Charge-remote fragmentation of odd-electron peptide ions

Comparison between the gas-phase fragmentation of odd-electron M+*, [M + H]2+*, and [M - 2H]-* ions of model peptides suggests that charge-remote radical-driven fragmentation pathways play an important role in the dissociation of odd-electron peptide ions. We have found that charge-remote processes are responsible for a variety of side-chain losses from the precursor ion and some backbone fragmentation. These fragmentation pathways most likely involve hydrogen abstraction by the radical site that initiates subsequent cleavages. These findings are generally relevant to our understanding of the fragmentation patterns of odd-electron peptide ions produced through various approaches including the capture of low-energy electrons, electron detachment, and electron transfer.     

Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions

Most algorithms for identifying peptides from tandem mass spectra use information only from the final spectrum, ignoring non-mass-based information acquired routinely in liquid chromatography tandem mass spectrometry analyses. One physiochemical property that is always obtained but rarely exploited is peptide chromatographic retention time. Efforts to use chromatographic retention time to improve peptide identification are complicated because of the variability of retention time in different experimental conditions-making retention time calculations nongeneralizable. We show that peptide retention time can be reliably predicted by training and testing a support vector regressor on a small collection of data from a single liquid chromatography run. This model can be used to filter peptide identifications with observed retention time that deviates from predicted retention time. After filtering, positive peptide identifications increase by as much as 50% at a false discovery rate of 3%. We demonstrate that our dynamically trained model generalizes well across diverse chromatography conditions and methods for generating peptides, in particular improving peptide identification using nonspecific proteases.     

Establishment of accuracy limits and standards for comparative thermal conductivity measurements

New techniques have been developed for reducing thermal conductivity data from thermal comparative measurements. The first of these techniques is based on making a Taylor-series expansion of the stack centerline temperature profile. The result is an expression giving the ratio of sample to reference conductivities at any temperature as a function of measured quantities, the stack thermocouple readings and stack element thicknesses. The conventional formula presently used to reduce comparative conductivity data is shown to be a special result of the general analysis. A second technique involves the use of linear least-squares (LS) techniques to derive both the sample and the reference conductivities from the measured data. The LS technique provides the coefficients for a polynomial temperature expansion of the reference and sample conductivities directly. Use of the new techniques is illustrated in a reduction of some comparative data on the conductivities of Pyrex 7740 and Pyroceram 9606. It is shown that a highly self-consistent pair of conductivity functions can be derived for these two commonly used reference materials if the conductivity vs temperature relation for Pyrex is modified slightly from its recommended value. The Pyroceram conductivity results from the comparative measurements are in good agreement with a conductivity derived from pulse diffusivity and differential scanning calorimetry measurements and also in good agreement with the recommended Pyroceram conductivity function.Paper presented at the Ninth Symposium on Thermophysical Properties, June 24–27, 1985, Boulder, Colorado, U.S.A.     

The accuracy of real-time computer spectrum analyzer calculations

A practical estimate of the accuracy of calculations of a software-hardware system consisting of an audio-frequency generator and a combined spectrum analyzer is presented. It is shown, using the example of a number of model measurements, that the frequency, amplitude, and phase errors of the calculations are very close to the theoretical limits. __________ Translated from Izmeritel’naya Tekhnika, No. 2, pp. 62–65, February, 2007.     

Fundamental limits of the accuracy of the photoelectric recording of radiation: Interferometric and anemometer aspects

The fundamental limits of the accuracy of the photoelectric recording of the amplitude, visibility and phase of an interference field are investigated using a semiclassical approach by methods of information theory and parameter estimation. A receiving scheme with moving scattering particles is analyzed, which enables the laser anemometer aspect to be included and enables the effect of the phase and number of fringes to be investigated. Translated from Izmeritel’naya Tekhnika, No. 8, pp. 26–30, August, 1996.     

On the limits of finite element perfectability

It has been shown² that a four-noded membrane element of trapezoidal shape must either lock or fail constant strain patch tests. That result is generalized here to establish similar limitations for all finite elements. A modal analysis is used to show that essential coupling exists between low modes whose displacement states can be exactly represented by an element's basis functions and higher modes whose displacement states cannot be so represented. Such coupling can be avoided only when an element has particular shapes. In all other cases the element designer is faced with the choice of patch test failure in a low mode or locking in a higher mode. Several examples are described.     

