Virtual Expert Mass Spectrometrist: iTRAQ tool for database‐dependent search, quantitation and result storage
Eva Rodríguez‐SuárezEwa GubbItziar FradesJuan Manuel Falcón‐PérezAntónio AmorimFélix ElortzaRune Matthiesen
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Abstract A frequent goal of MS‐based proteomics experiments nowadays is to quantify changes in the abundance of proteins across several biological samples. The iTRAQ labeling method is a powerful technique; when combined with LC coupled to MS/MS it allows relative quantitation of up to eight different samples simultaneously. Despite the usefulness of iTRAQ current software solutions have limited functionality and require the combined use of several software programs for analysis of the data from different MS vendors. We developed an integrated tool, now available in the virtual expert mass spectrometrist (VEMS) program, for database‐dependent search of MS/MS spectra, quantitation and database storage for iTRAQ‐labeled samples. VEMS also provides useful alternative report types for large‐scale quantitative experiments. The implemented statistical algorithms build on quantitative algorithms previously used in proposed iTRAQ tools as described in detail herein. We propose a new algorithm, which provides more accurate peptide ratios for data that show an intensity‐dependent saturation. The accuracy of the proposed iTRAQ algorithm and the performance of VEMS are demonstrated by comparing results from VEMS, MASCOT and PEAKS Q obtained by analyzing data from a reference mixture of six proteins. Users can download VEMS and test data from “ http://www.portugene.com/software.html ”.No abstract available.
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There are a number of reports on seismic quiescence phenomena before large earthquakes. The RTL algorithm is a weighted coefficient statistical method that takes into account the magnitude, occurrence time, and place of earthquake when seismicity pattern changes before large earthquakes are being investigated. However, we consider the original RTL algorithm to be overweighted on distance. In this paper, we introduce a modified RTL algorithm, called the RTM algorithm, and apply it to three large earthquakes in Japan, namely, the Hyogo-ken Nanbu earthquake in 1995 (MJMA7.3), the Noto Hanto earthquake in 2007 (MJMA 6.9), and the Iwate-Miyagi Nairiku earthquake in 2008 (MJMA 7.2), as test cases. Because this algorithm uses several parameters to characterize the weighted coefficients, multiparameter sets have to be prepared for the tests. The results show that the RTM algorithm is more sensitive than the RTL algorithm to seismic quiescence phenomena. This paper represents the first step in a series of future analyses of seismic quiescence phenomena using the RTM algorithm. At this moment, whole surveyed parameters are empirically selected for use in the method. We have to consider the physical meaning of the "best fit" parameter, such as the relation of ACFS, among others, in future analyses.
Earthquake simulation
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This paper propose an improved image filtering algorithm which is based on median filteringing algorithm and medium filteringing algorithm according to the simpleness of median filteringing algorithm and the significant denoising effect of medium filteringing algorithm. The new algorithm combines the two algorithms and thus gets a better filtering effect. We did the simulation using MATLAB, and then did the objective evaluation using the classical method PSNR. Simulation results showed that the new algorithm has a better denoising effect than the medium filteringing algorithm and reduces the denoising time as well. Thus the improved algorithm has a better practicalility.
Algorithm design
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article Free Access Share on Remarks on Algorithm 332: Jacobi polynomials: Algorithm 344: student's t-distribution: Algorithm 351: modified Romberg quadrature: Algorithm 359: factoral analysis of variance Author: Arthur H. J. Sale Univ. of Sydney, Sydney, Australia Univ. of Sydney, Sydney, AustraliaView Profile Authors Info & Claims Communications of the ACMVolume 13Issue 7July 1970 https://doi.org/10.1145/362686.362700Published:01 July 1970Publication History 0citation275DownloadsMetricsTotal Citations0Total Downloads275Last 12 Months10Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Quadrature (astronomy)
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Recently we developed a family of image reconstruction algorithms that look like emission maximum-likelihood expectation-maximization (ML-EM) algorithm. In this paper, we extend these algorithms to Bayesian algorithms. The family of emission-EM-lookalike algorithms uses multiplicative update scheme. The extension of these algorithms to Bayesian algorithms is achieved by introducing a new simple factor, which contains the Bayesian information. One of the extended algorithms can be applied to emission tomography, and another can be applied to transmission tomography. Computer simulations are performed and compared with the corresponding un-extended algorithms. The totalvariation (TV) norm is used as the Bayesian constraint in the computer simulations. The newly developed algorithms demonstrate stable performance. For any noise variance function, a simple Bayesian algorithm can be derived. The proposed algorithms have properties such as multiplicative update, non-negativity, faster convergence rate for the bright objects, and ease of implementation. Our algorithms are inspired by Green's one-step-late (OSL) algorithm. "One-step-late" is an undesirable feature. Our algorithms do not have this undesirable one-step-late feature.
Feature (linguistics)
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article Free AccessRemarks on algorithms 372: Algorithm 401: An algorithm to produce complex primes, csieve: an improved algorithm to produce complex primes Author: Paul Bratley Univ. de Montréal, Quebec, Canada Univ. de Montréal, Quebec, CanadaView Profile Authors Info & Claims Communications of the ACMVolume 13Issue 1101 November 1970https://doi.org/10.1145/362790.362805Published:01 November 1970Publication History 0citation192DownloadsMetricsTotal Citations0Total Downloads192Last 12 Months9Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
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