can't get m/z array and intensity array

[morestart]

this is my code

for spectrum in mzml.read(self.data, use_index=True):
    self.process_time.append(spectrum.get('scanList').get('scan')[0].get('scan start time'))
    self.mz.append(spectrum.get('m/z array'))
    self.intensity.append(spectrum.get('intensity array'))

m/z and intensity is empty, why?

xml version: version="1.0" system: macos python: 3.8

[mobiusklein]

If your mzML file was already centroided, it's not uncommon for some spectra, especially early in an acquisition, to contain no peaks above whatever noise threshold the peak picker sets. Are all the spectra empty?

[morestart]

if i use this code , i can get need data:

from pyteomics import mzml

data = mzml.read('/Users/cattree/PycharmProjects/BMIProject/data/test.mzML', use_index=True)
print(data.get_by_index(3890))

{'index': 3890, 'id': 'controllerType=0 controllerNumber=1 scan=3891', 'defaultArrayLength': 1763, 'scanList': {'count': 1, 'scan': [{'scanWindowList': {'count': 1, 'scanWindow': [{'scan window lower limit': 50.0, 'scan window upper limit': 2000.0}]}, 'scan start time': 14.626956666667, 'filter string': 'ITMS + c ESI Full ms [50.00-2000.00]', 'preset scan configuration': 0.0, 'ion injection time': 0.327597945929}], 'no combination': ''}, 'MS1 spectrum': '', 'ms level': 1, 'positive scan': '', 'centroid spectrum': '', 'base peak m/z': 1371.603881835938, 'base peak intensity': 767264.375, 'total ion current': 73670352.0, 'lowest observed m/z': 96.687423706055, 'highest observed m/z': 1999.616577148438, 'spectrum title': 'LAMS-POS-JUN-1064nm-1HZ-200MJ-NANOESI-05ULMIN_01.3891.3891. File:"LAMS-POS-JUN-1064nm-1HZ-200MJ-NANOESI-05ULMIN_01.raw", NativeID:"controllerType=0 controllerNumber=1 scan=3891"', 'count': 2, 'm/z array': array([ 96.68742371, 106.71133423, 110.47019958, ..., 1997.41137695, 1998.47338867, 1999.61657715]), 'intensity array': array([ 3213.50585938, 4366.23095703, 4368.14160156, ..., 12838.35742188, 3873.36865234, 4008.85546875])}

[mobiusklein]

You should be able to look at your data structure from the first note and look at the 3890th entry in self.mz and self.intensity and see the same arrays shown in the result of data.get_by_index(3890).

Looking at the scan data you just showed, these are already centroided ('centroid spectrum' key is present).

[morestart]

how can i get all index? self.intensity and self.mz is all empty like this : [array([], dtype=float64), array([], dtype=float64), array([], dtype=float64), array([], dtype=float64), array([], dtype=float64), array([], dtype=float64), array([], dtype=float64).....]

[morestart]

ok, i know why... we must use index=True... if dont use this param, spectrum.get('m/z array')) and spectrum.get('intensity array') will get None

mzml.read(file_path, use_index=True)

I hope this can be explained in the document 😊