IPO: a tool for automated optimization of XCMS parameters
Gunnar Libiseller,Michaela Dvorzak,Ulrike Kleb,Edgar Gander,Tobias Eisenberg,Frank Madeo,Steffen Neumann,Gert Trausinger,Frank Sinner,Frank Sinner,Thomas R. Pieber,Thomas R. Pieber,Christoph Magnes +12 more
TLDR
The software package IPO (‘Isotopologue Parameter Optimization’) was successfully applied to data derived from liquid chromatography coupled to high resolution mass spectrometry from three studies with different sample types and different chromatographic methods and devices and the potential of IPO to increase the reliability of metabolomics data was shown.Abstract:
Background
Untargeted metabolomics generates a huge amount of data. Software packages for automated data processing are crucial to successfully process these data. A variety of such software packages exist, but the outcome of data processing strongly depends on algorithm parameter settings. If they are not carefully chosen, suboptimal parameter settings can easily lead to biased results. Therefore, parameter settings also require optimization. Several parameter optimization approaches have already been proposed, but a software package for parameter optimization which is free of intricate experimental labeling steps, fast and widely applicable is still missing.read more
Citations
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Journal Article
The Design and Analysis of Experiments
TL;DR: This book by a teacher of statistics (as well as a consultant for "experimenters") is a comprehensive study of the philosophical background for the statistical design of experiment.
Journal ArticleDOI
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights.
Zhiqiang Pang,Jasmine Chong,Guangyan Zhou,David Anderson de Lima Morais,Le Chang,Michel Barrette,Carol Gauthier,Pierre-Étienne Jacques,Shuzhao Li,Jianguo Xia +9 more
TL;DR: The MetaboAnalyst 5.0 as mentioned in this paper is the latest version of the web-based platform for comprehensive metabolomics data analysis and interpretation, aiming to narrow the gap from raw data to functional insights for global metabolomics based on HRMS.
Journal ArticleDOI
Feature-based molecular networking in the GNPS analysis environment.
Louis-Félix Nothias,Louis-Félix Nothias,Daniel Petras,Daniel Petras,Robin Schmid,Kai Dührkop,Johannes Rainer,Abinesh Sarvepalli,Abinesh Sarvepalli,Ivan Protsyuk,Madeleine Ernst,Madeleine Ernst,Madeleine Ernst,Hiroshi Tsugawa,Markus Fleischauer,Fabian Aicheler,Alexander A. Aksenov,Alexander A. Aksenov,Oliver Alka,Pierre-Marie Allard,Aiko Barsch,Xavier Cachet,Andrés Mauricio Caraballo-Rodríguez,Andrés Mauricio Caraballo-Rodríguez,Ricardo Silva,Ricardo Silva,Tam Dang,Tam Dang,Neha Garg,Julia M. Gauglitz,Julia M. Gauglitz,Alexey Gurevich,Giorgis Isaac,Alan K. Jarmusch,Alan K. Jarmusch,Zdeněk Kameník,Kyo Bin Kang,Kyo Bin Kang,Kyo Bin Kang,Nikolas Kessler,Irina Koester,Irina Koester,Ansgar Korf,Audrey Le Gouellec,Marcus Ludwig,Christian Martin H,Laura-Isobel McCall,Jonathan McSayles,Sven W. Meyer,Hosein Mohimani,Mustafa Morsy,Oriane Moyne,Oriane Moyne,Steffen Neumann,Heiko Neuweger,Ngoc Hung Nguyen,Ngoc Hung Nguyen,Mélissa Nothias-Esposito,Mélissa Nothias-Esposito,Julien Paolini,Vanessa V. Phelan,Tomáš Pluskal,Robert A. Quinn,Simon Rogers,Bindesh Shrestha,Anupriya Tripathi,Anupriya Tripathi,Justin J. J. van der Hooft,Justin J. J. van der Hooft,Justin J. J. van der Hooft,Fernando Vargas,Fernando Vargas,Kelly C. Weldon,Kelly C. Weldon,Michael Witting,Heejung Yang,Zheng Zhang,Zheng Zhang,Florian Zubeil,Oliver Kohlbacher,Sebastian Böcker,Theodore Alexandrov,Theodore Alexandrov,Nuno Bandeira,Nuno Bandeira,Mingxun Wang,Mingxun Wang,Pieter C. Dorrestein +87 more
TL;DR: Feature-based molecular networking (FBMN) as discussed by the authors is an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools.
Journal ArticleDOI
MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics.
TL;DR: This work introduces MetaboAnalystR 3.0, a significantly improved pipeline with three key new features: efficient parameter optimization for peak picking; automated batch effect correction; and more accurate pathway activity prediction that offers an efficient pipeline to support high-throughput global metabolomics in the open-source R environment.
Journal ArticleDOI
Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data
TL;DR: MetaboAnalyst 5.0 as discussed by the authors extends the previous 2011 Nature Protocol by providing stepwise instructions to optimize parameters for LC-HRMS spectra processing; obtain functional insights from peak list data; integrate metabolomics data with transcriptomics data or combine multiple metabolomics datasets; conduct exploratory statistical analysis with complex metadata.
References
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Journal Article
The Design and Analysis of Experiments
TL;DR: This book by a teacher of statistics (as well as a consultant for "experimenters") is a comprehensive study of the philosophical background for the statistical design of experiment.
Journal ArticleDOI
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.
TL;DR: An LC/MS-based data analysis approach, XCMS, which incorporates novel nonlinear retention time alignment, matched filtration, peak detection, and peak matching, and is demonstrated using data sets from a previously reported enzyme knockout study and a large-scale study of plasma samples.
Journal ArticleDOI
Some New Three Level Designs for the Study of Quantitative Variables
George E. P. Box,D. W. Behnken +1 more
TL;DR: In this paper, a class of incomplete three level factorial designs useful for estimating the coefficients in a second degree graduating polynomial are described and the designs either meet, or approximately meet, the criterion of rotatability and for the most part can be orthogonally blocked.
Journal ArticleDOI
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
TL;DR: A new generation of a popular open-source data processing toolbox, MZmine 2 is introduced, suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.
Journal ArticleDOI
Metabolite profiles and the risk of developing diabetes
Thomas J. Wang,Martin G. Larson,Martin G. Larson,Ramachandran S. Vasan,Ramachandran S. Vasan,Susan Cheng,Susan Cheng,Susan Cheng,Eugene P. Rhee,Eugene P. Rhee,Elizabeth L. McCabe,Elizabeth L. McCabe,Gregory D. Lewis,Gregory D. Lewis,Caroline S. Fox,Caroline S. Fox,Paul F. Jacques,Céline Fernandez,Christopher J. O'Donnell,Christopher J. O'Donnell,Christopher J. O'Donnell,Stephen A Carr,Vamsi K. Mootha,Vamsi K. Mootha,Jose C. Florez,Jose C. Florez,Amanda Souza,Olle Melander,Clary B. Clish,Robert E. Gerszten,Robert E. Gerszten +30 more
TL;DR: Findings underscore the potential key role of amino acid metabolism early in the pathogenesis of diabetes and suggest that amino acid profiles could aid in diabetes risk assessment.
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