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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 - - 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 ...
Rogers Shane W - - 2007
Expedited site characterization and groundwater monitoring using direct-push technology and conventional monitoring wells were conducted at a former manufactured gas plant site. Biogeochemical data and heterotrophic plate counts support the presence of microbially mediated remediation. By superimposing solutions of a two-dimensional reactive transport analytical model, first-order degradation rate coefficients ((day-1) ...
Matthiesen Rune - - 2007
Mass spectrometry (MS) has recently become one of the most informative methods for studying proteins. Albiet, MS cannot compete with the detailed structural information obtained by methods such as nuclear magnetic resonance and X-ray crystallography. However, MS is much easier to automate and use as a large-scale technique. Large-scale proteomic ...
Boehm Andreas M - - 2007
BACKGROUND: Mass spectrometry based quantification of peptides can be performed using the iTRAQ reagent in conjunction with mass spectrometry. This technology yields information about the relative abundance of single peptides. A method for the calculation of reliable quantification information is required in order to obtain biologically relevant data at the ...
Faria-Campos A C - - 2007
Proteomics correspond to the identification and quantitative analysis of proteins expressed in different conditions or life stages of a cell or organism. Methods used in proteomics analysis include mainly chromatography, two-dimensional electrophoresis and mass spectrometry. Data generated in proteomics analysis vary significantly, and to identify a protein it is often ...
Oliver Arnau - - 2007
In this paper we propose a new approach for false positive reduction in the field of mammographic mass detection. The goal is to distinguish between the true recognized masses and the ones which actually are normal parenchyma. Our proposal is based on Local Binary Patterns (LBP) for representing salient micro-patterns ...
Zivy Michel - - 2007
The use of 2D electrophoresis for comparative proteomics allows the revelation of variations of protein relative amounts according to various physiological or genetic criteria. The statistical significance of these results is related to different factors, from the experimental design to the statistical tests. In this chapter we describe different parameters ...
Thysell Elin - - 2007
A strategy for processing of metabolomic GC/MS data is presented. By considering the relationship between quantity and quality of detected profiles, representative data suitable for multiple sample comparisons and metabolite identification was generated. Design of experiments (DOE) and multivariate analysis was used to relate the changes in settings of the ...
Khatami Mahin - - 2007
The purpose of this position article was to design a set of criteria (data elements) for a wide range of cancer biomarkers (CBs) in an attempt to standardize biomarkers features through a common language as a foundation for a database. Data elements are described as a set of generic criteria, ...
Fu Jingyuan - - 2007
We here describe the MetaNetwork protocol to reconstruct metabolic networks using metabolite abundance data from segregating populations. MetaNetwork maps metabolite quantitative trait loci (mQTLs) underlying variation in metabolite abundance in individuals of a segregating population using a two-part model to account for the often observed spike in the distribution of ...
Engkilde Kåre - - 2007
We present the background for multivariate data analysis on proteomics data with a hands-on section on how to transfer data between different software packages. The techniques can also be used for other biological and biochemical problems in which structures have to be found in a large amount of data. Digitalization ...
Sumner Lloyd W - - 2007
Metabolomics is the large-scale analysis of metabolites and as such requires bioinformatics tools for data analysis, visualization, and integration. This chapter describes the basic composition of chromatographically coupled mass spectrometry (MS) data sets used in metabolomics and describes in detail the steps necessary for extracting large-scale qualitative and quantitative information. ...
Culley Joan M - - 2007
This research proposes a comprehensive Information Conceptual Model for a Mass Casualty Continuum of Care. The conceptual model lays out the key relationships among entities/factors in mass casualty events needed to provide real-time visibility of data that track patients, personnel, resources and potential hazards to improve responders situational awareness. Validation ...
Gilar Martin - - 2007
A retention prediction model was developed for peptides separated in reversed-phase chromatography. The model was utilized to identify and exclude the false positive (FP) peptide identifications obtained via database search. The selected database included human proteins, as well as decoy sequences of random proteins. The FP peptide detection rate was ...
Lee Jean W - - 2007
Many candidate biomarkers emerging from genomics and proteomics research have the potential to serve as predictive indexes for guiding the development of safer and more efficacious drugs. Research and development of biomarker discovery, selection, and clinical qualification, however, is still a relatively new field for the pharmaceutical industry. Advances in ...
Huang Hongzhan - - 2007
In the post-genome era, researchers are systematically tackling gene functions and complex regulatory processes by studying organisms on a global scale; however, a major challenge lies in the voluminous, complex, and dynamic data being maintained in heterogeneous sources, especially from proteomics experiments. Advanced computational methods are needed for integration, mining, ...
Villanueva Josep - - 2007
Discovery of biomarker patterns using proteomic techniques requires examination of large numbers of patient and control samples, followed by data mining of the molecular read-outs (e.g., mass spectra). Adequate signal processing and statistical analysis are critical for successful extraction of markers from these data sets. The protocol, specifically designed for ...
