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Results 451 - 500 of 991
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Elkabes Stella - - 2007
The early and precise diagnosis, the prognosis, and the clinical management of multiple sclerosis, remain a considerable challenge. In recent years, the development of novel and powerful proteomic techniques prompted the use of these approaches for the search of unique biomarkers in the cerebrospinal fluid of multiple sclerosis patients. A ...
Nesvizhskii Alexey I - - 2007
The analysis of the large amount of data generated in mass spectrometry-based proteomics experiments represents a significant challenge and is currently a bottleneck in many proteomics projects. In this review we discuss critical issues related to data processing and analysis in proteomics and describe available methods and tools. We place ...
Orchard Sandra - - 2007
Over the last five years, the Human Proteome Organisation Proteomics Standards Initiative (HUPO PSI) has produced and released community-accepted XML interchange formats in the fields of mass spectrometry, molecular interactions and gel electrophoresis, have led the field in the discussion of the minimum information with which such data should be ...
Hendriks Margriet M W B - - 2007
SELDI-TOF-MS is rapidly gaining popularity as a screening tool for clinical applications of proteomics. Application of adequate statistical techniques in all the stages from measurement to information is obligatory. One of the statistical methods often used in proteomics is classification: the assignment of subjects to discrete categories, for example healthy ...
Parikh Nisha I - - 2007
Biomarkers in medicine have gained immense scientific and clinical interest in recent years. Biomarkers are potentially useful in the contexts of primary, secondary and tertiary prevention. Some of the characteristics of an ideal biomarker include that they are safe and easy to measure, are associated with acceptable costs (including those ...
Palandra Joe - - 2007
A fully automated protein precipitation technique for biological sample preparation has been developed for the quantitation of drugs in various biological matrixes. All liquid handling during sample preparation was automated using a Hamilton MicroLab Star Robotic workstation, which included the preparation of standards and controls from a Watson laboratory information ...
Harvey Gemma - - 2008
Body mass changes, hematocrit, specific gravity and urine colour were recorded during two games of soccer to determine which of these methods was the most practical in a field setting for monitoring dehydration. Members (n=13) of a premiership soccer team with a mean age of 22.6 (+/-4.9) years old, height ...
Morris Jeffrey S JS The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030-4009, USA. - - 2008
In this article, we apply the recently developed Bayesian wavelet-based functional mixed model methodology to analyze MALDI-TOF mass spectrometry proteomic data. By modeling mass spectra as functions, this approach avoids reliance on peak detection methods. The flexibility of this framework in modeling nonparametric fixed and random effect functions enables it ...
Cummings J - - 2008
Over recent years the role of biomarkers in anticancer drug development has expanded across a spectrum of applications ranging from research tool during early discovery to surrogate endpoint in the clinic. However, in Europe when biomarker measurements are performed on samples collected from subjects entered into clinical trials of new ...
Ulintz Peter J - - 2008
Improvements in ion trap instrumentation have made n-dimensional mass spectrometry more practical. The overall goal of the study was to describe a model for making use of MS(2) and MS(3) information in mass spectrometry experiments. We present a statistical model for adjusting peptide identification probabilities based on the combined information ...
Gabbard Carl - - 2007
This study examined the influence of target viewing time on perceived (estimates of) reachability. Right-handed participants were asked to judge the simulated reachability of midline targets using their dominant limb in viewing conditions of 150 ms, 500 ms, 1 s and 2 s. Responses were compared to actual maximum reach. ...
Flikka Kristian - - 2007
High-throughput proteomics experiments typically generate large amounts of peptide fragmentation mass spectra during a single experiment. There is often a substantial amount of redundant fragmentation of the same precursors among these spectra, which is usually considered a nuisance. We here discuss the potential of clustering and merging redundant spectra to ...
Jones Andrew R - - 2007
The use of gel electrophoresis to separate and, in some instances, to quantify the abundance of large numbers of proteins from complex mixtures, has been well established for several decades. The quantity of publicly available data is still relatively modest due to a lack of community accepted data standards, tools ...
