massdash.structs.TargetedDIAConfig

class massdash.structs.TargetedDIAConfig

Bases: object

A class representing the configuration for the extraction windows.

ms1_mz_tol

The m/z tolerance for MS1 spectra.

Type:

float

mz_tol

The m/z tolerance for MS2 spectra.

Type:

float

rt_window

The retention time window for spectra.

Type:

float

im_window

The ion mobility window for spectra.

Type:

float

mslevel

A list of MS levels to include.

Type:

list

update()

Update the configuration attributes using a dictionary.

get_im_upper_lower(im_apex: float) → Tuple[float, float]

Get the upper bound and lower bound of a target IM point for a given IM window, i.e. a window of 0.06 would be 0.03 points to either side of the target IM.

Parameters:

im_apex – (float) The target IM point to generate upper and lower bound IM coordinates for

Returns:

(tuple) a tuple of the lower and upper bound for target IM

get_rt_upper_lower(rt_apex: float) → Tuple[float, float]

Get the upper bound and lower bound of a target RT point for a given RT window, i.e. a window of 50 would be 25 points to either side of the target RT.

Parameters:

rt_apex – (float) The target RT point to generate upper and lower bound RT coordinates for

Returns:

(tuple) a tuple of the lower and upper bound for target RT

get_upper_lower_tol(target_mz: float) → Tuple[float, float]

Get the upper bound and lower bound mz around a target mz given a mz tolerance in ppm

Parameters:

• target_mz – (float) The target mz to generate upper and lower bound mz coordinates for

• mz_tol – (int) The m/z tolerance toget get upper and lower bounds arround target mz. Must be in ppm.

Returns:

(tuple) a tuple of the lower and upper bound for target mz

is_mz_in_product_mz_tol_window(check_mz: float, target_product_upper_lower_list: List[Tuple[float, float]]) → bool

Check to see if a target product ion mz is within upper and lower tolerance window

Parameters:

• check_mz – (float) The target product ion mz to check

• target_product_upper_lower_list – (list) A list of tuples that contain an upper and lower bound of a product mz

Return: (bool) Return a logical value

update(config_dict)

Update the configuration attributes using a dictionary.

Parameters:

config_dict (dict) – A dictionary containing configuration values.

Example

config_dict = {

‘rt_window’: 50, ‘im_window’: 0.06, ‘mslevel’: [1, 2]

} config.update(config_dict)