Check differences between RAW, mzXML and mzML data

I have compared mzXML and mzML scans (just one, exemplarily) for files 190321_Serum_Lipidextract_368723_01.mzML and 190321_Serum_Lipidextract_368723_01.mzXML. Comparison for scan numer 1 shows, that there are small deviations in the reported masses (fourth decimal position) and larger ones for the reported intensities (on average -2.3261 difference from mzML peaks to mzXML peaks). mzXML intensities seem to be higher all around, which also manifests itself in the comparative results with and without MSfilter and MSMSfilter.

scan1_comparison_mzML_MzXML.xlsx mzML_vs_mzXML_with_and_without_MSfilter_MSMSfilter.xlsx

Workflow Outline

LipidXplorer 1.2.8

MSFilter/MSMSfilter	Metric	Value	Input Format
0	No. of Peaks MS1		mzXML from PeakStrainer
	No. of Peaks MS2
0.6	No. of Peaks MS1		mzXML from PeakStrainer
	No. of Peaks MS2
0	No. of Peaks MS1	2123	mzXML from msConvert
	No. of Peaks MS2	278162
0.6	No. of Peaks MS1	1887	mzXML from msConvert
	No. of Peaks MS2	249344
0	No. of Peaks MS1	2126	mzML from msConvert
	No. of Peaks MS2	275956
0.6	No. of Peaks MS1	1884	mzML from msConvert
	No. of Peaks MS2	246412

RAW -> mzML || mzXML -> LX 1.2.7 || LX 1.2.8