Karp Natasha A - - 2007
Quantitative proteomics is the comparison of distinct proteomes which enables the identification of protein species which exhibit changes in expression or post-translational state in response to a given stimulus. Many different quantitative techniques are being utilized and generate large datasets. Independent of the technique used, these large datasets need robust ...
Pelikan Richard - - 2007
The 'reproducibility' of mass spectrometry proteomic profiling has become an intensely controversial topic. The mere mention of concern over the 'reproducibility' of data generated from any particular platform can lead to the anxiety over the generalizability of its results and its role in the future of discovery proteomics. In this ...
Karr T L - - 2008
Proteomics is a relatively new scientific discipline that merges protein biochemistry, genome biology and bioinformatics to determine the spatial and temporal expression of proteins in cells, tissues and whole organisms. There has been very little application of proteomics to the fields of behavioral genetics, evolution, ecology and population dynamics, and ...
Noy Karin - - 2007
Mass spectrometry (MS) is increasingly being used for biomedical research. The typical analysis of MS data consists of several steps. Feature extraction is a crucial step since subsequent analyses are performed only on the detected features. Current methodologies applied to low-resolution MS, in which features are peaks or wavelet functions, ...
Lv Lin-Li - - 2007
The antibody microarray is an intrinsically robust and quantitative system that delivers high-throughput and parallel measurements on particular sets of known proteins. It has become an important proteomics research tool, complementary to the conventional unbiased separation-based and mass spectrometry-based approaches. This review summarizes the technical aspects of production and the ...
Lau King Wai - - 2007
Whilst the array of techniques available for quantitative proteomics continues to grow, the attendant bioinformatic software tools are similarly expanding in number. The data capture and analysis of such quantitative data is obviously crucial to the experiment and the methods used to process it will critically affect the quality of ...
Taylor Chris F - - 2007
Both the generation and the analysis of proteomics data are now widespread, and high-throughput approaches are commonplace. Protocols continue to increase in complexity as methods and technologies evolve and diversify. To encourage the standardized collection, integration, storage and dissemination of proteomics data, the Human Proteome Organization's Proteomics Standards Initiative develops ...
Alterovitz Gil - - 2007
Biological and medical data have been growing exponentially over the past several years [1, 2]. In particular, proteomics has seen automation dramatically change the rate at which data are generated [3]. Analysis that systemically incorporates prior information is becoming essential to making inferences about the myriad, complex data [4-6]. A ...
Matthiesen Rune - - 2007
Computational MS-based proteomics is an emerging field arising from the demand of high throughput analysis in numerous large-scale experimental proteomics projects. The review provides a broad overview of a number of computational tools available for data analysis of MS-based proteomics data and gives appropriate literature references to detailed description of ...
Prakash Amol - - 2007
Mass spectrometry-based proteomics holds great promise as a discovery tool for biomarker candidates in the early detection of diseases. Recently much emphasis has been placed upon producing highly reliable data for quantitative profiling for which highly reproducible methodologies are indispensable. The main problems that affect experimental reproducibility stem from variations ...
Tokuda Isao T - - 2007
Voice instabilities were studied using excised human larynx experiments and biomechanical modeling. With a controlled elongation of the vocal folds, the experiments showed registers with chest-like and falsetto-like vibrations. Observed instabilities included abrupt jumps between the two registers exhibiting hysteresis, aphonic episodes, subharmonics, and chaos near the register transitions. In ...
Hinz Klaus-Peter - - 2007
On-line micro- and nanoparticle mass spectrometry has evolved into a prominent analytical method for the characterization of airborne particles, particle populations and aerosols over the recent years, driven by essential developments in instrumentation, data evaluation and validation. In this tutorial, the fundamental aspects of the technology and methodology for qualitative ...
