Baseline correction for GC-MS data
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@julienkermorvant-23634
Last seen 9 months ago

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 ?

Best regards, Julien Kermorvant

XCMS metaMS • 104 views
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ron.wehrens ▴ 20
@ronwehrens-7060
Last seen 3.4 years ago
Netherlands

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 ?

Best regards, Julien Kermorvant

Post tags: XCMS, metaMS

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https://support.bioconductor.org/p/131764/

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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