The effects of mass accuracy,data acquisition speed,and search algorithm choice on peptide identification rates in phosphoproteomics

Proteomic analyses via tandem mass spectrometry have been greatly enhanced by the recent development of fast, highly accurate instrumentation. However, successful application of these developments to high-throughput experiments requires careful optimization of many variables which adversely affect each other, such as mass accuracy and data collection speed. We examined the performance of three shotgun-style acquisition methods ranging in their data collection speed and use of mass accuracy in identifying proteins from yeast-derived complex peptide and phosphopeptide-enriched mixtures. We find that the combination of highly accurate precursor masses generated from one survey scan in the FT-ICR cell, coupled with ten data-dependent tandem MS scans in a lower-resolution linear ion trap, provides more identifications in both mixtures than the other examined methods. For phosphopeptide identifications in particular, this method identified over twice as many unique phosphopeptides as the second-ranked, lower-resolution method from triplicate 90-min analyses (744 ± 50 vs. 308 ± 50, respectively). We also examined the performance of four popular peptide assignment algorithms (Mascot, Sequest, OMSSA, and Tandem) in analyzing the results from both high-and low-resolution data. When compared in the context of a false positive rate of approximately 1%, the performance differences between algorithms were much larger for phosphopeptide analyses than for an unenriched, complex mixture. Based upon these findings, acquisition speed, mass accuracy, and the choice of assignment algorithm all largely affect the number of peptides and proteins identified in high-throughput studies. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Toward a high-throughput approach to quantitative proteomic analysis: Expression-dependent protein identification by mass spectrometry

The isotope-coded affinity tag (ICAT) [1] technology enables the concurrent identification and comparative quantitative analysis of proteins present in biological samples such as cell and tissue extracts and biological fluids by mass spectrometry. The initial implementation of this technology was based on microcapillary chromatography coupled on-line with electrospray ionization tandem mass spectrometry. This implementation lacked the ability to select proteins for identification based on their relative abundance and therefore to focus on differentially expressed proteins. In order to improve the sample throughput of this technology, we have developed a two-step approach that is focused on those proteins for which the abundance changes between samples: First, a new software program for the automated quantification of ICAT reagent labeled peptides analyzed by microcapillary electrospray ionization time-of-flight mass spectrometry determines those peptides that differ in their abundance and second, these peptides are identified by tandem mass spectrometry using an electrospray quadrupole time-of flight mass spectrometer and sequence database searching. Results from the application of this approach to the analysis of differentially expressed proteins secreted from nontumorigenic human prostate epithelial cells and metastatic cancerous human prostate epithelial cells are shown.     

Enhancement of second harmonic generation efficiency: Growth and characterization of magnesium(II)-doped tetrakis(thiourea)nickel(II) chloride crystals

The influence of magnesium doping on the properties of tetrakis(thiourea)nickel(II) chloride crystals has been described. The reduction in the intensity observed in powder X-ray diffraction of doped specimen and slight shifts in vibrational frequencies confirm the lattice stress as a result of doping. Surface morphological changes due to doping of the alkaline earth metal are observed by scanning electron microscopy. The incorporation of Mg(II) into the crystal lattice was confirmed by energy dispersive X-ray spectroscopy. Lattice parameters are determined by single crystal XRD analysis. The thermogravimetric and differential thermal analysis studies reveal the purity of the materials and no decomposition is observed up to the melting point. The crystal is further characterized by Kurtz powder technique and dielectric studies.     

