Proteome analysis of camptothecin-treated cortical neurons using isotope-coded affinity tags

Isotope-coded affinity tags (ICATs) were employed to identify and quantitate changes in protein expression between control and camptothecin-treated mouse cortical neurons. Proteins extracted from control cortical neurons and those treated with camptothecin were labeled with the light and heavy isotopic versions of the ICAT reagents, respectively. ICAT-labeled samples were combined, proteolytically digested, and the derivatized peptides isolated using immobilized avidin chromatography. The peptides thus isolated were analyzed by reversed-phase liquid chromatography coupled directly to either a conventional ion-trap mass spectrometer (IT-MS) or a Fourier transform ion cyclotron resonance mass spectrometer (FTICR). While a majority of the peptide identifications were accomplished using IT-MS, FTICR was used to quantitate the relative abundances of the ICAT-labeled peptides taking advantage of its high resolution, sensitivity, and duty cycle. By using this combination of MS technologies we have thus far identified and quantified the expression of greater than 125 proteins from control and camptothecin-treated mouse cortical neurons. While proteins from most functional classes of proteins were identified, a particularly large percentage of the enzymes involved in glycolysis and the tricarboxylic acid cycle were observed.     

Clinical and pharmaceutical applications of packed-column supercritical fluid chromatography

Packed-column supercritical fluid chromatography (pSFC) is a fast separation technique that combines the properties of HPLC and GC. pSFC with carbon dioxide as the mobile phase and packed silica column as the stationary phase possesses the properties of normal phase mechanism; however, the addition of modifiers to the mobile phase allows the separation of relatively polar compounds. In spite of its many positive attributes, pSFC has not been widely used in areas such as proteomics, where methods such as HPLC dominate. Packed column SFC has been extensively used in clinical and pharmaceutical laboratories, especially for separation of nonpolar and chiral drugs. This review will discuss recently published applications of pSFC, with a specific focus on its advantages and limitations for the analysis of pharmaceuticals with varying chemical properties.     

Two-dimensional liquid chromatography-capillary zone electrophoresis-sheathless electrospray ionization-mass spectrometry: evaluation for peptide analysis and protein identification

A peptide separation strategy that combines two-dimensional (2-D) liquid chromatography (LC)-capillary zone electrophoresis (CZE) with tandem mass spectrometry (MS/MS) is described for the identification of proteins in complex mixtures. To test the effectiveness of this strategy, a serum sample was depleted of the high-abundance proteins by methanol precipitation, digested with trypsin to generate a complex peptide mixture, and separated into 96 fractions by reversed-phase (RP)-LC. Compared to ion-exchange LC separations, RPLC provides much higher resolution and peak capacity. Fractions were collected off-line from the RPLC separation, and subjected to short 20 min CZE separations. The separated zones were introduced to the mass spectrometer through a sheathless electrospray ionization interface that is integrated on the separation capillary. The ease of fabrication of the interface and its durability allowed for the analysis of all fractions on a single capillary in a relatively short analysis time. A stable electrospray was produced at nanoliter flowrates by augmenting analyte electrophoretic and electroosmotic mobilities with pressure-assisted flow. Unlike first-dimensional ion-exchange LC fractionation, where there is a large degree of overlap, the CZE-MS results show less than 15% overlap between neighboring RPLC fractions.     

RNA-RNA noncovalent interactions investigated by microspray ionization mass spectrometry.

Electrospray ionization mass spectrometry is playing an increasing role in the study of noncovalent interactions involving biomolecules. RNA-RNA complexes are important in many areas of biology, including RNA catalysis, RNA splicing, ribosome function, and gene regulation. Here, microelectrospray mass spectrometry (microESI-MS) is used to study noncovalent base-pairing interactions between RNA oligonucleotides, an area not previously explored by this technique. Using a set of complementary RNA oligonucleotides, we demonstrate the formation of the expected double-helical RNA complexes composed of three distinct oligonucleotides. The ability to study specific RNA noncovalent interactions by microESI-MS has the potential to provide a unique method by which to analyze and assign precise molecular masses to RNA-RNA complexes.     

