Bruker-Specific processing
Several parameters can change how the bruker data is processed.
{
"bruker_config": {
"ms1": {
"mz_ppm": 15.0,
"ims_pct": 3.0
},
"ms2": {
"spectrum_processing_params": {
"smoothing_window": 1,
"centroiding_window": 1,
"calibration_tolerance": 0.1,
"calibrate": false
},
"frame_splitting_params": {
"Quadrupole": {
"UniformMobility": [[0.1, 0.05], null]
}
},
}
}
}MS1
These parameters modify the tolerances to centroid peaks along the mobility dimension of a frame.
This parameter is only used if the lfq option is enabled.
centroid_config
{
"bruker_config": {
"ms1": {
"mz_ppm": 15.0,
"ims_pct": 3.0
}
}MS2 Spectrum Processing Parameters
Default Parameters
{
"bruker_config": {
"ms2": {
"spectrum_processing_params": {
"smoothing_window": 1,
"centroiding_window": 1,
"calibration_tolerance": 0.1,
"calibrate": false
}
}
}
}(Experimental) Frame Splitting Parameters
These parameters can be used to search timsDIA data using Sage. In essence they describe how the frame should be split to generate spectra.
There are two major options that describe what subsets of the frame
should be considered an unit to split by; The options are Window
and Quadrupole. And Three minor options, null, UniformMobility,
and Even.
null, No splitting beyond the major group is done.UniformMobility, Splits each region in areas of a specified size, and that overlap by a specific value. For instance [0.1, 0.05] will combine regions of size 0.1 1/k0 and will overlap by 0.05 with each other.EvenWill evenly divide the mobility window intoNnumber of groups.
Default value:
{
"bruker_config": {
"ms2": {
"frame_splitting_params": {
// "Window": { // All internal options are also compatible with `Window`
"Quadrupole": {
"UniformMobility": [[0.1, 0.05], null]
// "Even": 10
// null
}
}
}
}
}