Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. More information on Cardinal
This tool provides options to filter (subset) pixels and m/z features of mass spectrometry imaging data.
Input data
MSI data: 3 types of input data can be used:
- imzml file (upload imzml and ibd file via the "composite" function) Introduction to the imzml format
- Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
- Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData
Optional file with pixel coordinates and annotation:
Tabular file: One column with x values, one column with y values
The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
Pixel with coordinates outside the coordinates of the input file are ignored
x_coord y_coord 1 1 2 1 3 1 ... ...Optional tabular file with m/z values:
One column with numeric m/z values (without empty fields or letters)
The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
m/z features outside the m/z range of the input file are ignored
m/z 100.0 100.01 100.02 ... ...
Options
Pixel filtering/annotation:
- Either with a tabular file containing x and y coordinates or by entering x-min, x-max, y-min, y-max manually
- Pixel that are not present in the dataset are ignored
- An error occurs if the input for filtering (tabular file, x-range or y-range) contains not a single coordinate that occurs in the input dataset
m/z feature filtering:
- Either with a tabular file containing m/z values or by entering m/z-min and m/z-max manually
- m/z values that are not present in the dataset are ignored
- An error occurs if the input for filtering (tabular file or mz-range) contains not a single m/z feature that occurs in the dataset
m/z feature removing:
- Perturbing m/z features such as matrix contaminants, tryptic peptides and internal calibrants can be removed by specifying their m/z value in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed
Tips
m/z feautre filtering with a tabular file:
- For matching the m/z features of the input dataset are rounded to the number of decimal points of the m/z values from the tabular file. In case the input had more than 4 digits m/z values of dataset and tabular file are rounded to 4 digits.
- Therefore, it is recommended to use the filtering tool only for m/z features which have been extracted from the same dataset. If the m/z values are from a different dataset, the tool 'Join two files on column allowing a small difference' should be used to find corresponding m/z values, which can then be used for filtering.
Problems to select tabular file:
- In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy might be different from 'tabular' - datatype can be changed by pressing the pen button of the dataset (edit attributes)
Output