Dutkowski Janusz - - 2007
BACKGROUND: Recent development of mass spectrometry technology enabled the analysis of complex peptide mixtures. A lot of effort is currently devoted to the identification of biomarkers in human body fluids like serum or plasma, based on which new diagnostic tests for different diseases could be constructed. Various biomarker selection procedures ...
Xia Qiangwei - - 2007
Differential analysis of whole cell proteomes by mass spectrometry has largely been applied using various forms of stable isotope labeling. While metabolic stable isotope labeling has been the method of choice, it is often not possible to apply such an approach. Four different label free ways of calculating expression ratios ...
Doerksen Shawna E - - 2007
ABSTRACT: BACKGROUND: Multiple sclerosis (MS) is a chronic neurological disease that is associated with physical inactivity. Understanding the factors that correlate with physical activity is important for developing effective physical activity promotion programs for this population. Thus, we conducted a cross-sectional study that examined the association between features of the ...
MacCoss Michael J - - 2007
Over the last few years, new proteomics methods have been developed for making quantitative comparisons using stable isotope labeling. Although these methods have paved the way for quantitative proteomics, the analysis of these data is often the rate-limiting step. In fact, many analyzes are still carried out manually, which adds ...
Fu Yan - - 2007
The assumption on the mass error distribution of fragment ions plays a crucial role in peptide identification by tandem mass spectra. Previous mass error models are the simplistic uniform or normal distribution with empirically set parameter values. In this paper, we propose a more accurate mass error model, namely conditional ...
Pham Tuan D - - 2007
Recent advent of mass-spectrometry data generated by proteomic technology provides a new type of biological information which is very promising in the search for diagnostic and therapeutic approaches that enables the early detection of fatal diseases and the development of personalized medicine. Successful analysis of such high-throughput proteomic data relies ...
Ruty Nicolas - - 2007
An experimental setup and human vocal folds replica able to produce self-sustained oscillations are presented. The aim of the setup is to assess the relevance and the accuracy of theoretical vocal folds models. The applied reduced mechanical models are a variation of the classical two-mass model, and a simplification inspired ...
Grau P - - 2007
In this paper, a new methodology for integrated modelling of the WWTP has been used for the construction of the Benchmark Simulation Model N degrees 2 (BSM2). The transformations-approach proposed in this methodology does not require the development of specific transformers to interface unit process models and allows the construction ...
Laures Alice M-F - - 2007
The results of an investigation of the parameters which have the most significant effect on the accuracy of mass measurements on a quadrupole orthogonal acceleration time-of-flight mass spectrometer (q-oaToF) are reported. The influence of eight factors is investigated: ion abundances of reference and analyte compounds, mass difference between analyte and ...
Aliferis Constantin F - - 2007
Sound data analysis is critical to the success of modern molecular medicine research that involves collection and interpretation of mass-throughput data. The novel nature and high-dimensionality in such datasets pose a series of nontrivial data analysis problems. This technical commentary discusses the problems of over-fitting, error estimation, curse of dimensionality, ...
Quandt Andreas - - 2007
Biomarker detection is one of the greatest challenges in Clinical Proteomics. Today, great hopes are placed into tandem mass spectrometry (MS/MS) to discover potential biomarkers. MS/MS is a technique that allows large scale data analysis, including the identification, characterization, and quantification of molecules. Especially the identification process, that implies to ...
Kiehntopf Michael - - 2007
Surface-enhanced laser desorption time of flight mass spectrometry (SELDI-TOF-MS) is an important proteomic technology that is immediately available for the high throughput analysis of complex protein samples. Over the last few years, several studies have demonstrated that comparative protein profiling using SELDI-TOF-MS breaks new ground in diagnostic protein analysis particularly ...
Matthiesen Rune - - 2007
The number of tools described in the literature for analysis of proteome data is growing fast. However, most tools are not able to communicate or exchange data with other tools. In Virtual Expert Mass Spectrometrist (VEMS) v3.0 an effort has been made to interface and export to already existing tools. ...
Deng Xutao - - 2007
Many studies showed inconsistent cancer biomarkers due to bioinformatics artifacts. In this paper we use multiple data sets from microarrays, mass spectrometry, protein sequences, and other biological knowledge in order to improve the reliability of cancer biomarkers. We present a novel Bayesian network (BN) model which integrates and cross-annotates multiple ...
Kage Andreas - - 2007
Mammography is the standard examination method for the early detection of breast cancer. In the last decade, computer assisted detection systems have been developed that assist the physician in the detection of suspicious regions in mammograms. However, recent clinical studies indicate that state of the art CAD systems might have ...
Orchard Sandra - - 2007
The ever increasing volumes of proteomic data now being produced by laboratories across the world have resulted in major issues in data storage and accessibility. The further demands of multilaboratory initiatives has highlighted issues when collaborators cannot import data generated within the same project but generated by different hardware types ...
Howes Charles G - - 2007
Technological advances in mass spectrometry and other detection methods are leading to larger and larger proteomics datasets. However, when papers describing such information are published the enormous volume of data can typically only be provided as supplementary data in a tabular form through the journal website. Several journals in the ...
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