I'm currently working on low-resolution GC-MS data with quite high baseline which pollute the features I extract with metaMS peakDetection wrapper (peak picking done with the matched filter method).
I would like to remove the baseline specifically for each ion (not on the TIC), do you have any library or function suggestions do to that ?
Hi Julien,
no, metaMS does not have such functions. It uses the peak picking
facilities of xcms (which already take into acccount local baselines if
I am not mistaken) - maybe tapping into the xcms community might help.
Finally, please note that I am no longer the maintainer of metaMS.
Cheers,Ron
-----Original Message-----From: julien.kermorvant [bioc] <
noreply@bioconductor.org>Reply-To:
reply+07d4f3a8+code@bioconductor.orgTo: ron.wehrens@gmail.comSubject:
[bioc] Baseline correctio for GC-MS dataDate: Mon, 15 Jun 2020 07:55:14
+0000
Activity on a post you are following on support.bioconductor.org
User julien.kermorvant wrote Question: Baseline correctio for GC-MS
data:
Hello,
I'm currently working on low-resolution GC-MS data with quite high
baseline which pollute the features I extract with metaMS peakDetection
wrapper (peak picking done with the matched filter method).
I would like to remove the baseline specifically for each ion (not on
the TIC), do you have any library or function suggestions do to that ?
Thank you for your answer.
The peak detection function works perfectly fine, but the extracted spectrum at a given retention time contains the ions of the compound of interest but also the background noise and bleeding which I would like to get rid of to create my standard database.
Dear Ron,
Thank you for your answer. The peak detection function works perfectly fine, but the extracted spectrum at a given retention time contains the ions of the compound of interest but also the background noise and bleeding which I would like to get rid of to create my standard database.
Take care, Julien