Electron capture/transfer versus collisionally activated/induced dissociations: Solo or duet?

New ion fragmentation technologies--electron capture dissociation (ECD) and electron-transfer dissociation (ETD)--are based on interaction of multiply charged polypeptides with either free electrons (ECD) or anionic species (ETD). After initial difficulties, these ECD/ETD (ExD) technologies are now being increasingly implemented in high-throughput proteomics work. This critical analysis presents arguments for the combined use of ExD with the conventional low-energy collisional excitation CID/CAD (CxD). It is argued that the database search, a key technology in MS/MS-based proteomics, is vulnerable with respect to the incomplete sequence information obtainable with either of the techniques, peptide MS/MS homology being a major complicating factor. De novo sequencing is viewed as the only adequate answer to this challenge and it can be achieved only with combined use of ExD and CxD. The payoff in the form of additional sequence information is projected to exceed the costs of such implementation. The greatest impact of combining ExD and CxD is expected in high-resolution instruments.     

Electron capture dissociation of weakly bound polypeptide polycationic complexes

We have previously reported that, in electron capture dissociation (ECD), rupture of strong intramolecular bonds in weakly bound supramolecular aggregates can proceed without dissociation of weak intermolecular bonds. This is now illustrated on a series of non-specific peptide-peptide dimers as well as specific complexes of modified glycopeptide antibiotics with their target peptide. The weak nature of bonding is substantiated by blackbody infrared dissociation, low-energy collisional excitation and force-field simulations. The results are consistent with a non-ergodic ECD cleavage mechanism.     

Mass spectrometric study of peptides secreted by the skin glands of the brown frog Rana arvalis from the Moscow region

A high‐performance liquid chromatography nano‐electrospray ionization Fourier transform mass spectrometry (HPLC/nanoESI‐FTMS) approach involving recording of collision‐activated dissociation (CAD) and electron‐capture dissociation (ECD) spectra of an intact sample and two its modifications after performic oxidation and reduction followed by carboxamidomethylation helps to establish peptide profiles in the crude secretion of frog species at mid‐throughput level, including de novo sequencing. The proposed derivatization procedures allow increasing of the general sequence coverage in the backbone, providing complementary information and, what is more important, reveal the amino acid sequence in the cystine ring (‘rana box’). Thus purely mass spectrometric efficient sequencing becomes possible for longer than usual proteolytic peptides. Seventeen peptides belonging to four known families were identified in the secretion of the European brown frog Rana arvalis inhabiting the Moscow region in Russia. Ranatuerins, considered previously a unique feature of the North American species, as well as a new melittin‐related peptide, are worth special mention. The developed approach was previously successfully used for the identification of peptides in the skin secretion of the Caucasian green frog Rana ridibunda. Copyright © 2009 John Wiley & Sons, Ltd.     

Rheological properties of polydisperse magnetic fluids. Effect of chain aggregates

A theoretical model of medium-density polydisperse magnetic fluids is proposed. The model takes into account that the major fraction of particles in typical ferrofluids is characterized by a magnetic core diameter of about 10 nm. In addition, there is a certain proportion of large particles with a core diameter of about 16 nm. As a result of the magnetic dipole interaction, the large particles form chain aggregates. Small particles, for which the magnetic dipole interaction energy (both with each other and with large particles) is smaller than the thermal energy, remain in the individual nonaggregated state. The distribution of chains with respect to the number of (large) particles and some rheological characteristics of the ferrofluids are determined. The proposed model is capable of explaining, in principle, the giant magnetoviscosity effect and a strong dependence of the rheological properties of ferrofluids on the shear rate observed in some recent experiments.     

Dynamics of the free surface of a conducting liquid in a near-critical electric field

Near-critical behavior of the free surface of a perfectly conducting liquid in an external electric field is considered. Based on an analysis of three-wave processes using the method of integral estimates, sufficient criteria for hard instability of a planar surface are formulated. It is shown that the higher-order nonlinearities do not saturate the instability, for which reason the growth of disturbances has an explosive character.     

Applicability of the critical chromatography concept to proteomics problems: Experimental study of the dependence of peptide retention time on the sequence of amino acids in the chain

Experimental data on the separation of synthetic and natural peptides are presented as treated in terms of the separation model proposed by the authors, which allows for the chain connectivity of amino acid residues and the cooperative character of their interaction with the surface. It was shown that the model accurately predicts the separation of peptides with identical amino acid contents and different sequences of units in the chain. The differences in the sequence may be permutation of amino acid residues and the presence of terminal groups, amino acid isomers, or mirror sequences in the chain. The separation model was used to predict the retention times of peptides prepared via the enzymatic hydrolysis of E. coli proteins and bovine serum albumin with trypsin. It was shown that in general the model accurately explains the array of experimental data on the separation of such peptides, thus being the first successful attempt to relate the chain sequence to the retention volume.     

Structural transformations in magnetic suspensions

Structural transformations in dispersions of micron-sized iron particles suspended in a magnetite ferrofluid (the colloidal suspension of ferromagnetic nanoparticles in nonmagnetic liquid) are theoretically considered. An attempt is made to explain the tendency of iron particles to form doublets and longer chain aggregates with finite distance between particles in external magnetic field observed in recent experiments; in colloidal ferrofluid, micron-sized iron particles approach one another to finite distance that is equal approximately to the particle diameter. At moderate magnetic fields, minimal distance between approached particles is nearly independent of the strength of magnetic field. In ordinary magnetorheological dispersions, which are suspensions of magnetizing micron-sized particles in nonmagnetic liquid, the approach of particles practically does not occur up to their physical contact.     

Two-parametric family of exact solutions for the profile of the surface of a conducting liquid in a nonuniform electric field

Possible equilibrium configurations of the free surface of a conducting liquid in an external nonuniform electric field are investigated. The liquid is at the tip of a wedge-shaped electrode, and the counter-elecrode is a thin straight conducting filament parallel to the edge of the wedge. The conformal mapping method is used to obtain a two-parametric family of exact solutions for the shape of the surface. The solutions describe the deformation of the surface right to separation of a drop from the electrode.