Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry

<p>Abstract</p> <p>Background</p> <p>Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC/TOF-MS) has been used for metabolite profiling in metabolomics. However, there is still much experimental variation to be controlled including both within-experiment and between-experiment variation. For efficient analysis, an ideal peak alignment method to deal with such variations is in great need.</p> <p>Results</p> <p>Using experimental data of a mixture of metabolite standards, we demonstrated that our method has better performance than other existing method which is not model-based. We then applied our method to the data generated from the plasma of a rat, which also demonstrates good performance of our model.</p> <p>Conclusions</p> <p>We developed a model-based peak alignment method to process both homogeneous and heterogeneous experimental data. The unique feature of our method is the only model-based peak alignment method coupled with metabolite identification in an unified framework. Through the comparison with other existing method, we demonstrated that our method has better performance. Data are available at <url>http://stage.louisville.edu/faculty/x0zhan17/software/software-development/mspa</url>. The R source codes are available at <url>http://www.biostat.iupui.edu/~ChangyuShen/CodesPeakAlignment.zip</url>.</p> <p>Trial Registration</p> <p>2136949528613691</p

An empirical Bayes model using a competition score for metabolite identification in gas chromatography mass spectrometry

<p>Abstract</p> <p>Background</p> <p>Mass spectrometry (MS) based metabolite profiling has been increasingly popular for scientific and biomedical studies, primarily due to recent technological development such as comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC/TOF-MS). Nevertheless, the identifications of metabolites from complex samples are subject to errors. Statistical/computational approaches to improve the accuracy of the identifications and false positive estimate are in great need. We propose an empirical Bayes model which accounts for a competing score in addition to the similarity score to tackle this problem. The competition score characterizes the propensity of a candidate metabolite of being matched to some spectrum based on the metabolite's similarity score with other spectra in the library searched against. The competition score allows the model to properly assess the evidence on the presence/absence status of a metabolite based on whether or not the metabolite is matched to some sample spectrum.</p> <p>Results</p> <p>With a mixture of metabolite standards, we demonstrated that our method has better identification accuracy than other four existing methods. Moreover, our method has reliable false discovery rate estimate. We also applied our method to the data collected from the plasma of a rat and identified some metabolites from the plasma under the control of false discovery rate.</p> <p>Conclusions</p> <p>We developed an empirical Bayes model for metabolite identification and validated the method through a mixture of metabolite standards and rat plasma. The results show that our hierarchical model improves identification accuracy as compared with methods that do not structurally model the involved variables. The improvement in identification accuracy is likely to facilitate downstream analysis such as peak alignment and biomarker identification. Raw data and result matrices can be found at <url>http://www.biostat.iupui.edu/~ChangyuShen/index.htm</url></p> <p>Trial Registration</p> <p>2123938128573429</p

Challenges and complexities in application of LCA approaches in the case of ICT for a sustainable future

In this work, three of many ICT-specific challenges of LCA are discussed. First, the inconsistency versus uncertainty is reviewed with regard to the meta-technological nature of ICT. As an example, the semiconductor technologies are used to highlight the complexities especially with respect to energy and water consumption. The need for specific representations and metric to separately assess products and technologies is discussed. It is highlighted that applying product-oriented approaches would result in abandoning or disfavoring of new technologies that could otherwise help toward a better world. Second, several believed-untouchable hot spots are highlighted to emphasize on their importance and footprint. The list includes, but not limited to, i) User Computer-Interfaces (UCIs), especially screens and displays, ii) Network-Computer Interlaces (NCIs), such as electronic and optical ports, and iii) electricity power interfaces. In addition, considering cross-regional social and economic impacts, and also taking into account the marketing nature of the need for many ICT's product and services in both forms of hardware and software, the complexity of End of Life (EoL) stage of ICT products, technologies, and services is explored. Finally, the impact of smart management and intelligence, and in general software, in ICT solutions and products is highlighted. In particular, it is observed that, even using the same technology, the significance of software could be highly variable depending on the level of intelligence and awareness deployed. With examples from an interconnected network of data centers managed using Dynamic Voltage and Frequency Scaling (DVFS) technology and smart cooling systems, it is shown that the unadjusted assessments could be highly uncertain, and even inconsistent, in calculating the management component's significance on the ICT impacts.Comment: 10 pages. Preprint/Accepted of a paper submitted to the ICT4S Conferenc

An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure

Motivation: Comprehensive two-dimensional gas chromatography mass spectrometry (GC × GC–MS) brings much increased separation capacity, chemical selectivity and sensitivity for metabolomics and provides more accurate information about metabolite retention times and mass spectra. However, there is always a shift of retention times in the two columns that makes it difficult to compare metabolic profiles obtained from multiple samples exposed to different experimental conditions

Interpretation of comprehensive two-dimensional gas chromatography data using advanced chemometrics

The power of comprehensive two-dimensional gas chromatography (GC × GC) for the study of complex mixtures has been indisputably proved in the past several decades. This review encompasses the whole of GC × GC-related data processing and summarizes relevant applications. We include theoretical introduction to some specific methods and studies to aid readers&#039; understanding of chemometrics strategies for advanced data interpretation

The metaRbolomics Toolbox in Bioconductor and beyond

Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub