Reading in mass spec imaging data -mzMLb

[Ana-Maria Nastase]

Good morning,

I am trying to use pyteomics to read in an mzMLb file. The file was generated from mass spectrometry imaging data by conversion from Waters .raw file to mzMLb through ProteoWizard msconvert. My question is: Would you know whether the pixel coordinates information for each spectrum is retained in the mzMLb file and whether pyteomics accesses this information?

In the imzML file this information looks something like this: 

<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="223”/>

An example output I get from pyteomics when reading in the data looks like this:

file.get_by_index(17639)

{'index': 17639, 'id': 'function=1 process=0 scan=17640', 'defaultArrayLength': 22649, 'scanList': {'count': 1, 'scan': [{'scanWindowList': {'count': 1, 'scanWindow': [{'scan window lower limit': 50.0 m/z, 'scan window upper limit': 1200.0 m/z}]}, 'preset scan configuration': 1.0, 'scan start time': 102.720802307129 minute}], 'no combination': ''}, 'MS1 spectrum': '', 'ms level': 1, 'positive scan': '', 'profile spectrum': '', 'base peak m/z': 348.181885, 'base peak intensity': 1622.0, 'total ion current': 246812.0, 'count': 2, 'm/z array': array([ 49.99884415, 50.15951157, 50.16260529, ..., 1199.61010742, 1199.62524414, 1199.98815918]), 'intensity array': array([ 0., 0., 26., ..., 17., 0., 0.], dtype=float32)}

Thank you. Your help is very much appreciated.

Best wishes,

Ana-Maria