MS scan visualization
In case you need a demo data file.
Visualize a single MS1 or MS/MS scan
Plot by scan index:
from masscube import read_raw_file_to_obj
d = read_raw_file_to_obj("demo_data.mzML")
# by index
scan_index = 10 # index of the scan to visualize
scan = d.scans[scan_index] # get the scan object
# example 1
scan.plot_scan()Example output 1
Plot the scan by index:
Plot MS/MS scans by searching for a specific m/z value and retention time:
from masscube import read_raw_file_to_obj
d = read_raw_file_to_obj("demo_data.mzML")
# by m/z and retention time
target_mz_arr = 138.0521 # m/z value of the precursor ion.
target_rt = 1.774 # target retention time in minutes. Set it to None to plot the whole retention time range
mz_tol = 0.005, # m/z tolerance in Da
rt_tol = 0.3, # retention time tolerance in minutes
# search all available MS/MS scans
scans = d.find_ms2_by_mzrt(target_mz_arr, target_rt, mz_tol=0.005, rt_tol=0.3)
# example 2
for scan in scans:
scan.plot_scan()Example output 2
The first MS/MS scan by m/z and retention time:
The second MS/MS scan by m/z and retention time:
