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Command chr

Runs the R interactive script to extract chromatogram(s) from raw MS1 data files (mzXML, mzData and mzML) and saves to PNG image(s) file(s).

Depending on the provided parameters this can be a total ion chromatogram (TIC), a base peak chromatogram (BPC) or an extracted ion chromatogram (XIC) extracted from each sample/file.

In the interactive prompt is possible to select a mz and/or retention time window to better visualize interesting parts of the sample's chromatograms. The plots can be grouped by data collection batch, by a selection of samples, or all the samples can be plotted together.

Parameters

For the complete list of parameters run:

node np3_workflow.js chr --help

Parameters for the command chr:

  • -n, --data_name [name] : the data collection name. Used for verbosity (default: -)
  • -b, --metadata <file> : path to the metadata table CSV file
  • -d, --raw_data_path <path> : path to the folder containing the input LC-MS/MS raw spectra data in mzXML, mzData and mzML format
  • -h, --help output usage information

Results

PNG image(s) file(s) with the extracted chromatogram(s) of the selected sample(s) and grouped as specified in the options.

Examples

Fake example to execute the MS¹ Viewer command:

node np3_workflow.js chr --metadata "/path/to/the/metadata/file/test_np3_metadata.csv" 
--data_name "test_np3" --raw_data_path "/path/to/the/raw/data/directory"

node np3_workflow.js chr -b "/path/to/the/metadata/file/test_np3_metadata.csv" 
-d "/path/to/the/raw/data/directory"