Simões Joana - - 2007
The possibility of discrimination of the anomeric configuration (alpha or beta) of underivatized reducing glucopyranosyl-glucose disaccharides, using a hybrid mass spectrometer Q-TOF 2 (Micromass), a linear ion trap LXQ (Thermo), and a triple quadrupole Quattro (Micromass) with an electrospray source (ESI) was investigated. Differences observed in the relative abundances of ...
Page Steven J - - 2007
Researchers at the National Institute for Occupational Safety and Health (NIOSH) have long used stationary tapered element oscillating microbalances (TEOMs) in laboratory settings. They have served to assess the mass concentration of laboratory-generated particulates in experimental dust chambers and they provide a reference method for comparison with other particulate-measuring instruments. ...
Borges Chad R - - 2007
A chemometrics-based data analysis concept has been developed as a substitute for manual inspection of extracted ion chromatograms (XICs), which facilitates rapid, analyst-mediated interpretation of GC- and LC/MS(n) data sets from samples undergoing qualitative batchwise screening for prespecified sets of analytes. Automatic preparation of data into two-dimensional row space-derived scatter ...
Ervens Barbara - - 2007
The organic fraction of atmospheric aerosols affects the physical and chemical properties of the particles and their role in the climate system. Current models greatly underpredict secondary organic aerosol (SOA) mass. Based on a compilation of literature studies that address SOA formation, we discuss different parameters that affect the SOA ...
Lemelin Pierre - - 2007
The hands and feet of primates fulfill a variety of biological roles linked with food acquisition and positional behavior. Current explanations of shape differences in cheiridial morphology among prosimians are closely tied to body size differences. Although numerous studies have examined the relationships between body mass and limb morphology in ...
Cannataro Mario - - 2007
We connect in a grid-enabled pipeline an ontology-based environment for proteomics spectra management with a machine learning platform for unbiased predictive analysis. We exploit two existing software platforms (MS-Analyzer and BioDCV), the emerging proteomics standards, and the middleware and computing resources of the EGEE Biomed VO grid infrastructure. In the ...
Myers Tamra - - 2007
The community of proteomic researchers has been generating openly available software infrastructure for systematic proteomic data analyses and data management for the past several years. The Computational Proteomics Analysis System (CPAS) integrates many of these efforts into a single Web-based platform for mining liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic experiments. ...
Reid Jennifer D - - 2007
The value of biomarker research in the field of diagnostics and predictive medicine has long been acknowledged. Diagnostic tests have evolved from single-molecule monitoring to multiplexed assays for entire panels of biomarkers, resulting in comprehensive data that clinicians can use to efficiently and effectively treat patients. Thus, the focus of ...
Eriksson Jan - - 2007
Truly comprehensive proteome analysis is highly desirable in systems biology and biomarker discovery efforts. But complete proteome characterization has been hindered by the dynamic range and detection sensitivity of experimental designs, which are not adequate to the very wide range of protein abundances. Experimental designs for comprehensive analytical efforts involve ...
Viarengo A - - 2007
The paper outlines a 2-tier approach for wide-scale biomonitoring programmes. To obtain a high level of standardization, we suggest the use of caged organisms (mussels or fish). An "early warning", highly sensitive, low-cost biomarker is employed in tier 1 (i.e. lysosomal membrane stability (LMS) and survival rate, a marker for ...
Erny Guillaume L - - 2007
It has been demonstrated that CE-MS is a very useful hyphenated technique for proteomic studies. However, the huge amount of data stored in a single CE-MS run makes it necessary to account with procedures able to extract all the relevant information made available by CE-MS. In this work, we present ...
Smit Suzanne - - 2007
A strategy is presented for the statistical validation of discrimination models in proteomics studies. Several existing tools are combined to form a solid statistical basis for biomarker discovery that should precede a biochemical validation of any biomarker. These tools consist of permutation tests, single and double cross-validation. The cross-validation steps ...
Thalassinos Konstantinos - - 2007
Novel software has been developed to aid the interpretation of tandem mass spectrometry (MS/MS) data from synthetic polymers. The software is particularly focused toward aiding the end-group determination of these materials by significantly speeding up the interpretation process. This allows information on the initiator and/or chain transfer agents, used to ...