Chemistry of crown ethers: Synthesis of crown ethers based on α,β-bis(halomethyl)- or α,β-bis(hydroxymethyl)-substituted aromatics

Two types of novel crown ethers in which a polyether chain is linked, via C atoms, with two adjacent C atoms of an aromatic or heteroaromatic ring have been synthesized by reaction of α,β-bis(halomethyl)-substituted aromatics with polyethylene glycolates. Both 1:1 and 2:2 cyclic reaction products were formed, in yields varying from 1 to 53% and from 0 to 24%, respectively. The relatively high yields of these macrocyclic polyethers (rings containing from 11 to 34 atoms), obtained without operating at high dilution, depend both on the chain length of the glycol and on the nature of the cation. This can be explained in terms of a “template” effect of the cation in the cyclization step. Experimental evidence supporting such an effect was obtained from the relationship between the 1:1 product selectivity and the glycol chain length for cations with different ionic radii (L⁺, Na⁺ and K⁺). Furthermore, a correlation has been established between the ratio of the yields of 1:1 and 2:2 cyclic products from the reaction of 1,2-bis(bromomethyl)benzene and dipotassium triethylene glycolate and the ratio of the relative complexation constants of these compounds with potassium salts.     

Rashba spin-splitting control at the surface of the topological insulator Bi2Se3

The electronic structure of Bi(2)Se(3) is studied by angle-resolved photoemission and density functional theory. We show that the instability of the surface electronic properties, observed even in ultrahigh-vacuum conditions, can be overcome via in situ potassium deposition. In addition to accurately setting the carrier concentration, new Rashba-like spin-polarized states are induced, with a tunable, reversible, and highly stable spin splitting. Ab initio slab calculations reveal that these Rashba states are derived from 5-quintuple-layer quantum-well states. While the K-induced potential gradient enhances the spin splitting, this may be present on pristine surfaces due to the symmetry breaking of the vacuum-solid interface.     

Quantitative proteomic analysis of inorganic phosphate-induced murine MC3T3-E1 osteoblast cells

Cleavable isotope-coded affinity tag (cICAT) reagents were utilized to identify and quantitate protein expression differences in control and inorganic phosphate-treated murine MC3T3-E1 osteoblast cells. Proteins extracted from control and treated cells were labeled with the light and heavy isotopic versions of cICAT reagents, respectively. The cICAT-labeled samples were combined, proteolytically digested, and the cICAT-derivatized peptides isolated using immobilized avidin chromatography. The cICAT-labeled peptides were resolved into 96 fractions by strong cation-exchange (SCX) liquid chromatography (LC). Analysis of the SCX-LC cICAT peptide fractions by microcapillary reversed-phase LC-tandem mass spectrometry resulted in the identification and quantitation of 7227 unique peptides corresponding to 2501 proteins, or roughly 9% of the proteins currently predicted to be encoded by the mouse genome. A false positive analysis indicated a 98% confidence in the peptide identifications. To corroborate changes in abundance measured by cICAT with those detectable in traditionally prepared cell lysate, we chose to analyze cyclin D1. Cyclin D1 has been previously identified as a phosphate-responsive gene and was likewise identified as a phosphate-responsive protein in the current analysis. The 1.76-fold increase in abundance in cyclin D1 determined from cICAT corresponds well with the 2.41-fold increase as determined by Western blotting. These results demonstrate that quantitative proteomics is capable of providing a quantitative view of thousands of proteins in mammalian cells within a defined set of experiments.     

Analysis of concentration polarization phenomenon in ultrafiltration under turbulent flow conditions

An ultrafiltration data set previously reported by Gekas and Olund is used to test three concentration polarization models. The data consist of testing eight ultrafiltration membranes representing different polymer materials and molecular weight cut-offs with 0.5 wt% Dextran T10 at 25°C and 0.5 MPa under turbulent flow conditions. The tested concentration polarization models include the modified film theory model, the original film theory model and the Sherwood correlation model. The Chilton-Colburn analogy is the common foundation of the these models.