xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data

BMC Bioinformatics - Tập 14 Số 1 - 2013
Karan Uppal1,2, Quinlyn A. Soltow3, Frederick H. Strobel4, W. Stephen Pittard1, Kim M. Gernert1, Tianwei Yu5, Dean P. Jones3
1BimCore, School of Medicine, Emory University, Atlanta, USA
2School of Biology, Georgia Institute of Technology, Atlanta, USA
3Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Emory University, Atlanta, USA
4Mass Spectrometry Center, Emory University, Atlanta, USA
5Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, USA

Tóm tắt

Abstract Background Detection of low abundance metabolites is important for de novo mapping of metabolic pathways related to diet, microbiome or environmental exposures. Multiple algorithms are available to extract m/z features from liquid chromatography-mass spectral data in a conservative manner, which tends to preclude detection of low abundance chemicals and chemicals found in small subsets of samples. The present study provides software to enhance such algorithms for feature detection, quality assessment, and annotation. Results xMSanalyzer is a set of utilities for automated processing of metabolomics data. The utilites can be classified into four main modules to: 1) improve feature detection for replicate analyses by systematic re-extraction with multiple parameter settings and data merger to optimize the balance between sensitivity and reliability, 2) evaluate sample quality and feature consistency, 3) detect feature overlap between datasets, and 4) characterize high-resolution m/z matches to small molecule metabolites and biological pathways using multiple chemical databases. The package was tested with plasma samples and shown to more than double the number of features extracted while improving quantitative reliability of detection. MS/MS analysis of a random subset of peaks that were exclusively detected using xMSanalyzer confirmed that the optimization scheme improves detection of real metabolites. Conclusions xMSanalyzer is a package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. The program was designed to integrate with existing packages such as apLCMS and XCMS, but the framework can also be used to enhance data extraction for other LC/MS data software.

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BMC Bioinformatics

Tập 14 Số 1

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