De novo peptide sequencing based on a divide-and-conquer algorithm and peptide tandem spectrum simulation

Mass spectrometry-based de novo peptide sequencing is generally more reliable on high-resolution instruments owing to their high resolution and mass accuracy. On a lower resolution instrument such as the more widely used quadrupole ion traps, de novo peptide sequencing is not so reliable or requires more MS(3) experiments. However, the peptide CID spectrum has been demonstrated to be quite reproducible on an ion trap instrument and can be predicted with good accuracy. A new de novo peptide sequencing technique, DACSIM, combining a divide-and-conquer algorithm for deriving sequence candidates and spectrum simulation for sequence refinement, is developed for spectra acquired on an ion trap instrument. When DACSIM was used to sequence peptides 500-1900 u in mass generated from proteolytic digests of hemoglobin and myoglobin, the success rate was 70% with a false positive rate of only 6%, when isoleucine and leucine residues were not distinguished.     

On Kaplun limits and the generalized boundary layer theory

In the present work, Kaplun limits will be used to derive a generalized version of the boundary layer theory. The intermediate variable technique will be applied to the Navier-Stokes equations and, through the concept of principal equation proposed by Kaplun, a set of partial differential equations will be obtained which represents the asymptotic limit of the momentum equations as the Reynolds number approaches infinite. These equations combine the inviscid flow formulation and the classical boundary layer equations into a single and more general theory that disregards the needs for any type of viscid-inviscid interaction. The proposed formulation will be used to study the flow over a flat plate, and a quasi-similar ordinary differential equation will be deduced which represents an extension of the Blasius equation. The domain of validity of the quasi-similar equation will be analyzed and the asymptotic character of the Blasius solution, which is valid only as Reynolds number tends to infinity, will be studied.     

On the accuracy of the polynomial chaos approximation

Polynomial chaos representations for non-Gaussian random variables and stochastic processes are infinite series of Hermite polynomials of standard Gaussian random variables with deterministic coefficients. Finite truncations of these series are referred to as polynomial chaos (PC) approximations. This paper explores features and limitations of PC approximations. Metrics are developed to assess the accuracy of the PC approximation. A collection of simple, but relevant examples is examined in this paper. The number of terms in the PC approximations used in the examples exceeds the number of terms retained in most current applications. For the examples considered, it is demonstrated that (1) the accuracy of the PC approximation improves in some metrics as additional terms are retained, but does not exhibit this behavior in all metrics considered in the paper, (2) PC approximations for strictly stationary, non-Gaussian stochastic processes are initially nonstationary and gradually may approach weak stationarity as the number of terms retained increases, and (3) the development of PC approximations for certain processes may become computationally demanding, or even prohibitive, because of the large number of coefficients that need to be calculated. However, there have been many applications in which PC approximations have been successful.     

On the temperature dependence of flammability limits of gases

Flammability limits of several combustible gases were measured at temperatures from 5 to 100 °C in a 12-l spherical flask basically following ASHRAE method. The measurements were done for methane, propane, isobutane, ethylene, propylene, dimethyl ether, methyl formate, 1,1-difluoroethane, ammonia, and carbon monoxide. As the temperature rises, the lower flammability limits are gradually shifted down and the upper limits are shifted up. Both the limits shift almost linearly to temperature within the range examined. The linear temperature dependence of the lower flammability limits is explained well using a limiting flame temperature concept at the lower concentration limit (LFL)--'White's rule'. The geometric mean of the flammability limits has been found to be relatively constant for many compounds over the temperature range studied (5-100 °C). Based on this fact, the temperature dependence of the upper flammability limit (UFL) can be predicted reasonably using the temperature coefficient calculated for the LFL. However, some compounds such as ethylene and dimethyl ether, in particular, have a more complex temperature dependence.     

On the flammability limits of saturated vapours of hydrocarbons

The upper flammability limits of saturated vapours of four hydrocarbons (cyclohexane, benzene, toluene and ethylbenzene) in oxygen—nitrogen and oxygeThe different reactivity of the four hydrocarbons is discussed, taking into account the pressure dependence of the flammability limits, which appeared     

Improving the accuracy of experimental prediction of the detectability of nonlinear objects by radar

The possibility of calibration of nonlinear radar measuring systems using a physical standard scatterer is investigated. Suggestions on the shape of such a scatterer at super-high frequencies are formulated. Translated from Izmeritel'naya Tekhnika, No. 11, pp. 44–48, November, 1999.     

Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation

A database of 5500 unique peptide tandem mass spectra acquired in an ion trap mass spectrometer was assembled for peptides derived from proteins digested with trypsin. Peptides were identified initially from their tandem mass spectra by the SEQUEST algorithm and subsequently validated manually. Two different statistical methods were used to identify sequence-dependent fragmentation patterns that could be used to improve fragmentation models incorporated into current peptide sequencing and database search algorithms. The currently accepted "mobile proton" model was expanded to derive a new classification scheme for peptide mass spectra, the "relative proton mobility" scale, which considers peptide ion charge state and amino acid composition to categorize peptide mass spectra into peptide ions containing "nonmobile", "partially mobile", or "mobile" protons. Quantitation of amide bond fragmentation, both N- and C-terminal to any given amino acid, as well as the positional effect of an amino acid in a peptide and peptide length on such fragmentation, has been determined. Peptide bond cleavage propensities, both positive (i.e., enhanced) and negative (i.e., suppressed), were determined and ranked in order of their cleavage preferences as primary, secondary, or tertiary cleavage effects. For example, primary positive cleavage effects were observed for Xaa-Pro and Asp-Xaa bond cleavage for mobile and nonmobile peptide ion categories, respectively. We also report specific pairwise interactions (e.g., Asn-Gly) that result in enhanced amide bond cleavages analogous to those observed in solution-phase chemistry. Peptides classified as nonmobile gave low or insignificant scores, below reported MS/MS score thresholds (cutoff filters), indicating that incorporation of the relative proton mobility scale classification would lead to improvements in current MS/MS scoring functions.     

On the dynamic fragmentation of glass: a meso-damage model

This paper presents an anisotropic damage model to deal with the fragmentation induced by impact loadings on glass samples. As small-scale (i.e. sub-element) damage is described as well as cracks extending above the element scale, an approach referred to as “meso-damage” is developed. The latter, which is based on the knowledge of random distributions of initiation sites, predicts different regimes such as single or multiple fragmentation. The experimental opening crack pattern obtained in edge-on-impact test is reproduced numerically.     

Impact of peptide modifications on the isobaric tags for relative and absolute quantitation method accuracy

In this study, the impact of amino acid modifications on the accuracy of the iTRAQ (isobaric tags for relative and absolute quantitation) method was evaluated. MCF-7 breast cancer cells, cultured in the presence of 17β-estradiol and tamoxifen, were used as a model system. The cells were labeled and analyzed by reversed-phase liquid chromatography and pulsed Q dissociation ion trap tandem mass spectrometry detection. Database searching was performed by using various combinations of amino acid modification allowances, i.e, Lys/Tyr/Cys and amino terminal iTRAQ labeling, Lys methylation, acetylation and carbamylation, and Cys/Met oxidation. Other than the intended Lys/amino terminal iTRAQ labeling, such modifications occur as a result of either enzymatic or sample preparation related reactions and are typically ignored in quantitation analysis to minimize the rate of false-positive peptide identifications. The study revealed that the modifications with the greatest impact on protein identification and quantitation pertain to Lys and Tyr amino acid residues, that by enabling such modifications the number and type of identified proteins will change (by up to 10%), and that the rate of false-positive protein identifications can be maintained below an upper threshold of 5% if appropriate data filtering conditions are used. In addition, the interference of possible posttranslational modifications (i.e., phosphorylation) with iTRAQ quantitation was examined.     

On the accuracy of the Haar wavelet discretization method

Current study contains adaption of Haar wavelet discretization method (HWDM) for FG beams and its accuracy estimates. The convergence analysis is performed for differential equations covering a wide class of composite and nanostructures. Corresponding error bound has been derived. It has been shown that the order of convergence of the HWDM can be increased from two to four by applying Richardson extrapolation method. The theoretical estimates are validated by numerical samples considering FGM beam as a model problem. The results obtained by applying HWDM are compared with the results of finite difference method (FDM).