Phosphopeptide fragmentation and analysis by mass spectrometry

Reversible phosphorylation is a key event in many biological processes and is therefore a much studied phenomenon. The mass spectrometric (MS) analysis of phosphorylation is challenged by the substoichiometric levels of phosphorylation and the lability of the phosphate group in collision‐induced dissociation (CID). Here, we review the fragmentation behaviour of phosphorylated peptides in MS and discuss several MS approaches that have been developed to improve and facilitate the analysis of phosphorylated peptides. CID of phosphopeptides typically results in spectra dominated by a neutral loss of the phosphate group. Several proposed mechanisms for this neutral loss and several factors affecting the extent at which this occurs are discussed. Approaches are described to interpret such neutral loss‐dominated spectra to identify the phosphopeptide and localize the phosphorylation site. Methods using additional activation, such as MS³ and multistage activation (MSA), have been designed to generate more sequence‐informative fragments from the ion produced by the neutral loss. The characteristics and benefits of these methods are reviewed together with approaches using phosphopeptide derivatization or specific MS scan modes. Additionally, electron‐driven dissociation methods by electron capture dissociation (ECD) or electron transfer dissociation (ETD) and their application in phosphopeptide analysis are evaluated. Finally, these techniques are put into perspective for their use in large‐scale phosphoproteomics studies. Copyright © 2009 John Wiley & Sons, Ltd.     

Top–down glycolipidomics: fragmentation analysis of ganglioside oligosaccharide core and ceramide moiety by chip‐nanoelectrospray collision‐induced dissociation MS2–MS6

We developed a straightforward approach for high‐throughput top–down glycolipidomics based on fully automated chip‐nanoelectrospray (nanoESI) high‐capacity ion trap (HCT) multistage mass spectrometry (MSⁿ) by collision‐induced dissociation (CID) in the negative ion mode. The method was optimized and tested on a polysialylated ganglioside fraction (GT1b), which was profiled by MS¹ and sequenced in tandem MS up to MS⁶ in the same experiment. Screening of the fraction in the MS¹ mode indicated the occurrence of six [M ? 2H]^2? ions which, according to calculation, support 13 GT1 variants differing in their relative molecular mass due to dissimilar ceramide (Cer) constitutions. By stepwise CID MS²–MS⁵ on the doubly charged ion at m/z 1077.20 corresponding to a ubiquitous GT1b structure, the complete characterization of its oligosaccharide core including the identification of sialylation sites was achieved. Structure of the lipid moiety was further elucidated by CID MS⁶ analysis carried out using the Y₀ fragment ion, detected in MS⁵, as a precursor. MS⁶ fragmentation resulted in a pattern supporting a single ceramide form having the less common (d20 : 1/18 : 0) configuration. The entire top–down experiment was performed in a high‐throughput regime in less than 3 min of measurement, with an analysis sensitivity situated in the subpicomolar range. Copyright © 2009 John Wiley & Sons, Ltd.     

Hydrophobic guar gum derivatives prepared by controlled grafting processes–Part II: rheological and degradation properties toward fracturing fluids applications

Introduction of polyalkoxyalkyleneamide grafts to guar gum produces new water soluble guar derivatives as described in an earlier publication. 10 In this paper, the rhelogical behavior of these products was explored in more detail at 25 and 65°C. In addition, the viscosity was measured at high temperatures (90 and 120°C) and pressure (150 psi) to partially simulate the down hole conditions of oil wells. Upon treatment with zirconium lactate, the cross‐linked hydrophobically‐modified CMG derivatives exhibited better high‐temperature stability and higher gel viscosities than the corresponding CMHPG derivatives. The cross‐linked gel viscosities indicate that gels will be capable of supporting a high proppant carrying capacity. To facilitate removal of the gels from the formation, the hydrophobically modified derivatives were treated with an enzyme breaker system which produced fragments capable of producing stable emulsions when extracted with toluene. Thus, the clean up process will be enhanced by emulsification of the gel fragments produced by the gel hydrolysis. The low viscosities of the linear derivatives, the rapid formation of high viscosity gels upon cross‐linking and generation of emulsifiers during the gel removal suggest that these new derivatives are good candidates for fracturing fluid applications. Copyright © 2007 John Wiley & Sons, Ltd.     

A property of certain multistage linear programs and some applications

In this paper, we present a property of certain linear multistage problems. To solve them, a method which takes this property into account is presented. It requires the resolution of 2N–1 subproblems, if there areN stages in the original problem. A sufficient condition is given on the matrix of the constraints for the property to be true. When only a submatrix has this property, we propose to use the Dantzig-Wolfe decomposition principle. We then can solve the subproblem with the proposed method. Applications to linear and nonlinear programming are presented.This work was done while the author was Visiting Scholar at the Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California.     

