Suggested starting parameters for GC-MS data

[ckeeling]

Can you suggest starting parameters for GC-MS data?

[jorainer]

For which algorithm(s)? I've never worked with GC-MS data, but I would suggest to try/check the code in the xcms tutorials related to chrom peak detection maybe?

[sneumann]

Also depends on your instrument and settings. The W4M team also has great tutorials using xcms behind the scenes https://workflow4metabolomics.org/howto, including https://download.workflow4metabolomics.org/docs/w4e2018/2018-10_EC_W4E%20-%20MSprocessing_GC-MS_processing.pdf Yours, Steffen

[ckeeling]

Thanks @sneumann, the pdf link is broken but @yguitton is now aware of this, and directed me to additional information, including metaMS and the metaRbolomics Toolbox.