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Images #46

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XinsongDu opened this issue May 2, 2020 · 19 comments
Open

Images #46

XinsongDu opened this issue May 2, 2020 · 19 comments

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@XinsongDu
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This issue includes all images that are used in the documentation
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XinsongDu commented May 2, 2020 •
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Metabolomics_Pipeline_V6

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design_file_format

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XinsongDu commented Jul 9, 2020 •
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mass_detection

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chromatogram_builder

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smoothing

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chromatogram_deconvolution

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isotupe_grouping

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group_aligner

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peak_finder

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duplicate_filter

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Open MZmine-2.53 batch mode
Screen Shot 2020-07-12 at 1 40 51 PM

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Add mass detection to batch queue.
Screen Shot 2020-07-12 at 1 54 26 PM

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default mass detection algorithm of RUMP is centroid, now change it to local maxima:

  • click "configure"

Screen Shot 2020-07-12 at 1 59 19 PM

- click "..." and set the parameter for local maxima algorithm

Screen Shot 2020-07-12 at 1 59 31 PM

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Click OK and use "save..." button to save config file to your computer
Screen Shot 2020-07-12 at 1 59 55 PM

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Open saved config file, copy the mass detection module to clipboard
Screen Shot 2020-07-12 at 2 00 19 PM

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XinsongDu commented Jul 12, 2020 •
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Open "rump/batchfile_generator_pos_253.py" and replace mass detection module with your new mass detection module by pasting from your clipboard
Screen Shot 2020-07-12 at 3 03 20 PM

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XinsongDu commented Jul 12, 2020 •
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add "\n" to the end of each line you copied, then the file will be like the following:
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XinsongDu commented Jul 12, 2020 •
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Add "\" to quotes in your new mass detection module:
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@nishachachad
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@XinsongDu @nishachachad