of nitration exist, tandem mass spectrometry (MS/MS) methods provide unique tools to locate the nitro-tyrosine(s) precisely. Electron capture dissociation (ECD) is a powerful MS/MS method, different in its mechanisms to the “slow-heating” threshold fragmentation methods, such as collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD). Generally, ECD provides more homogeneous cleavage of the protein backbone and preserves labile PTMs. However recent studies in our laboratory demonstrated that ECD of doubly charged nitrated peptides is inhibited by the large electron affinity of the nitro group, while CID efficiency remains unaffected by nitration. Here, we have investigated the efficiency of ECD versus CID and IRMPD for top-down MS/MS analysis of multiply charged intact nitrated protein ions of myoglobin, lysozyme, and cytochrome c in a commercial Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. CID and IRMPD produced more cleavages in the vicinity of the sites of nitration than ECD. However the total number of ECD fragments was greater than those from CID or IRMPD, and many ECD fragments contained the site(s) of nitration. We conclude that ECD can be used in the top-down analysis of nitrated proteins, but precise localization of the sites of nitration may require either of the “slow-heating” methods

On Fabry P\'erot Etalon based Instruments. I. The Isotropic Case

Here we assess the spectral and imaging properties of Fabry P\'erot etalons when located in solar magnetographs. We discuss the chosen configuration (collimated or telecentric) for both ideal and real cases. For the real cases, we focus on the effects caused by the polychromatic illumination of the filter by the irregularities in the optical thickness of the etalon and by deviations from the ideal illumination in both setups. We first review the general properties of Fabry P\'erots and we then address the different sources of degradation of the spectral transmission profile. We review and extend the general treatment of defects followed by different authors. We discuss the differences between the point spread functions (PSFs) of the collimated and telecentric configurations for both monochromatic and (real) quasi-monochromatic illumination of the etalon. The PSF corresponding to collimated mounts is shown to have a better performance, although it varies from point to point due to an apodization of the image inherent to this configuration. This is in contrast to the (perfect) telecentric case, where the PSF remains constant but produces artificial velocities and magnetic field signals because of its strong spectral dependence. We find that the unavoidable presence of imperfections in the telecentrism produces a decrease of flux of photons and a shift, a broadening and a loss of symmetrization of both the spectral and PSF profiles over the field of view, thus compromising their advantages over the collimated configuration. We evaluate these effects for different apertures of the incident beam.Comment: 20 pages 22 figures 2 Appendice

A Theoretical Framework for Lagrangian Descriptors

This paper provides a theoretical background for Lagrangian Descriptors (LDs). The goal of achieving rigourous proofs that justify the ability of LDs to detect invariant manifolds is simplified by introducing an alternative definition for LDs. The definition is stated for $n$-dimensional systems with general time dependence, however we rigorously prove that this method reveals the stable and unstable manifolds of hyperbolic points in four particular 2D cases: a hyperbolic saddle point for linear autonomous systems, a hyperbolic saddle point for nonlinear autonomous systems, a hyperbolic saddle point for linear nonautonomous systems and a hyperbolic saddle point for nonlinear nonautonomous systems. We also discuss further rigorous results which show the ability of LDs to highlight additional invariants sets, such as $n$-tori. These results are just a simple extension of the ergodic partition theory which we illustrate by applying this methodology to well-known examples, such as the planar field of the harmonic oscillator and the 3D ABC flow. Finally, we provide a thorough discussion on the requirement of the objectivity (frame-invariance) property for tools designed to reveal phase space structures and their implications for Lagrangian descriptors

Evershed clouds as precursors of moving magnetic features around sunspots

The relation between the Evershed flow and moving magnetic features (MMFs) is studied using high-cadence, simultaneous spectropolarimetric measurements of a sunspot in visible (630.2 nm) and near-infrared (1565 nm) lines. Doppler velocities, magnetograms, and total linear polarization maps are calculated from the observed Stokes profiles. We follow the temporal evolution of two Evershed clouds that move radially outward along the same penumbral filament. Eventually, the clouds cross the visible border of the spot and enter the moat region, where they become MMFs. The flux patch farther from the sunspot has the same polarity of the spot, while the MMF closer to it has opposite polarity and exhibits abnormal circular polarization profiles. Our results provide strong evidence that at least some MMFs are the continuation of the penumbral Evershed flow into the moat. This, in turn, suggests that MMFs are magnetically connected to sunspots.Comment: To appear in ApJ Letters, Vol 649, 2006 September 20 issu

The formation and disintegration of magnetic bright points observed by Sunrise/IMaX

The evolution of the physical parameters of magnetic bright points (MBPs) located in the quiet Sun (mainly in the interwork) during their lifetime is studied. First we concentrate on the detailed description of the magnetic field evolution of three MBPs. This reveals that individual features follow different, generally complex, and rather dynamic scenarios of evolution. Next we apply statistical methods on roughly 200 observed MBP evolutionary tracks. MBPs are found to be formed by the strengthening of an equipartition field patch, which initially exhibits a moderate downflow. During the evolution, strong downdrafts with an average velocity of 2.4 km/s set in. These flows, taken together with the concurrent strengthening of the field, suggest that we are witnessing the occurrence of convective collapses in these features, although only 30% of them reach kG field strengths. This fraction might turn out to be larger when the new 4 m class solar telescopes are operational as observations of MBPs with current state of the art instrumentation could still be suffering from resolution limitations. Finally, when the bright point disappears (although the magnetic field often continues to exist) the magnetic field strength has dropped to the equipartition level and is generally somewhat weaker than at the beginning of the MBP's evolution. Noteworthy is that in about 10% of the cases we observe in the vicinity of the downflows small-scale strong (exceeding 2 km/s) intergranular upflows related spatially and temporally to these downflows.Comment: 19 pages, 13 figures; final version published in "The Astrophysical Journal