Qualitative improvement and quantitative assessment of N-terminomics.

Proteolysis represents one of the most tightly controlled physiological processes, as proteases create events that will typically commit pathways in an irreversible manner. Despite their implication in nearly all biological systems, our understanding of the role of proteases in disease pathology is often limited. Several approaches to studying proteolytic activity as it relates to biology, pathophysiology, and drug therapy have been published, including the recently described terminal amine isotopic labeling of substrates (TAILS) strategy by Kleifeld and colleagues. Here, we investigate TAILS as a methodology based on targeted enrichment and mass spectrometric detection of endogenous N-terminal peptides from clinically relevant biological samples and its potential to provide quantitative information on proteolysis and elucidation of the protease cleavage sites. While optimizing the most current protocol, by switching to a streamlined one-tube format and simplifying the reagents' removal steps, we demonstrate the advantages over previously published methods and provide solutions to some of the technical challenges presented in the Kleifeld publication. We also identify some of the current and unresolved limitations. We use human plasma as a model system to provide data, which illustrates some of the key analytical parameters of the modified TAILS procedure, including specificity, sensitivity, quantitative precision, and accuracy.

Discovering new bioactive neuropeptides in the striatum secretome using in vivo microdialysis and versatile proteomics.

The striatum, a major component of the brain basal nuclei, is central for planning and executing voluntary movements and undergoes lesions in neurodegenerative disorders such as Huntington disease. To perform highly integrated tasks, the striatum relies on a complex network of communication within and between brain regions with a key role devoted to secreted molecules. To characterize the rat striatum secretome, we combined in vivo microdialysis together with proteomics analysis of trypsin digests and peptidomics studies of native fragments. This versatile approach, carried out using different microdialysis probes and mass spectrometer devices, allowed evidencing with high confidence the expression of 88 proteins and 100 processed peptides. Their secretory pathways were predicted by in silico analysis. Whereas high molecular weight proteins were mainly secreted by the classical mode (94%), low molecular weight proteins equally used classical and non-classical modes (53 and 47%, respectively). In addition, our results suggested alternative secretion mechanisms not predicted by bioinformatics tools. Based on spectrum counting, we performed a relative quantification of secreted proteins and peptides in both basal and neuronal depolarization conditions. This allowed detecting a series of neuropeptide precursors and a 6-fold increase for neurosecretory protein VGF and proenkephalin (PENK) levels. A focused investigation and a long peptide experiment led to the identification of new secreted non-opioid PENK peptides, referred to as PENK 114-133, PENK 239-260, and PENK 143-185. Moreover we showed that injecting synthetic PENK 114-133 and PENK 239-260 into the striatum robustly increased glutamate release in this region. Thus, the combination of microdialysis and versatile proteomics methods shed new light on the secreted protein repertoire and evidenced novel neuropeptide transmitters.

Effect of two different UVA doses on the rabbit cornea and lens.

The aim of the present paper was to examine the irradiation effect of two doses of UVA rays (365 nm) on the rabbit cornea and lens. Corneas of anesthetized adult albino rabbits were irradiated with UVA rays for 5 days (daily dose 1.01 J cm(-2) in one group of rabbits and daily dose 2.02 J cm(-2) in the second group of animals). The third day after the last irradiation, the rabbits were killed, and their eyes were employed for spectrophotometrical, biochemical and immunohistochemical investigations. Normal eyes served as controls. Absorption spectra of the whole corneal centers were recorded over the UV-VIS (visible) spectral range. Levels of antioxidant and prooxidant enzymes, nitric oxide synthases and nitric oxide (indirectly measured as nitrate concentration) were investigated in the cornea. Malondialdehyde, a byproduct of lipid peroxidation, was examined in the cornea and lens. The results show that the staining for endothelial nitric oxide synthase was more pronounced in corneas irradiated with the higher UVA dose. Otherwise, UVA rays at either dose did not significantly change corneal light absorption properties and did not cause statistically significant metabolic changes in the cornea or lens. In conclusion, UVA rays at the employed doses did not evoke harmful effects in the cornea or lens.

Prospects for monolithic nano-LC columns in shotgun proteomics.

We report a premier side-by-side comparison of two leading types of monolithic nano-LC column (silica-C(18), polystyrene) in shotgun proteomics experiments. Besides comparing the columns in terms of the number of peptides from a real-life sample (Arabidopsis thaliana chloroplast) that they identified, we compared the monoliths in terms of peak capacity and retention behavior for standard peptides. For proteomics applications where the mobile phase composition is constrained by electrospray ionization considerations (i.e., there is a restricted choice of ion-pairing modifiers), the polystyrene nano-LC column exhibited reduced identification power. The silica monolith column was superior in all measured values and compared very favorably with traditional packed columns. Finally, we investigated the performances of the monoliths at high flow rates in an attempt to demonstrate their advantages for high-throughput identification.

Light absorption properties of the rabbit cornea repeatedly irradiated with UVB rays.

Under normal conditions, the cornea absorbs the majority of UVB (ultraviolet B, 280-320 nm) rays, which is very important for the protection of the inner eye against their damaging effect. Our previous studies have shown that repeated irradiation of the rabbit cornea with UVB rays for 5 days (daily dose of 1.01 J cm(- 2)) caused photokeratitis accompanied by swelling (hydration) of the corneal stroma, thinning of the corneal epithelium and decrease in antioxidants. The purpose of this study was to examine the light absorption properties of such damaged rabbit cornea. Results of both spectrophotometry of the whole corneal buttons and corneal tissue dissolved in sodium hydroxide show that because of above mentioned disturbances, UVB-irradiated cornea absorbs more light throughout the whole measurable UV-VIS spectral range than the normal cornea. Increased corneal thickness (result of hydration), changes of corneal transparency (the cornea becomes grayish) and some increase in protein content all contribute to the increased light absorption of UVB irradiated corneas. We suggest that the UVB-irradiated cornea, although damaged and nearly without antioxidants, might actually through its higher UV absorbance protect the inner eye against further damage from UVB rays.

