8. Data processing parameters modification

Steps of data processing

Mass detection -> Chromatogram builder -> Smoothing -> Chromatogram deconvolution -> Isotopics peaks grouper -> Join aligner -> Peak finder -> Duplicate peak filter

Corresponding files that need to be modified

"rump/batchfile_generator_pos_253.py" contains parameters for positive data processing; "rump/batchfile_generator_neg_253.py" contains parameters for negative data processing.

Parameter Modification with The Aid of MZmine-2.53

Suppose I want to change mass detection parameters for positive data

Open MZmine-2.53 batch mode
Add mass detection to batch queue
Default mass detection algorithm of RUMP is centroid, now change it (e.g., change to local maxima)

Click "Configure"
Click "..." and set parameters for local maxima algorithm
Note: make sure "Those created by previous batch step" is selected for "Raw data files"

Click "OK" and use "Save..." button to save config file to your computer
Open saved config file, copy the mass detection module to clipboard
Open "rump/batchfile_generator_pos_253.py" and replace mass detection module with your new mass detection module by pasting from your clipboard
Add "\n\" to the end of each line you copied, then the file will be like the following
Add "\" to quotes in your new mass detection module

Modifying Parameter by Directly Editing Code

Open corresponding file

Open files containing data processing parameters: "rump/batchfile_generator_pos_253.py" contains parameters for positive data processing; "rump/batchfile_generator_neg_253.py" contains parameters for negative data processing.