Dataset Information

HD desktop: an integrated platform for the analysis and visualization of H/D exchange data.

ABSTRACT: Here we describe an integrated software platform titled HD Desktop designed specifically to enhance the analysis of hydrogen/deuterium exchange (HDX) mass spectrometry data. HD Desktop integrates tools for data extraction with visualization components within a single web-based application. The interface design enables users to navigate from the peptide view to the sample and experiment levels, tracking all manipulations while updating the aggregate graphs in real time. HD Desktop is integrated with a relational database designed to provide performance enhancements, as well as a robust model for data storage and retrieval. Additional features of the software include retention time determination, which is achieved with the use of theoretical isotope fitting; here, we assume that the best theoretical fit will occur at the correct retention time for any given peptide. Peptide data consolidation for the rendering of data in 2D was realized by automating known and novel approaches. Designed to address broad needs of the HDX community, the platform presented here provides an efficient and manageable workflow for HDX data analysis and is freely available as a web tool at the project home page http://hdx.florida.scripps.edu.

SUBMITTER: Pascal BD

PROVIDER: S-EPMC2792908 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature

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Publications

HD desktop: an integrated platform for the analysis and visualization of H/D exchange data.

Pascal Bruce D BD Chalmers Michael J MJ Busby Scott A SA Griffin Patrick R PR

Journal of the American Society for Mass Spectrometry 20081206 4

Here we describe an integrated software platform titled HD Desktop designed specifically to enhance the analysis of hydrogen/deuterium exchange (HDX) mass spectrometry data. HD Desktop integrates tools for data extraction with visualization components within a single web-based application. The interface design enables users to navigate from the peptide view to the sample and experiment levels, tracking all manipulations while updating the aggregate graphs in real time. HD Desktop is integrated w ...[more]

PMID: 19135386

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Project description:BACKGROUND:One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytical workflows that guarantee reproducibility, repeatability, and result provenance are essential requirements of modern microbiome research. For nearly a decade, several state-of-the-art bioinformatics tools have been developed for understanding microbial communities living in a given sample. However, most of these tools are built with many functions that require an in-depth understanding of their implementation and the choice of additional tools for visualizing the final output. Furthermore, microbiome analysis can be time-consuming and may even require more advanced programming skills which some investigators may be lacking. RESULTS:We have developed a wrapper named iMAP (Integrated Microbiome Analysis Pipeline) to provide the microbiome research community with a user-friendly and portable tool that integrates bioinformatics analysis and data visualization. The iMAP tool wraps functionalities for metadata profiling, quality control of reads, sequence processing and classification, and diversity analysis of operational taxonomic units. This pipeline is also capable of generating web-based progress reports for enhancing an approach referred to as review-as-you-go (RAYG). For the most part, the profiling of microbial community is done using functionalities implemented in Mothur or QIIME2 platform. Also, it uses different R packages for graphics and R-markdown for generating progress reports. We have used a case study to demonstrate the application of the iMAP pipeline. CONCLUSIONS:The iMAP pipeline integrates several functionalities for better identification of microbial communities present in a given sample. The pipeline performs in-depth quality control that guarantees high-quality results and accurate conclusions. The vibrant visuals produced by the pipeline facilitate a better understanding of the complex and multidimensional microbiome data. The integrated RAYG approach enables the generation of web-based reports, which provides the investigators with the intermediate output that can be reviewed progressively. The intensively analyzed case study set a model for microbiome data analysis.

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Dataset Information

HD desktop: an integrated platform for the analysis and visualization of H/D exchange data.

Publications

HD desktop: an integrated platform for the analysis and visualization of H/D exchange data.

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