crux param-medic [options] <spectrum-file>


Examine the spectra in a file to estimate the best precursor and fragment error tolerances for database search and to infer the presence of various types of modifications, including stable-isotope labeling, isobaric labeling, tandem mass tags, and enrichment of phosphorylated peptides. For details on how param-medic works, see these publications:

Damon H. May, Kaipo Tamura, William Stafford Noble. "Param-Medic: A tool for improving MS/MS database search yield by optimizing parameter settings." Journal of Proteome Research. 16(4):1817-1824, 2017.

Damon May, Kaipo Tamura, William Stafford Noble. "Detecting modifications in proteomics experiments with Param-Medic." Journal of Proteome Research. 18(4):1902-1906, 2019.
Note that you can access some of the functionality of Param-Medic by using the --auto-precursor-window and --auto-mz-bin-width options in tide-search.



The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created: