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Deutsch Eric W - - 2010
The Trans-Proteomic Pipeline (TPP) is a suite of software tools for the analysis of MS/MS data sets. The tools encompass most of the steps in a proteomic data analysis workflow in a single, integrated software system. Specifically, the TPP supports all steps from spectrometer output file conversion to protein-level statistical ...
Alymani Nayef A NA Section of Translational Medical Sciences, Division of Applied Medicine, School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, United - - 2010
A priority translational research objective in cancer medicine is the discovery of novel therapeutic targets for solid tumours. Ideally, co-discovery of predictive biomarkers occurs in parallel to facilitate clinical development of agents and ultimately personalise clinical use. However, the identification of clinically useful predictive biomarkers for solid tumours has proven ...
Christ John A - - 2010
Models that link simplified descriptions of dense non-aqueous phase liquid (DNAPL) source zone architecture with predictions of mass flux can be effective screening tools for evaluation of source zone management strategies. Recent efforts have focused on the development and implementation of upscaled models to approximate the relationship between mass removal ...
Nasso Sara - - 2010
As an emerging field, MS-based proteomics still requires software tools for efficiently storing and accessing experimental data. In this work, we focus on the management of LC-MS data, which are typically made available in standard XML-based portable formats. The structures that are currently employed to manage these data can be ...
MacLean Brendan - - 2010
Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected ...
García Alonso J Ignacio - - 2010
A procedure for the determination of the uncertainties in the theoretical mass isotopomer distribution of molecules due to natural variations in the isotope composition of their constituting elements is described here for the first time. For this purpose, a Visual Basic macro for Microsoft Excel was written by adapting the ...
Jain Rachana - - 2010
Peptide Mass Fingerprinting (PMF) uses proteolytic peptide masses and a prespecified search database to identify proteins. At the core of a PMF database search algorithm lies a quality statistic that gauges the level to which an experimentally obtained peak list agrees with a list of theoretically observable mass-to-charge ratios for ...
Liby Bruce W - - 2010
Center-of-mass perception in dot patterns arranged into triangular and quadrilateral configurations was investigated. In Exp. 1, the length, orientation, and direction of dots forming right triangles were varied. Errors in center-of-mass perception by 19 participants increased with the length of the triangles. In Exp. 2, 27 participants estimated the centers ...
Draisma Harmen H M - - 2010
Combination of data sets from different objects (for example, from two groups of healthy volunteers from the same population) that were measured on a common set of variables (for example, metabolites or peptides) is desirable for statistical analysis in "omics" studies because it increases power. However, this type of combination ...
Boccard Julien - - 2010
While metabolomics attempts to comprehensively analyse the small molecules characterising a biological system, MS has been promoted as the gold standard to study the wide chemical diversity and range of concentrations of the metabolome. On the other hand, extracting the relevant information from the overwhelming amount of data generated by ...
Goloborodko Anton A - - 2010
Estimation of false discovery rate (FDR) for identified peptides is an important step in large-scale proteomic studies. We introduced an empirical approach to the problem that is based on the FDR-like functions of sets of peptide spectral matches (PSMs). These functions have close values for equal-sized sets with the same ...
Nowatzke William - - 2010
The use of biomarkers during clinical drug-development programs may expedite pipeline decision making by adding critical information about the pharmacological mechanism and efficacy of a potential therapeutic agent. Currently, advice for laboratorians conducting method development and analytical validation of biomarker methods is provided by published White Paper recommendations from industry ...
Yang Anxiong A Department of Phoniatrics and Pediatric Audiology, University Hospital Erlangen, Medical School, Bohlenplatz 21, 91054 Erlangen, Germany. - - 2010
Human voice originates from the three-dimensional (3D) oscillations of the vocal folds. In previous studies, biomechanical properties of vocal fold tissues have been predicted by optimizing the parameters of simple two-mass-models to fit its dynamics to the high-speed imaging data from the clinic. However, only lateral and longitudinal displacements of ...
Marengo Emilio - - 2010
The field of biomarkers discovery is one of the leading research areas in proteomics. One of the most exploited approaches to this purpose consists of the identification of potential biomarkers from spot volume datasets produced by 2D gel electrophoresis. In this case, problems may arise due to the large number ...
Barkauskas Donald A DA Children's Oncology Group, 440 E. Huntington Drive Suite 402, Arcadia, CA 91006, USA. - - 2010
A common feature of many modern technologies used in proteomics--including nuclear magnetic resonance imaging and mass spectrometry--is the generation of large amounts of data for each subject in an experiment. Extracting the signal from the background noise, however, poses significant challenges. One important part of signal extraction is the correct ...
Reinert Knut - - 2010
The automatic analysis of mass spectrometry data is becoming more and more important since increasingly larger datasets are readily available that cannot be evaluated manually. This has triggered the development of several open-source software libraries for the automatic analysis of such data. Among those is OpenMS together with TOPP (The ...
Kim Ethan Dh - - 2010
Affinity purification followed by mass spectrometry identification (AP-MS) is an increasingly popular approach to observe protein-protein interactions (PPI) in vivo. One drawback of AP-MS, however, is that it is prone to detecting indirect interactions mixed with direct physical interactions. Therefore, the ability to distinguish direct interactions from indirect ones is ...
Parnell Andrew C - - 2010
Stable isotope analysis is increasingly being utilised across broad areas of ecology and biology. Key to much of this work is the use of mixing models to estimate the proportion of sources contributing to a mixture such as in diet estimation. By accurately reflecting natural variation and uncertainty to generate ...
Tang Kai-Lin - - 2010
BACKGROUND: Recent advances in proteomics technologies such as SELDI-TOF mass spectrometry has shown promise in the detection of early stage cancers. However, dimensionality reduction and classification are considerable challenges in statistical machine learning. We therefore propose a novel approach for dimensionality reduction and tested it using published high-resolution SELDI-TOF data ...
Sui Weiguo - - 2010
Uremia is a term used to loosely describe the illness accompanying renal failure, in particular the nitrogenous waste products associated with the failure of this organ. At present, the diagnosis of uremia could be implemented by clinical symptoms, laboratory examinations, or image analysis. To develop alternative methods and potential new ...
Caffrey Rebecca E - - 2010
Surface Enhanced Laser/Desorption Ionization-time of flight (SELDI-TOF) mass spectrometry is a technique uniquely suited to the study of the urine proteome due to its salt tolerance, high-throughput, and small sample requirements. However, due to the extreme sensitivity of the technique, sample collection and storage conditions, as well as instrument protocols ...
Pluskal Tomás - - 2010
BACKGROUND: Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, ...
Sellers Kimberly F - - 2010
Numerous gel-based and nongel-based technologies are used to detect protein changes potentially associated with disease. The raw data, however, are abundant with technical and structural complexities, making statistical analysis a difficult task. Low-level analysis issues (including normalization, background correction, gel and/or spectral alignment, feature detection, and image registration) are substantial ...
Mischnick Petra - - 2010
Starch and cellulose are the most abundant and important representatives of renewable biomass. Since the mid-19th century their properties have been changed by chemical modification for commercial and scientific purposes, and there substituted polymers have found a wide range of applications. However, the inherent polydispersity and supramolecular organization of starch ...
Pedrioli Patrick G A - - 2010
Mass spectrometry has quickly become an essential tool in molecular biology laboratories. Here, we describe the Trans-Proteomic Pipeline, a collection of software tools, to facilitate the analysis, exchange, and comparison of MS data. The pipeline is instrument-independent and supports most commonly used proteomics workflows, including quantitative applications such as ICAT, ...
Toward Martin G R - - 2010
Models of the vertical apparent mass of the human body are mostly restricted to a sitting posture unsupported by a backrest and ignore the variations in apparent mass associated with changes in posture and changes in the magnitude of vibration. Using findings from experimental research, this study fitted a single ...
Deng Xutao - - 2010
High-throughput technologies can routinely assay biological or clinical samples and produce wide data sets where each sample is associated with tens of thousands of measurements. Such data sets can be mined to discover biomarkers and develop statistical models capable of predicting an endpoint of interest from data measured in the ...
ZieliƄski Andrzej - - 2010
Structured sanitary preparation to mass gatherings is based on the set of instructions and legal requirements which are different for different jurisdictions. In many countries special checklists are used for itemized scrutiny of the sanitary preparation to the event. Those checklists are present in two forms. One is relatively short ...
Stephan Christian - - 2010
In Proteomics, fast enhancements with regard to technology are responsible for the creation of huge data sets. Consequently, in 2006 the European Commission funded a Coordination Action named ProDaC (Proteomics Data Collection) within the 6th EU Framework Programme to foster a community-wide data collection and data sharing. The aims of ...
Coca Daniel - - 2010
High-throughput, MS-based proteomics studies are generating very large volumes of biologically relevant data. Given the central role of proteomics in emerging fields such as system/synthetic biology and biomarker discovery, the amount of proteomic data is expected to grow at unprecedented rates over the next decades. At the moment, there is ...
Cuomo Alessandro - - 2010
Stable isotope labeling with amino acids in cell culture (SILAC) has become increasingly popular as a quantitative proteomics (qProteomics) method. In combination with high-resolution mass spectrometry (MS) and new efficient algorithms for the analysis of quantitative MS data, SILAC has proven to be a potent tool for the in-depth characterization ...
Velikova Marina - - 2010
Despite their promising application, current Computer-Aided Detection (CAD) systems face difficulties, especially in the detection of malignant masses -a major mammographic sign for breast cancer. One of the main problems is the large number of false positives prompted, which is a critical issue in screening programs where the number of ...
Budu-Grajdeanu Paula - - 2010
Although the prognosis for Lupus Nephritis (LN) has dramatically improved with aggressive immunosuppressive therapies, these drugs carry significant side effects. To improve the effectiveness of these drugs, biomarkers of renal flare cycle could be used to detect the onset, severity, and responsiveness of kidney relapses, and to modify therapy accordingly. ...
Kuschner Karl W - - 2010
Time-of-flight mass spectrometry (TOF-MS) has the potential to provide non-invasive, high-throughput screening for cancers and other serious diseases via detection of protein biomarkers in blood or other accessible biologic samples. Unfortunately, this potential has largely been unrealized to date due to the high variability of measurements, uncertainties in the distribution ...
