9.2 Default numeric limits and tolerances

The functions in patRoon use various numeric limits and tolerances to configure e.g. tolerances applied to match retention times and m/z values. Since patRoon 3.0 the defaults for these limits are centralized, which simplifies configuration and switching defaults between different HRMS instruments.

The configuration is done through the limits.yml file. This is an easily editable YAML text file, and by default looks like this:

general:
    version: 1
    IMS: bruker
retention:
    very_narrow: 2
    narrow: 6
    medium: 12
    wide: 30
mz:
    very_narrow: 0.001
    narrow: 0.002
    medium: 0.005
    wide: 0.02
    narrow_rel: 5
    medium_rel: 10
mobility_bruker:
    very_narrow: 0.01
    narrow: 0.02
    medium: 0.04
    wide: 0.2
    medium_rel: 0.05
mobility_agilent:
    very_narrow: 0.1
    narrow: 0.2
    medium: 0.4
    wide: 2
    medium_rel: 0.05
CCS:
    medium: 10
    medium_rel: 0.05

The IMS setting under general specifies which IMS defaults are applied: this should be bruker or agilent. Depending on this setting, defaults are either taken from the mobility_buker or mobility_agilent setting blocks.

If you used the newProject tool to create a new project, the limits.yml file is automatically copied to the project directory. Otherwise, it can be created by the genLimitsFile() function:

genLimitsFile() # copy default limits.yml file to current working directory
genLimitsFile("my/path/limits.yml", IMS = "agilent") # generate `my/path/limits.yml` with Agilent IMS defaults

More information on the limits can be found in the reference manual (?limits).