Shin Hyunjin - - 2008
In recent years, proteomic profiling by mass spectrometry has opened up a new realm of methods for identifying potential biomarkers. Mass spectrometry data, like other proteomic and genomic data, are challenging to analyze because of their high dimensionality and the availability of few samples. Hence, feature selection is extremely important ...
Nie Lei - - 2007
Recent advances in high-throughput technologies enable quantitative monitoring of the abundance of various biological molecules and allow determination of their variation between biological states on a genomic scale. Two popular platforms are DNA microarrays that measure messenger RNA transcript levels, and gel-free proteomic analyses that quantify protein abundance. Obviously, no ...
Noid W G - - 2007
A statistical mechanical framework elucidates the significance of structural correlations between coarse-grained (CG) sites in the multiscale coarse-graining (MS-CG) method (Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469; J. Chem. Phys. 2005, 123, 134105). If no approximations are made, then the MS-CG method yields a many-body ...
Smith David - - 2007
The potential of breath analysis for clinical diagnosis and the strengths and weaknesses of the analytical methods used are discussed. Special attention is given to selected ion flow tube mass spectrometry, SIFT-MS, using which on-line real-time analyses of single breath exhalations can be carried out. Illustrative data on the concentration ...
Santos Agostinho - - 2007
The use of inductively coupled plasma-mass spectrometry (ICP-MS) in the study of gunshot residues (GSR) is relatively recent, and only a few studies have been published on the subject. In the present paper, this instrumental technique has been used to study the deposit pattern of the GSR around the bullet ...
Koch Boris P - - 2007
Ultrahigh-resolution mass spectrometry via the Fourier transform ion cyclotron resonance technique (FT-ICR-MS) allows the identification of thousands of different molecular formulas in natural organic matter and petroleum samples. Molecular formula assignment from mass data is most critical and time-consuming for these samples, and in many cases, several formulas can be ...
DiMaggio Peter A PA Jr Department of Chemical Engineering Princeton University, Princeton, New Jersey 08544-5263, - - 2007
A novel methodology for the automated de novo identification of peptides via integer linear optimization (also referred to as integer linear programming or ILP) and tandem mass spectrometry is presented in this article. The various features of the mathematical model are presented and examples are used to illustrate the key ...
Bogdan Istvan - - 2007
High-resolution mass spectrometers generate large data files that are complex, noisy and require extensive processing to extract the optimal data from raw spectra. This processing is readily achieved in software and is often embedded in manufacturers' instrument control and data processing environments. However, the speed of this data processing is ...
Kaur Parminder - - 2007
Isotope variability due to natural processes provides important information for studying a variety of complex natural phenomena from the origins of a particular sample to the traces of biochemical reaction mechanisms. These measurements require high-precision determination of isotope ratios of a particular element involved. Isotope ratio mass spectrometers (IRMS) are ...
Kohlbacher Oliver - - 2007
MOTIVATION: Experimental techniques in proteomics have seen rapid development over the last few years. Volume and complexity of the data have both been growing at a similar rate. Accordingly, data management and analysis are one of the major challenges in proteomics. Flexible algorithms are required to handle changing experimental setups ...
Listgarten Jennifer - - 2007
MOTIVATION: There is a pressing need for improved proteomic screening methods allowing for earlier diagnosis of disease, systematic monitoring of physiological responses and the uncovering of fundamental mechanisms of drug action. The combined platform of LC-MS (Liquid-Chromatography-Mass-Spectrometry) has shown promise in moving toward a solution in these areas. In this ...
Kaltenbach, Hans-Michael
We investigate several mathematical and algorithmical aspects of peptide mass fingerprinting (PMF). In a PMF experiment, a purified protein sample is digested by a protease using an enzymatic cleavage reaction, the masses of the resulting peptides are measured by mass spectrometry, yielding the mass fingerprint, and compared to predicted mass ...
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