DMA of D. magna - Galaxy workflows

Overview

The three Galaxy workflows used for the Daphnia magna deep metabolome annotation.

These Galaxy workflows were specifically developed to handle and conduct metabolite annotation across the diverse data types generated, encompassing (U)HPLC-HRMS(/MS) and DI-HRMS(MSn) from LC fractionation. By leveraging the extensive replication provided by the experimental workflow, data averaging and filtering were applied to both (U)HPLC-HRMS(/MS) and DI-HRMS(MSn) datasets to ensure that high-quality, reproducible fragment peaks were utilized for various complementary computational metabolite annotation strategies.

Abbreviations:

• (U)HPLC-HRMS(/MS): (Ultra)high-performance liquid chromatography-high resolution tandem mass spectrometry
• DI-HRMS(MSn): Direct infusion-high resolution mass spectrometry with multiple-stage fragmentation

Workflows

The three workflows are:

• W1 (Galaxy-Workflow-W1_LC-MSMS_DIMS_DIMSn_FRAC_DMA.ga): Full (U)HPLC-HRMS(/MS) and DI-HRMS(MSn) from the LC fractionation
• W2 (Galaxy-Workflow-W2_LC-MSMS_DMA.ga): Just (U)HPLC-HRMS(/MS) analysis
• W3 (Galaxy-Workflow-W3_LC-MSMS_MSM_DMA.ga): (U)HPLC-HRMS(/MS) specifically for the analysis of the metabolite standard mixture (MSM) used to assess the performance of the full experimental and computational DMA workflow

Availability and Access

Complete Galaxy workflows, analysis histories, and detailed tool version information are accessible through the dedicated Galaxy instance at https://dma.galaxy.bham.ac.uk/histories/list_published and https://dma.galaxy.bham.ac.uk/workflows/list_published. The workflows are also downloadable from this repository under the GPL-3.0 license.

These resources encompass the complete Galaxy workflow analysis; however, re-running all analyses of the DMA of D. magna, especially outside of the provided Galaxy instances, would require additional setup due to both the high computational resource demands of this large dataset, as well as software updates to some of the underlying Galaxy tools since the analysis in this manuscript was performed.

Software and Galaxy tools summary

Pre-existing software and Galaxy tools

Project name	Galaxy tools	Galaxy tool code home page	Underlying software code home page	Licence	Language
MSnBase	MSnBase.readMSData	https://github.com/workflow4metabolomics/tools-metabolomics	https://www.bioconductor.org/packages/release/bioc/html/MSnbase.html	Underlying software: Artistic-2.0; Galaxy tool: GPL-3.0	R
XCMS	xcms.findChromPeaks; xcms.findChromPeaks Merger; xcms.groupChromPeaks	https://github.com/workflow4metabolomics/tools-metabolomics	http://bioconductor.org/packages/release/bioc/html/xcms.html	GPL (≥2)	R
CAMERA	CAMERA.annotate	https://github.com/workflow4metabolomics/tools-metabolomics	https://www.bioconductor.org/packages/release/bioc/html/CAMERA.html	GPL (≥2)	R
BEAMSpy	BEAMSpy	https://github.com/computational-metabolomics/beamspy-galaxy	https://github.com/computational-metabolomics/beamspy; https://more.bham.ac.uk/beams/	GPL-3.0	R
DIMSpy	dimspy.processScans; dimspy.mergePeaklists; dimspy.alignSamples; dimspy.blankFilter; dimspy.getPeaklist	https://github.com/computational-metabolomics/dimspy-galaxy	https://github.com/computational-metabolomics/dimspy	GPL-3.0	Python

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Software and/or Galaxy tools developed by authors

Project name	Galaxy tools	Galaxy tool code home page	Underlying software code home page	Licence	Language
msPurity	msPurity.purityA; msPurity.flagRemove; msPurity.frag4feature; msPurity.filterFragSpectra; msPurity.averageFragSpectra; msPurity.createMSP; msPurity.createDatabase; msPurity.spectralMatching; msPurity.combineAnnotations; msPurity.dimsPredictPurity	https://github.com/computational-metabolomics/mspurity-galaxy	https://www.bioconductor.org/packages/release/bioc/html/msPurity.html	GPL-3.0	R
MSnPy	MSnPy.group-scans; MSnPy.process-scans; MSnPy.create-spectral-trees; MSnPy.annotate-trees; MSnPy.convert-spectral-trees	https://github.com/computational-metabolomics/msnpy-galaxy	https://github.com/computational-metabolomics/msnpy	GPL-3.0	Python
msp2db	msp2db	https://github.com/computational-metabolomics/dmatools-galaxy	https://github.com/computational-metabolomics/msp2db	GPL-3.0	Python
CAMERA DIMS	CAMERA DIMS	https://github.com/computational-metabolomics/dmatools-galaxy	https://github.com/computational-metabolomics/cameraDIMS	GPL (≥2)	R
SIRIUS CSI:FingerID †	SIRIUS CSI:FingerID	https://github.com/computational-metabolomics/sirius-csifingerid-galaxy	https://bio.informatik.uni-jena.de/software/sirius/	Underlying software: GNU AGPL; Galaxy tool: GPL-3.0	Java (Python for Galaxy wrapper)
MetFrag †	MetFrag	https://github.com/computational-metabolomics/metfrag-galaxy	https://ipb-halle.github.io/MetFrag/	Underlying software: GPL (≥2); Galaxy tool: GPL-3.0	Java (Python for Galaxy wrapper)
LC fractionation processor	LC fractionation processor	https://github.com/computational-metabolomics/lcfrac-galaxy	(all functionality within Galaxy tool)	GPL-3.0	Python
deconrank §	deconrank	https://github.com/computational-metabolomics/dmatools-galaxy	https://github.com/computational-metabolomics/deconrank	GPL-3.0	Python

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Footnotes: bold: New underlying software and Galaxy tool developed by authors
†Galaxy tool developed by authors
§Not used directly in the annotation workflows but used in the directed acquisition workflows described in the supplemental of publication

License

This project is licensed under the GPL-3.0 License - see the LICENSE file for details.