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Higdon Roger - - 2010
Large amounts of mass spectrometry (MS) proteomics data are now publicly available; however, little attention has been given to how to best combine these data and assess the error rates for protein identification. The objective of this article is to show how variation in the type and amount of data ...
Yu Kebing - - 2010
Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab-based automated ...
Halevy Itay - - 2010
Sulfur isotopes in ancient sediments provide a record of past environmental conditions. The long-time-scale variability and apparent asymmetry in the magnitude of minor sulfur isotope fractionation in Archean sediments remain unexplained. Using an integrated biogeochemical model of the Archean sulfur cycle, we find that the preservation of mass-independent sulfur is ...
Niu Qian - - 2010
To identify novel serum protein biomarkers and establish diagnostic pattern for rheumatoid arthritis (RA) by using proteomic technology. Serum proteomic spectra were generated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) combined with weak cationic exchange magnetic beads. A training set of spectra, derived from analyzing sera from 22 patients ...
Cazzola Mario - - 2010
Although there is increasing interest in using pulmonary biomarkers for a more complete and clinically relevant assessment of COPD and a plethora of biomarkers are becoming available, there is little information regarding their reproducibility and correlation with other outcome measurements in COPD. The lack of well-validated biomarkers that can be ...
Menschaert Gerben - - 2010
The term peptidomics for a new promising "omics" field was not introduced until the beginning of 2000. The approach has been proven successful in several domains such as neuroendocrine research and biomarker or drug discovery. This review reports on bioinformatics tools and methodologies within the peptidomics field and the application ...
Zhu Qi - - 2010
The enzymatic (18)O-labeling is a useful technique for reducing the influence of the between-spectrum variability on the results of mass-spectrometry experiments. A limitation of the technique is the possibility of an incomplete labeling, which may result in biased estimates of the relative peptide abundance. We propose a Markov-chain-based regression model ...
Cerqueira Fabio R - - 2010
The target-decoy search strategy has been successfully applied in shotgun proteomics for validating peptide and protein identifications. If, on one hand, this method has proven to be very efficient for error estimation, on the other hand, little attention has been paid to the resulting sensitivity. Only two scores are normally ...
Kirchner Marc - - 2010
Despite the efforts of the mass spectrometry (MS) community to migrate data representation toward modern file formats, legacy text formats still play an important role in MS data processing workflows. We provide a formal grammar and a portable, efficient C++ implementation for a Mascot Generic Format (MGF) parser. Software and ...
Courtiol Alexandre - - 2010
Many studies use representations of human body outlines to study how individual characteristics, such as height and body mass, affect perception of body shape. These typically involve reality-based stimuli (e.g., pictures) or manipulated stimuli (e.g., drawings). These two classes of stimuli have important drawbacks that limit result interpretations. Realistic stimuli ...
Gabbiani Chiara - - 2010
Since the discovery of cisplatin and its introduction in the clinics, metal compounds have been intensely investigated in view of their possible application in cancer therapy. In this frame, a deeper understanding of their mode of action, still rather obscure, might turn crucial for the design and the obtainment of ...
Wacey David - - 2010
The 3426-3350 Ma Strelley Pool Formation (SPF) is a silicified, dominantly sedimentary unit within the Pilbara Supergroup, Western Australia. It is found widely across the East Pilbara Terrane, and it forms a prominent marker horizon and separates the largely volcanic 3520-3427 Ma Warrawoona and 3350-3315 Ma Kelly groups. It has ...
Jarcuska Peter - - 2010
INTRODUCTION: Fibrogenesis is a typical reaction of the liver to injury. In the case of overstimulation of fibrogenesis clinically significant fibrosis and, eventually, cirrhosis occur. Treatment of liver cirrhosis is limited, therefore it is important to screen and monitor patients at risk of cirrhosis. Noninvasive parameters are ideal for this ...
Chao Tzu-Chiao - - 2010
The use of proteomics to profile biological fluids and identify therein biomarkers for cancer and other diseases was initially received with considerable excitement. However, results have fallen short of the expectations. Traditionally, protein biomarkers have been identified by measurement of relative expression changes between case and control samples from which ...
Souady Jamal - - 2010
Glycosphingolipids (GSLs) are major components of the outer leaflet of the cell membrane. These lipids are involved in many cell surface events and show disease-related expression changes. GSLs could thus serve as useful targets for biomarker discovery. The GSL structure is characterized by two entities: a hydrophilic glycan and a ...
