Similarity between condensed phase and gas phase chemistry: Fragmentation of peptides containing oxidized cysteine residues and its implications for proteomics

Amino acid residues containing thioethers are easily oxidized during protein purification, derivatization, and/or digestion. For instance, oxidation of methionine residues in proteins during SDS-PAGE is commonly observed. Under low energy collision induced dissociation this gives rise to a second series of fragment ion of lower abundance that are shifted by -64 Da when compared to the oxidized methionine-containing fragments. We report here that alkylated cysteine residues can be found in their oxidized form too, indicating that the oxidation of thioethers can occur during and following protein digestion and not only during SDS-PAGE or reduction and alkylation. Collision induced dissociation experiments on the singly- and multiply-charged species reveals that these peptides preferentially undergo elimination reactions that forms a dehydroalanine from the oxidized, alkylated cysteine residue. This contrasts to the less abundant elimination reaction of peptides containing oxidized methionines which cannot form an alpha,beta-unsaturated compound, but parallels the condensed phased chemistry of sulfoxides. The masses of both precursor and product ions are shifted such that these peptides cannot be identified in database searches with current algorithms. Incorporation of this fragmentation pattern is important for the isotope-coded affinity tag approach since this method is based on peptides containing cysteine residues.     

Scattering Theory for Quantum Fields¶with Indefinite Metric

In this work, we discuss the scattering theory of local, relativistic quantum fields with indefinite metric. Since the results of Haag–Ruelle theory do not carry over to the case of indefinite metric [4], we propose an axiomatic framework for the construction of in- and out-states, such that the LSZ asymptotic condition can be derived from the assumptions. The central mathematical object for this construction is the collection of mixed vacuum expectation values of local, in- and out-fields, called the “form factor functional”, which is required to fulfill a Hilbert space structure condition. Given a scattering matrix with polynomial transfer functions, we then construct interpolating, local, relativistic quantum fields with indefinite metric, which fit into the given scattering framework. Received: 13 September 1999/ Accepted: 1 August 2000     

Profiling recombinant major birch pollen allergen Bet v 1a and carbamylated variants with CZE and CIEF

A preparation of recombinant birch pollen allergen of Betula verrucosa isoform 1a (Bet v 1a) containing chemically modified (carbamylated) variants has been analyzed by CZE and CIEF. In CZE, employing a 100 mmol/L MES buffer at pH 6.50, with 0.4 mmol/L tetraethylenepentamine (TEPA) added, allowed for the resolution of 17 protein fractions. The CIEF profiling of the allergen preparation required a combination of a wide-pH-range carrier ampholyte (CA) of pH 3-10 with two narrow-range CAs of pH 5-6 and 5-7. For CIEF, 91 mmol/L of glycine at pH 2.12 and 20 mmol/L of CHES at pH 10.00 were applied as anolyte and catholyte, respectively. The generated pH gradient was nonlinear with a flat slope for pH 4-6, thus providing an improved resolution. In CIEF, up to 18 protein fractions were distinguished as well. The pI of the target allergen Bet v 1a was 4.9 as determined by means of two pI marker compounds flanking the allergen. Relative purity of the target allergen within the preparation containing carbamylated variants was in accordance for both separation systems and varied between 40.7 and 42.8%.     

Abelian Chern-Simons theory, Stokes’ theorem, and generalized connections

Generalized connections and their calculus have been developed in the context of quantum gravity. Here we apply them to abelian Chern-Simons theory. We derive the expectation values of holonomies in U(1) Chern-Simons theory using Stokes’ theorem, flux operators and generalized connections. A framing of the holonomy loops arises in our construction, and we show how, by choosing natural framings, the resulting expectation values nevertheless define a functional over gauge invariant cylindrical functions.The abelian theory considered in the present article is the test case for our method. It can also be applied to the non-abelian theory. Results will be reported in a companion article.     

Uniqueness of Diffeomorphism Invariant States on Holonomy–Flux Algebras

Loop quantum gravity is an approach to quantum gravity that starts from the Hamiltonian formulation in terms of a connection and its canonical conjugate. Quantization proceeds in the spirit of Dirac: First one defines an algebra of basic kinematical observables and represents it through operators on a suitable Hilbert space. In a second step, one implements the constraints. The main result of the paper concerns the representation theory of the kinematical algebra: We show that there is only one cyclic representation invariant under spatial diffeomorphisms.While this result is particularly important for loop quantum gravity, we are rather general: The precise definition of the abstract *-algebra of the basic kinematical observables we give could be used for any theory in which the configuration variable is a connection with a compact structure group. The variables are constructed from the holonomy map and from the fluxes of the momentum conjugate to the connection. The uniqueness result is relevant for any such theory invariant under spatial diffeomorphisms or being a part of a diffeomorphism invariant theory.