Primal—Dual Constraint Aggregation with Application to Stochastic Programming

The special constraint structure and large dimension are characteristic for multistage stochastic optimization. This results from modeling future uncertainty via branching process or scenario tree. Most efficient algorithms for solving this type of problems use certain decomposition schemes, and often only a part of the whole set of scenarios is taken into account in order to make the problem tractable.We propose a primal–dual method based on constraint aggregation, which constructs a sequence of iterates converging to a solution of the initial problem. At each iteration, however, only a reduced sub-problem with smaller number of aggregate constraints has to be solved. Number of aggregates and their composition are determined by the user, and the procedure for calculating aggregates can be parallelized. The method provides a posteriori estimates of the quality of the current solution approximation in terms of the objective function value and the residual.Results of numerical tests for a portfolio allocation problem with quadratic utility function are presented.     

How to identify dislocations in molecular dynamics simulations?

Dislocations are of great importance in revealing the underlying mechanisms of deformed solid crystals.With the development of computational facilities and technologies,the observations of dislocations at atomic level through numerical simulations are permitted.Molecular dynamics(MD)simulation suggests itself as a powerful tool for understanding and visualizing the creation of dislocations as well as the evolution of crystal defects.However,the numerical results from the large-scale MD simulations are not very illuminating by themselves and there exist various techniques for analyzing dislocations and the deformed crystal structures.Thus,it is a big challenge for the beginners in this community to choose a proper method to start their investigations.In this review,we summarized and discussed up to twelve existing structure characterization methods in MD simulations of deformed crystal solids.A comprehensive comparison was made between the advantages and disadvantages of these typical techniques.We also examined some of the recent advances in the dynamics of dislocations related to the hydraulic fracturing.It was found that the dislocation emission has a significant effect on the propagation and bifurcation of the crack tip in the hydraulic fracturing.     

基于灰色关联法的水平井压裂参数优化研究

针对低渗透薄互砂岩油藏A油田C9区块水平井井区储层物性差、非均质性强、开发难度大等问题,为改善水平井井区开发效果、提高水平井单井产能,应用灰色关联法,结合数值模拟软件,分析影响压裂水平井产能的主要因素,开展水平井压裂参数优化研究,结果表明裂缝半长和裂缝间距是影响压裂水平井产能的主要因素,优选出水平井压裂方案:裂缝半长为150m,裂缝间距为40m,裂缝导流能力为50μm~2·cm;裂缝与水平段夹角为90°.应用灰色关联分析法明确水平井压裂效果的主控因素,为低渗透薄互砂岩油藏现场水平井压裂施工提供了思路和借鉴,具有一定的理论指导意义.     

Transboundary extraction of groundwater in the presence of hydraulic fracturing

We studied transboundary groundwater management problems in the presence of hydraulic fracturing. We found that the presence of risk suggests there should be caution when considering hydraulic fracturing. Our results from the cooperative solution show a decrease in hydraulic fracturing and increase in the steady state survival rate of groundwater. We also provide a Pigouvian type tax that could be imposed on natural gas developers.     

Specific UV photodissociation of tyrosyl-containing peptides in multistage mass spectrometry

UV photodissociation (UVPD) at 262 nm has been carried out on protonated tyrosyl-containing peptides formed by trypsin digestion of apo-transferrin. Under UVPD, the main event is the fragmentation of the C(alpha)-C(beta) bond of the tyrosyl residues leading to a radical ion 107 Da below the precursor ion. The dissociation rate of this specific cleavage appears to be strongly dependent on the peptide sequence and is more prominent on the singly protonated species than on the doubly protonated state. The fragmentation spectra resulting from collisional activation of the protonated even-electron native peptides and of the odd-electron radical species prepared by UVPD are dominated by y-type backbone cleavages. A comparison of their respective y-ion pattern shows complementarities since the combination of both increases the sequence coverage of the peptide sequence. The specific detection of the neutral loss of 107 Da from peptides witnesses the content of at least one tyrosyl residue and, though preliminary, is proposed as a potential new filtering strategy during protein database searching.     

基于DEM-CFD耦合的泵内颗粒流动特性研究

随着我国加快深海、深地资源的开发力度,对此类应用环境下的液体提升泵的可靠性提出了更高的要求。而泵内固体颗粒引起的磨损破坏是其中一个严重问题。本文基于DEM-CFD耦合方法,针对自开发的两级混流泵研究了颗粒在泵内部与流体相互作用下的流动特性和对泵的磨损规律,并基于该泵分析了不同颗粒形状、颗粒浓度下的运动特性和泵磨损分布,发现颗粒主要沿着叶轮工作面以及导叶凹面运动,且随着浓度增加,磨损速率会逐渐达到一个饱和值。本文分析探讨了颗粒在泵内的流动特性、颗粒与叶轮导叶发生碰撞的形式及磨损严重区域,对设计抗磨损多级混流泵提供了理论支撑。