Phenoxythiazoline (FTz)-Cobalt(II) Precatalysts Enable C(sp2)–C(sp3) Bond-Formation for Key Intermediates in the Synthesis of Toll-like Receptor 7/8 Antagonists**

Evaluation of the relative rates of the cobalt-catalyzed C(sp²)–C(sp³) Suzuki–Miyaura cross-coupling between the neopentylglycol ester of 4-fluorophenylboronic acid and N-Boc-4-bromopiperidine established that smaller N-alkyl substituents on the phenoxyimine (FI) supporting ligand accelerated the overall rate of the reaction. This trend inspired the design of optimal cobalt catalysts with phenoxyoxazoline (FOx) and phenoxythiazoline (FTz) ligands. An air-stable cobalt(II) precatalyst, (FTz)CoBr(py)₃ was synthesized and applied to the cross-coupling of an indole-5-boronic ester nucleophile with a piperidine-4-bromide electrophile that is relevant to the synthesis of reported toll-like receptor (TLR) 7/8 antagonist molecules including afimetoran. Addition of excess KOMe⋅B(OⁱPr)₃ improved catalyst lifetime due to attenuation of alkoxide basicity that otherwise resulted in demetallation of the FI chelate. A first-order dependence on the cobalt precatalyst and a saturation regime in nucleophile were observed, supporting turnover-limiting transmetalation and the origin of the observed trends in N-imine substitution.     

Water confined in nanotubes and between graphene sheets: a first principle study

Water confined at the nanoscale has been the focus of numerous experimental and theoretical investigations in recent years, yet there is no consensus on such basic properties as diffusion and the nature of hydrogen bonding (HB) under confinement. Unraveling these properties is important to understand fluid flow and transport at the nanoscale, and to shed light on the solvation of biomolecules. Here we report on a first principle, computational study focusing on water confined between prototypical nonpolar substrates, i.e., single-wall carbon nanotubes and graphene sheets, 1-2.5 nm apart. The results of our molecular dynamics simulations show the presence of a thin, interfacial liquid layer (approximately 5 A) whose microscopic structure and thickness are independent of the distance between confining layers. The properties of the HB network are very similar to those of the bulk outside the interfacial region, even in the case of strong confinement. Our findings indicate that the perturbation induced by the presence of confining media is extremely local in liquid water, and we propose that many of the effects attributed to novel phases under confinement are determined by subtle electronic structure rearrangements occurring at the interface with the confining medium.     

Photoreactive stapled BH3 peptides to dissect the BCL-2 family interactome

Defining protein interactions forms the basis for discovery of biological pathways, disease mechanisms, and opportunities for therapeutic intervention. To harness the robust binding affinity and selectivity of structured peptides for interactome discovery, we engineered photoreactive stapled BH3 peptide helices that covalently capture their physiologic BCL-2 family targets. The crosslinking α helices covalently trap both static and dynamic protein interactors, and enable rapid identification of interaction sites, providing a critical link between interactome discovery and targeted drug design.     

Fluidized and vibrofluidized shallow beds of fresh leaves

The fluid dynamics behavior of shallow fluidized and vibrofluidized beds operating with fresh leaves was investigated with the aim of exploring drying applications in a modified conveyor belt (MCB) system,which may be operated in a fixedor fluidized-bed mode.Leaves of the specimens Duranta repens,Schinus molle,Coleus barbatus,Buxus sempervirens,and Bougainvillea spectabilis were tested with a range of sphericities from 0.063 to 0.213,bulk densities from 0.038 to 0.251 g/cm 3,apparent densities from 0.52 to ...     

Towards an assessment of the accuracy of density functional theory for first principles simulations of water. II

A series of 20 ps ab initio molecular dynamics simulations of water at ambient density and temperatures ranging from 300 to 450 K are presented. Car-Parrinello (CP) and Born-Oppenheimer (BO) molecular dynamics techniques are compared for systems containing 54 and 64 water molecules. At 300 K, an excellent agreement is found between radial distribution functions (RDFs) obtained with BO and CP dynamics, provided an appropriately small value of the fictitious mass parameter is used in the CP simulation. However, we find that the diffusion coefficients computed from CP dynamics are approximately two times larger than those obtained with BO simulations for T>400 K, where statistically meaningful comparisons can be made. Overall, both BO and CP dynamics at 300 K yield overstructured RDFs and slow diffusion as compared to experiment. In order to understand these discrepancies, the effect of proton quantum motion is investigated with the use of empirical interaction potentials. We find that proton quantum effects may have a larger impact than previously thought on structure and diffusion of the liquid.