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Results 401 - 450 of 974
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Carpentier Sebastien Christian - - 2008
After separation through two-dimensional gel electrophoresis (2DE), several hundreds of individual protein abundances can be quantified in a cell population or sample tissue. Both a good experimental setup and a valid statistical approach are essential to get insight into the data and to draw correct conclusions. High-throughput 2DE proteomics yield ...
Hand David J - - 2008
The performance results of a wide range of different classifiers applied to proteomic mass spectra data, in a blind comparative assessment organised by Bart Mertens, are reviewed. The different approaches are summarised, issues of how to evaluate and compare the predictions are described, and the results of the different methods ...
Mertens Bart - - 2008
This paper gives a description of the structure of the classification competition on mass spectrometry proteomic data which is presented in this issue. All steps according to which the competition was run, leading up to the joint meeting, are explained. The paper gives further details on the data analyzed by ...
Böcker Sebastian - - 2008
Mass spectrometry has become one of the most popular analysis techniques in Proteomics and Systems Biology. With the creation of larger datasets, the automated recalibration of mass spectra becomes important to ensure that every peak in the sample spectrum is correctly assigned to some peptide and protein. Algorithms for recalibrating ...
Madhusudanan K P - - 2008
The ion abundances in the tandem mass spectra of oxocarbenium ions generated from aldohexoses and ketohexoses under electrospray ionization conditions depend on their stereochemistry. The ratios of the abundances of two of the major ions m/z 85 and 91 are different in the aldohexoses and the ketohexoses. Principal component analysis ...
Stanislaus Romesh - - 2008
In spite of two-dimensional gel electrophoresis (2-DE) being an effective and widely used method to screen the proteome, its data standardization has still not matured to the level of microarray genomics data or mass spectrometry approaches. The trend toward identifying encompassing data standards has been expanding from genomics to transcriptomics, ...
Pérès Sabine - - 2008
In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which ...
Nikamanon Pornpat - - 2008
Protein-amide proton hydrogen-deuterium exchange (HDX) is used to investigate protein conformation, conformational changes and surface binding sites for other molecules. To our knowledge, software tools to automate data processing and analysis from sample fractionating (LC-MALDI) mass-spectrometry-based HDX workflows are not publicly available. An integrated data pipeline (Solvent Explorer/TOF2H) has been ...
Lange Eva - - 2008
Liquid chromatography coupled to mass spectrometry (LC-MS) has become a prominent tool for the analysis of complex proteomics and metabolomics samples. In many applications multiple LC-MS measurements need to be compared, e. g. to improve reliability or to combine results from different samples in a statistical comparative analysis. As in ...
Soh Josephine L P - - 2008
The purpose of this research was to investigate the effects of particle size on the wet massing behavior of microcrystalline cellulose (MCC). In this study, a series of six fractionated MCC grades were customized and specially classified to yield different particle size varieties of the standard grade, Comprecel M101. All ...
Cairns David A - - 2008
Proteomic profiling using mass spectrometry (MS) is one of the most promising methods for the analysis of complex biological samples such as urine, serum and tissue for biomarker discovery. Such experiments are often conducted using MALDI-TOF (matrix-assisted laser desorption/ionisation time-of-flight) and SELDI-TOF (surface-enhanced laser desorption/ionisation time-of-flight) MS. Using such profiling ...
Sturm Marc - - 2008
Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever increasing amounts of data. Consequently, analysis of the ...
Zhang Jiyang - - 2008
Analysis of complex samples with tandem mass spectrometry (MS/MS) has become routine in proteomic research. However, validation of database search results creates a bottleneck in MS/MS data processing. Recently, methods based on a randomized database have become popular for quality control of database search results. However, a consequent problem is ...
Southey Bruce R - - 2008
Neuropeptides and hormones are signaling molecules that support cell-cell communication in the central nervous system. Experimentally characterizing neuropeptides requires significant efforts because of the complex and variable processing of prohormone precursor proteins into neuropeptides and hormones. We demonstrate the power and flexibility of the Python language to develop components of ...
Reich Eike E CAMAG Laboratory, Sonnenmattstrasse 11, CH-4132 Muttenz, Switzerland. - - 2008
Current Good Manufacturing Practices (cGMP) for botanicals stipulates the use of appropriate methods for identification of raw materials. Due to natural variability, chemical analysis of plant material is a great challenge and requires special approaches. This paper presents a comprehensive proposal to the process of validating qualitative high-performance thin-layer chromatographic ...
Rojas-Galeano Sergio S Division of Parasitology, National Institute for Medical Research, London, United - - 2008
The analysis of complex proteomic and genomic profiles involves the identification of significant markers within a set of hundreds or even thousands of variables that represent a high-dimensional problem space. The occurrence of noise, redundancy or combinatorial interactions in the profile makes the selection of relevant variables harder. Here we ...
Maletić-Savatić M M Departments of Neurology and Electrical and Computer Engineering, Stony Brook University, Stony Brook, New York 11790, - - 2008
Finding biomarkers of human neurological diseases is one of the most pressing goals of modern medicine. Most neurological disorders are recognized too late because of the lack of biomarkers that can identify early pathological processes in the living brain. Late diagnosis leads to late therapy and poor prognosis. Therefore, during ...