Porous polyacrylamide monoliths in hydrophilic interaction capillary electrochromatography of oligosaccharides.

Capillary electrochromatography (CEC) of oligosaccharides in porous polyacrylamide monoliths has been explored. While it is possible to alter separation capacity for various compounds by copolymerization of suitable separation ligands in the polymerization backbone, "blank" acrylamide matrix is also capable of sufficient resolution of oligosaccharides in the hydrophilic interaction mode. The "blank" acrylamide network, formed with a more rigid crosslinker, provides maximum efficiency for separations (routinely up to 350,000 theoretical plates/m for fluorescently-labeled oligosaccharides). These columns yield a high spatial resolution of the branched glycan isomers and large column permeabilities. From the structural point of view, some voids are observable in the monoliths at the mesoporous range (mean pore radius ca. 35 nm, surface area of 74 m2/g), as measured by intrusion porosimetry in the dry state.

Surface morphology of contact lenses probed with microscopy techniques.

The present study is bringing a comparison of surface morphology for various types of contact lenses. A novel method--scanning electron microscopy under aqueous conditions (cryo-SEM)--was tested for visualization of lenses at magnifications up to 2000x. For imaging lens surface on nanometre scale, we employed atomic force microscopy (AFM) in aqueous media. Various materials of lenses, based on silicone hydrogels or conventional hydrogels, were investigated. Total, 10 types of contact lenses from five manufacturers were selected and probed. We found that different methods of lens manufacture (lathe-cutting, cast-moulding, and spin casting) led to different values of surface roughness. In the swollen state, roughness values of lens surfaces lie between 4 and 140 nm. Lenses manufactured by lathe-cutting exhibit notable higher values, so that they could be easily distinguished from others. In cast-moulded lenses, the surface roughness decreased with increasing water content. Moreover, additional treatments of lenses introduced unique structural motifs onto surface. For instance, porous structure was found on lens surface finalized with plasma oxidation.

Automated sample preparation platform for mass spectrometry-based plasma proteomics and biomarker discovery.

The identification of novel biomarkers from human plasma remains a critical need in order to develop and monitor drug therapies for nearly all disease areas. The discovery of novel plasma biomarkers is, however, significantly hampered by the complexity and dynamic range of proteins within plasma, as well as the inherent variability in composition from patient to patient. In addition, it is widely accepted that most soluble plasma biomarkers for diseases such as cancer will be represented by tissue leakage products, circulating in plasma at low levels. It is therefore necessary to find approaches with the prerequisite level of sensitivity in such a complex biological matrix. Strategies for fractionating the plasma proteome have been suggested, but improvements in sensitivity are often negated by the resultant process variability. Here we describe an approach using multidimensional chromatography and on-line protein derivatization, which allows for higher sensitivity, whilst minimizing the process variability. In order to evaluate this automated process fully, we demonstrate three levels of processing and compare sensitivity, throughput and reproducibility. We demonstrate that high sensitivity analysis of the human plasma proteome is possible down to the low ng/mL or even high pg/mL level with a high degree of technical reproducibility.

Topographical properties of polymer films deposited in capillaries for electrophoretic separations of large organic molecules.

Topography and thickness of hydrophilic polymer coatings of fused-silica capillaries for capillary electrophoresis (CE) were investigated using atomic force microscopy (AFM), scanning electron microscopy (SEM), and profilometry. Three hydrogels, poly(2-hydroxyethyl methacrylate) [poly(HEMA)], poly(diethylene glycol monomethacrylate) [poly(DEGMA)], and poly(triethylene glycol monomethacrylate) [poly(TEGMA)], were deposited using two procedures, either by simple physical sorption of the polymers, or by derivatization of the capillary wall surface with glycidyl methacrylate (EPMA) followed by polymerization of the appropriate monomers. The performance of the modified capillaries was tested under CE conditions (decrease in the electroosmotic flow, EOF dependence on pH, separation of milk and standard proteins). It has been found that the most important property of the polymer coating is its thickness, whereas its topography and the degree of its hydrophobicity are less significant. Film deposition by physical adsorption is preferable to polymerization on the derivatized surface.

Modification of capillary electrophoresis capillaries by poly(hydroxyethyl methacrylate), poly(diethylene glycol monomethacrylate) and poly(triethylene glycol monomethacrylate).

Modification of capillary electrophoresis (CE) capillaries by poly(hydroxyethyl methacrylate) (poly(HEMA), poly(diethylene glycol monomethacrylate) (poly(DEGMA) and poly(triethylene glycol monomethacrylate) (poly(TEGMA), was studied. Methods based on physical adsorption of the modifier and on its chemical binding were compared on the basis of the electroosmotic flow (EOF) reproducibility, the EOF dependence on the pH, the symmetry of the peak of positively charged tyramine, the stability of the coating and the separation of standard and milk proteins in the modified capillaries. Reproducible coatings were obtained by chemical binding of the polymers to the capillary walls and by coating with a solution of a polymer, as also demonstrated by the atomic force microscopy.