GC MS using XCMS

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

Associated Tutorial

This workflows is part of the tutorial GC MS using XCMS, available in the GTN

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

Tutorial Contributor(s): Helena Rasche

Workflow Author(s): RECETOX

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

Added/updated 4 files

Open master c5fbaa4

Added/updated 4 files

Frozen 5.0 18c4cb4