Author(s) Ron Wehrens (ron.wehrens@gmail.com), Georg Weingart, Fulvio Mattivi
Galaxy wrapper and scripts developpers Guitton Yann LABERCA yann.guitton@oniris-nantes.fr and Saint-Vanne Julien julien.saint-vanne@sb-roscoff.fr
Please cites
metaMS : Wehrens, R.; Weingart, G.; Mattivi, F. Journal of Chromatography B.
xcms : Smith, C. A.; Want, E. J.; O’Maille, G.; Abagyan, R.; Siuzdak, G. Anal. Chem. 2006, 78, 779–787.
CAMERA : Kuhl, C.; Tautenhahn, R.; Böttcher, C.; Larson, T. R.; Neumann, S. Analytical Chemistry 2012, 84, 283–289.
metaMS.runGC is a function dedicated to GCMS data processing from converted files to the generation of pseudospectra (compounds) table. Current version for metaMS R package: 1.18.1
Process: Each of the converted data (cdf, mzML...) is profiled by a combination of xcms and CAMERA functions. Then all the mass spectra of detected peaks are compared and clustered. For more details see metaMS : Wehrens, R.; Weingart, G.; Mattivi, F. Journal of Chromatography B (10.1016/j.jchromb.2014.02.051) link
Main outputs: A PeakTable is generated with one line per "compound" and one column per sample. A dataMatrix.csv file is generated and can be used for PCA or for further analysis. A peakspectra.mps file is generated that contains all the spectra of the detected compounds in MSP format. That file can be used for database search online (Golm, MassBank) or locally (NIST MSSEARCH) for NIST search a tutorial is available here.
Upstream tools
You can start from here (XCMS 1.x) or use result file from (XCMS 3.x) :
Name | output file | format | parameter |
---|---|---|---|
xcms.xcmsSet | xset.RData RData | RData | file |
Downstream tools
Name | Output file | Format |
---|---|---|
Determine Vdk or Lowess | dataMatrix.tsv | Tabular |
Normalization Vdk/Lowess | dataMatrix.tsv | Tabular |
Anova | dataMatrix.tsv | Tabular |
PCA | dataMatrix.tsv | Tabular |
Hierarchical Clustering | dataMatrix.tsv | Tabular |
Golm Metabolome Search | peakspectra.msp | Text |
General schema of the metabolomic workflow for GCMS
If you choose to use results from xcms.xcmsSet with XCMS > 3.0
Parameter : num + label | Format |
---|---|
1 : RData file from XCMS | RData |
Or converted GCMS files (mzML, CDF...) in your local libray with XCMS < 3.0 (from metaMS)
Parameters are described in metaMS R package and mainly correspond to those of xcms.xcmsSet
Reference Data for testing are taken from:
Dittami,S.M. et al. (2012) Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae): Adaptation to low salinities in Ectocarpus. The Plant Journal
RData file from XCMS -> xset_merged.RData
Settings -> DefaultDB option -> show | DB file: -> W4M0004_database_small.msp...all default option values
RData file -> rungc.RData
Version 3.0 - 20/05/2019
Version 2.1 - 08/06/2017
Version 1.1 - 11/07/2016
Version 1.0 - 01/06/2015