Workflow Type: Galaxy

XCMS and RAMClustR based workflow for data processing and annotation using library matching via matchms.

Associated Tutorial

This workflows is part of the tutorial Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms), available in the GTN

Features

Thanks to...

Workflow Author(s): RECETOX

Tutorial Author(s): Matej Troják, Helge Hecht, Maxim Skoryk

Tutorial Contributor(s): Helena Rasche, Matej Troják, Mélanie Petera, Saskia Hiltemann, Björn Grüning

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Input Dataset Collection #main/Input Dataset Collection Mass spectrometry data to be processed in the workflow. Please ensure the format is supported by msconvert and only use the peak picking option if the input data was acquired in profile mode.
  • array containing
    • File
Reference compound list (alkanes) #main/Reference compound list (alkanes) List of retention indexed reference compounds. Either a table with columns `rt` and `ri` or an MSP with retention time and index metadata.
  • File
Reference spectra #main/Reference spectra Spectral library to use for annotation in MSP or MGF format.
  • File
sample_metadata.tsv #main/sample_metadata.tsv Sample metadata sheet, containing sample name, type (QC, blank, sample, etc.), batch number and injection order.
  • File

Steps

ID Name Description
4 msconvert toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2
5 MSnbase readMSData toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0
6 xcms findChromPeaks (xcmsSet) toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0
7 xcms findChromPeaks Merger toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0
8 xcms groupChromPeaks (group) toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0
9 xcms adjustRtime (retcor) toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0
10 xcms groupChromPeaks (group) toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0
11 xcms fillChromPeaks (fillPeaks) toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0
12 RAMClustR toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2
13 RIAssigner toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1
14 matchms similarity toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0
15 matchms scores formatter toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0

Outputs

ID Name Description Type
CosineGreedy scores of input dataset(s) #main/CosineGreedy scores of input dataset(s) n/a
  • File
Deconvoluted spectra #main/Deconvoluted spectra n/a
  • File
Feature (peak) intensities #main/Feature (peak) intensities n/a
  • File
Feature (peak) metadata (mz, rt, ...) #main/Feature (peak) metadata (mz, rt, ...) n/a
  • File
Feature (spectra) intensities #main/Feature (spectra) intensities n/a
  • File
Retention indexed spectra #main/Retention indexed spectra n/a
  • File
matchms_scores #main/matchms_scores n/a
  • File
xcmsObj (XCMSnExp) #main/xcmsObj (XCMSnExp) n/a
  • File

Version History

2.0 (earliest) Created 2nd Jun 2025 at 10:59 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:59

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