Karp Natasha A - - 2010
iTRAQ (isobaric tags for relative or absolute quantitation) is a mass spectrometry technology that allows quantitative comparison of protein abundance by measuring peak intensities of reporter ions released from iTRAQ-tagged peptides by fragmentation during MS/MS. However, current data analysis techniques for iTRAQ struggle to report reliable relative protein abundance estimates ...
Buyse Marc - - 2010
Biomarkers and surrogate end points have great potential for use in clinical oncology, but their statistical validation presents major challenges, and few biomarkers have been robustly confirmed. Provisional supportive data for prognostic biomarkers, which predict the likely outcome independently of treatment, is possible through small retrospective studies, but it has ...
Reemtsma Thorsten - - 2010
A two-dimensional diagram is proposed, in which the carbon number of each formula is plotted against its nominal mass, to visualize large sets of molecular formula data that can be derived from data generated by ultrahigh-resolution Fourier transform ion cyclotron resonance-MS. In such a carbon versus mass (CvM) diagram, each ...
Ray Patrick - - 2010
A biomarker may provide a diagnosis, assess disease severity or risk, or guide other clinical interventions such as the use of drugs. Although considerable progress has been made in standardizing the methodology and reporting of randomized trials, less has been accomplished concerning the assessment of biomarkers. Biomarker studies are often ...
Tseng George C - - 2010
High-throughput experiments have become more and more prevalent in biomedical research. The high-dimensional data have brought new challenges. Effective data reduction, summarization and visualization are important keys to initial exploration in the data mining. In this paper, we introduce a visualization tool, namely quantile map, to present information contained in ...
Huang Qizhi - - 2010
Biomarkers are needed to screen multiple stages in the clinical pathway of Barrett's oesophagus patients; from disease diagnosis to risk stratification and predicting response to therapy. Routes to the identification of biomarkers have been recognized by known molecular features of the disease and more recently through transcriptomic, methylation and proteomic ...
Christin Christin - - 2010
Time alignment of complex LC-MS data remains a challenge in proteomics and metabolomics studies. This work describes modifications of the Dynamic Time Warping (DTW) and the Parametric Time Warping (PTW) algorithms that improve the alignment quality for complex, highly variable LC-MS data sets. Regular DTW or PTW use one-dimensional profiles ...
Yunes Nicol?s - - 2010
We present the first models of extreme-mass-ratio inspirals within the effective-one-body (EOB) formalism, focusing on quasicircular orbits into nonrotating black holes. We show that the phase difference and (Newtonian-normalized) amplitude difference between analytical EOB and numerical Teukolsky-based gravitational waveforms can be reduced to less than or approximately 10{-1} rad and ...
Djidja Marie-Claude - - 2010
The development of tissue micro-array (TMA) technologies provides insights into high-throughput analysis of proteomics patterns from a large number of archived tumour samples. In the work reported here, matrix-assisted laser desorption/ionisation-ion mobility separation-mass spectrometry (MALDI-IMS-MS) profiling and imaging methodology has been used to visualise the distribution of several peptides and ...
Mart?nez-Bartolom? Salvador - - 2010
The Human Proteome Organization's Proteomics Standards Initiative aims to develop new standards for data representation and exchange. The Proteomics Standards Initiative has defined the Minimum Information About a Proteomics Experiment (MIAPE) guidelines that specify the information that should be reported with a published experiment. With the aim of promoting the ...
Albrecht Daniela - - 2010
Gel-based proteomics is a widely applied technique to measure abundances of proteins in various biological systems. Comparison of two or more biological groups involves matching of 2-D gels. Depending on the software, this can result in spots showing missing values on several gels. Most studies ignore this fact or substitute ...
Stephan Christian - - 2010
The organization and storage of proteomics data are challenging issues today and even more for the rising amount of information in the future. This review article describes the advantages of using Laboratory Information Management Systems (LIMS) in proteomics laboratories. Seven typical LIMS are explored in detail to describe their role ...
Park Sung Kyu - - 2010
Quantitative analysis has become increasingly important in the proteomics field; however, the large amount of mass spectrometric data and the different types of quantitative strategies make data analysis ever challenging. Here we describe a quantitative software tool called Census to analyze high-throughput mass spectrometry data from shotgun proteomics experiments in ...
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 - - 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 - - 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, ...
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