Maldease is a tool for rapidly processing MALDI mass spectra. It is currently in-development, but is usable in its current form. Maldease uses the excellent MALDIquant library.
maldease --negative-control=<path> --output=<path> --definitions=<tsv> <experiments>...Usage:
maldease --negative-control=<path> --output=<path> --definitions=<tsv>... [--peaks-only|--include-only=<ranges>] [options] <experiments>...
maldease --generate-example-definitions
maldease -v | --version
maldease -h | --help
Options:
-h --help Print this help and exit
-v --version Print program version and exit
-n <path> --negative-control=<path> Path to negative control MALDI results
-o <path> --output=<path> Output directory path
--half-window-size=<int> Half-window size for smoothing and peak
detection [default: 20]
--include-only=<ranges> Consider only these mass ranges for
peak reporting. Lower and upper bounds
are inclusive and separated by a dash.
Multiple ranges can be specified and
are comma delimited,
e.g.--include-only '123-456,1000-2000'
[default: 0-Inf]
--peaks-only Only report peaks within the tolerance
specified by --definitions
-d <tsv> --definitions=<tsv> One or more paths to tab-separated
defintions of target peaks
--generate-example-definitions Generate an example definitions file
and write it to stdout
Example BoNT-A peaks are described in:
Kalb, et al. 2015. "Detection of Botulinum Toxins A, B, E, and F in Foods by Endopep-MS" https://pubs.acs.org/doi/10.1021/jf505482b