Clarke Robert R Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3970 Reservoir Road NW, Washington, DC 20057, - - 2008
High-throughput genomic and proteomic technologies are widely used in cancer research to build better predictive models of diagnosis, prognosis and therapy, to identify and characterize key signalling networks and to find new targets for drug development. These technologies present investigators with the task of extracting meaningful statistical and biological information ...
Befekadu Getachew K GK Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, - - 2008
In this paper, a framework of probabilistic-based mixture regression models (PMRM) is presented for multi-class alignment of liquid chromatography-mass spectrometry (LC-MS) data. The proposed framework performs the alignment in both time and measurement spaces of the LC-MS spectra. The expectation maximization (EM) algorithm is used to estimate the joint parameters ...
Oberg Ann L AL Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA. - - 2008
Statistical tools enable unified analysis of data from multiple global proteomic experiments, producing unbiased estimates of normalization terms despite the missing data problem inherent in these studies. The modeling approach, implementation, and useful visualization tools are demonstrated via a case study of complex biological samples assessed using the iTRAQ relative ...
Petyuk Vladislav A VA Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, - - 2008
The high mass measurement accuracy and precision available with recently developed mass spectrometers is increasingly used in proteomics analyses to confidently identify tryptic peptides from complex mixtures of proteins, as well as post-translational modifications and peptides from nonannotated proteins. To take full advantage of high mass measurement accuracy instruments, it ...
Choi Hyungwon - - 2008
Development of robust statistical methods for validation of peptide assignments to tandem mass (MS/MS) spectra obtained using database searching remains an important problem. PeptideProphet is one of the commonly used computational tools available for that purpose. An alternative simple approach for validation of peptide assignments is based on addition of ...
Tabb David L DL Department of Biomedical Informatics and Biochemistry, Vanderbilt University, Nashville, Tennessee 37232-8575, USA. - - 2008
The "Paris Guidelines" have begun the process of standardizing reporting for proteomics. New bioinformatics tools have improved the process for estimating error rates of peptide identifications. This perspective seeks to consider these advances in the context of proteomics' short history. As increasing numbers of proteomics papers come from biologists rather ...
Choi Hyungwon - - 2008
Reliable statistical validation of peptide and protein identifications is a top priority in large-scale mass spectrometry based proteomics. PeptideProphet is one of the computational tools commonly used for assessing the statistical confidence in peptide assignments to tandem mass spectra obtained using database search programs such as SEQUEST, MASCOT, or X! ...
Choi Hyungwon - - 2008
Development of statistical methods for assessing the significance of peptide assignments to tandem mass spectra obtained using database searching remains an important problem. In the past several years, several different approaches have emerged, including the concept of expectation values, target-decoy strategy, and the probability mixture modeling approach of PeptideProphet. In ...
Orchard Sandra - - 2008
The amount of data currently being generated by proteomics laboratories around the world is increasing exponentially, making it ever more critical that scientists are able to exchange, compare and retrieve datasets when re-evaluation of their original conclusions becomes important. Only a fraction of this data is published in the literature ...
Collings Fitz B FB Renal Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine, Rm 550, 4 Blackfan Circle, Boston, MA 02115, United States. - - 2008
Reliable biomarkers of toxicity are necessary both for the safe conduct of pre-clinical and clinical trials, and are increasingly needed for accurate clinical evaluation of treatment regimens with the potential to cause tissue injury. Recent advances in technology have added several new tools to the biomarker screening toolkit and improved ...
Klie Sebastian - - 2008
Since the advent of public data repositories for proteomics data, readily accessible results from high-throughput experiments have been accumulating steadily. Several large-scale projects in particular have contributed substantially to the amount of identifications available to the community. Despite the considerable body of information amassed, very few successful analyses have been ...
Hsieh Sen-Yung - - 2008
Accurate and rapid identification of pathogenic microorganisms is of critical importance in disease treatment and public health. Conventional work flows are time-consuming, and procedures are multifaceted. MS can be an alternative but is limited by low efficiency for amino acid sequencing as well as low reproducibility for spectrum fingerprinting. We ...
Vakhrushev Sergey Y - - 2008
Identification of single glycoconjugate components in a complex mixture from the urine of a patient suffering from a congenital disorder of glycosylation was probed by MALDIMS analysis on a hybrid quadrupole time-of-flight instrument. In negative ion mode, complex maps containing more than 50 ionic species were obtained and a number ...
Weyermann Céline - - 2008
The main objectives of the European project "Collaborative Harmonization of Methods for Profiling of Amphetamine Type Stimulants" (CHAMP) funded by the sixth framework programme of the European Commission, included the harmonization of MDMA profiling methods and the creation of a common database in a drug intelligence perspective. In the preliminary ...
Mantini Dante - - 2008
MOTIVATION: Independent component analysis (ICA) is a signal processing technique that can be utilized to recover independent signals from a set of their linear mixtures. We propose ICA for the analysis of signals obtained from large proteomics investigations such as clinical multi-subject studies based on MALDI-TOF MS profiling. The method ...
Lee Kiju - - 2007
Over the past several decades a number of O(n) methods for forward and inverse dynamics computations have been developed in the multi-body dynamics and robotics literature. A method was developed in 1974 by Fixman for O(n) computation of the mass-matrix determinant for a serial polymer chain consisting of point masses. ...
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, ...
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