Piruzian Eleonora - - 2010
Psoriasis is complex inflammatory skin pathology of autoimmune origin. Several cell types are perturbed in this pathology, and underlying signaling events are complex and still poorly understood. In order to gain insight into molecular machinery underlying the disease, we conducted a comprehensive meta-analysis of proteomics and transcriptomics of psoriatic lesions ...
Carroll Adam J - - 2010
Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS) makes it an obvious target for such development. While a ...
Denery Judith R - - 2010
Development of robust, sensitive, and reproducible diagnostic tests for understanding the epidemiology of neglected tropical diseases is an integral aspect of the success of worldwide control and elimination programs. In the treatment of onchocerciasis, clinical diagnostics that can function in an elimination scenario are non-existent and desperately needed. Due to ...
Emanuele Vincent A VA - - 2010
Surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI) is a proteomics tool for biomarker discovery and other high throughput applications. Previous studies have identified various areas for improvement in preprocessing algorithms used for protein peak detection. Bottom-up approaches to preprocessing that emphasize modeling SELDI data acquisition are promising avenues of ...
Witton Mark P - - 2010
The size and flight mechanics of giant pterosaurs have received considerable research interest for the last century but are confused by conflicting interpretations of pterosaur biology and flight capabilities. Avian biomechanical parameters have often been applied to pterosaurs in such research but, due to considerable differences in avian and pterosaur ...
Eriksson Jan - - 2010
The complexity of proteomes makes good experimental design essential for their successful investigation. Here, we describe how proteomics experiments can be modeled and how computer simulations of these models can be used to improve experimental designs.
Deutsch Eric W - - 2010
PeptideAtlas is a multi-species compendium of peptides observed with tandem mass spectrometry methods. Raw mass spectrometer output files are collected from the community and reprocessed through a uniform analysis and validation pipeline that continues to advance. The results are loaded into a database and the information derived from the raw ...
Ling Xuefeng B XB Department of Pediatrics, Stanford University, Stanford, California, USA. - - 2010
Urine-based proteomic profiling is a novel approach that may result in the discovery of noninvasive biomarkers for diagnosing patients with different diseases, with the aim to ultimately improve clinical outcomes. Given new and emerging analytical technologies and data mining algorithms, the urine peptidome has become a rich resource to uncover ...
Winograd Nicholas N Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA. - - 2010
This article reviews the new physics and new applications of secondary ion mass spectrometry using cluster ion probes. These probes, particularly C(60), exhibit enhanced molecular desorption with improved sensitivity owing to the unique nature of the energy-deposition process. In addition, these projectiles are capable of eroding molecular solids while retaining ...
Elias Joshua E JE Department of Cell Biology, Harvard Medical School, Boston, MA, - - 2010
Accurate and precise methods for estimating incorrect peptide and protein identifications are crucial for effective large-scale proteome analyses by tandem mass spectrometry. The target-decoy search strategy has emerged as a simple, effective tool for generating such estimations. This strategy is based on the premise that obvious, necessarily incorrect "decoy" sequences ...
Aminian Minoo M Departments of Mathematical Science and Computer Science, Rensselaer Polytechnic Institute, Troy, New York, USA. - - 2010
We present a novel conformal Bayesian network (CBN) to classify strains of Mycobacterium tuberculosis Complex (MTBC) into six major genetic lineages based on two high-throuput biomarkers: mycobacterial interspersed repetitive units (MIRU) and spacer oligonucleotide typing (spoligotyping). MTBC is the causative agent of tuberculosis (TB), which remains one of the leading ...
Ruiz-Romero C - - 2010
OBJECTIVE: Osteoarthritis (OA) is the most common rheumatic pathology. It is related to aging and is characterized primarily by cartilage degradation. Despite its high prevalence, the diagnostic methods currently available are limited and lack sensitivity. The focus of this review is the application of proteomic technologies in the search of ...
Xu Cheng-Jian - - 2010
Principal component analysis (PCA) is much used in exploring time-course biological data sets, but does not distinguish variation between time and subjects. This study proposes a new integrated approach by combining analysis of variance (ANOVA) and three component modeling methods. The former was used to separate the between- and within-subject ...
De Bock Muriel - - 2010
Protein profiling using SELDI-TOF-MS has gained over the past few years an increasing interest in the field of biomarker discovery. The technology presents great potential if some parameters, such as sample handling, SELDI settings, and data analysis, are strictly controlled. Practical considerations to set up a robust and sensitive strategy ...
Abazov V M - - 2009
We present a direct measurement of the width of the W boson using the shape of the transverse mass distribution of W --> enu candidate events. Data from approximately 1 fb(-1) of integrated luminosity recorded at square root of s = 1.96 TeV by the D0 detector at the Fermilab ...
Tourlomousis Panagiotis - - 2010
Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology to profile complex microbial communities over time and in response to different stimuli. However, inherent gel-to-gel variability has always been a barrier toward meaningful interpretation of DGGE profiles obtained from multiple gels. To address this problem, we developed a ...
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