Issue in reading MS2 level data with mzML files converted from .raw files in MS convert: /home/support

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Issue in reading MS2 level data with mzML files converted from .raw files in MS convert	shanthini kannan	2024-12-12 14:01


I use the version : Version: 3.0.24196-4dd34ff in MS convert I acquire data from Waters Vion qTOF in MSe mode. When I try to convert the UEP files to mzML files, I can see both the MS level data. To look at the data i use Msnbase package in R , by loading the data with readMSData function. When I try to convert the Masslynx. raw files to mzML files with MS convert , then load in R with the function mentioned above. It reads all the spectra as MS1 .. Kindly please help.. I am hereby attaching a sample file..