Guitton Yann

How to query Thermo AIF MS2 data?

1

Hi, Is there a specific way to query an LC-MS file with All Ion Fragmentation (AIF) MS2 with massQL? If yes can you give me an example? Or should i...

fillPeaks function enhancement ChromPeakAreaParam

2

Hi, A new way of using fillpeaks is present in xcms and might be intersting to update the wrapper. See #https://community.france-bioinformatique.fr/t/fillchrompeaks-parameters/3425 `xcms_fillpeaks.r` : https://github.com/workflow4metabolomics/tools-metabolomics/blob/e9183269ad5b2e8f4551f301dc736df330aa73c6/tools/xcms/xcms_fillpeaks.r#L83 In `abims_xcms_fillpeaks.xml` : maybe add a...

Add a function to manage the automatic conversion (in the background) of the sampleMetadata. To avoid having to do a SM with the original file names and another with the...

findChromPeaks Merger with "bad " samplenames format auto correction

1

Hi, in xcms findChromPeaks Merger Merge xcms findChromPeaks RData into a unique file to be used by group (Galaxy Version 3.6.1+galaxy0) in that tool if we use a sampleMetadata.tsv created...

Hi, just a note it seems that with xcms process history (xcms_summary) not all parameters are exported. example if xcms is used before CAMERA then only CAMERA settings seems exported...

In CAMERA.groupFWHM the advanced option **use all the samples (automatic selection) - optional** is linked to the xsAnnotate sample parameter and this is not explained. By default it NA for...

Hi would be cool to add a new wrapper that will help building a custom adduct list to use as input in CAMERA Yann

In CAMERA tools the citation of the paper contains a typo Kuhl, C., Tautenhahn, R., **Böttcher, C.**, Larson, T. R., & Neumann, S. (2011). CAMERA: An Integrated Strategy for Compound...