# read file and convert to intensity matrix andi_file = "/x/PyMS/data/gc01_0812_066.cdf" data = ANDI_reader(andi_file) im = build_intensity_matrix_i(data) # Get the scan of a known TIC peak (at RT 31.17 minutes) # get the index of the scan nearest to 31.17 minutes (converted to seconds) scan_i = im.get_index_at_time(31.17*60.0) # get the MassSpectrum Object ms = im.get_ms_at_index(scan_i) # create a Peak object peak = Peak(31.17, ms, minutes=True) print peak.get_UID() # modify the range and null TMS ions peak.crop_mass(60, 450) peak.null_mass(73) peak.null_mass(147) # New UID after modification print peak.get_UID() # Create another peak from an isomer of the first peak (at RT 31.44 minutes) scan_i = im.get_index_at_time(31.44*60.0) ms = im.get_ms_at_index(scan_i) peak2 = Peak(31.44, ms, minutes=True) # modify the range and null TMS ions
from pyms.GCMS.IO.ANDI.Function import ANDI_reader from pyms.Peak.Class import Peak # read file and convert to intensity matrix andi_file = "/x/PyMS/data/gc01_0812_066.cdf" data = ANDI_reader(andi_file) im = build_intensity_matrix_i(data) # Get the scan of a known TIC peak (at RT 31.17 minutes) # get the index of the scan nearest to 31.17 minutes (converted to seconds) scan_i = im.get_index_at_time(31.17 * 60.0) # get the MassSpectrum Object ms = im.get_ms_at_index(scan_i) # create a Peak object peak = Peak(31.17, ms, minutes=True) # Get the retention time (in seconds) print peak.get_rt() # Get the peaks unique ID # Consists of the two most abundant ions and their ratio, # and the retention time (in the format set by minutes=True or False) print peak.get_UID() # Create another peak from an isomer of the first peak (at RT 31.44 minutes) scan_i = im.get_index_at_time(31.44 * 60.0) ms = im.get_ms_at_index(scan_i) peak2 = Peak(31.44, ms, minutes=True) print peak2.get_UID()
