So I am trying to use MetaboliteSpectralMatcher node but unfortunately it does not work always. I am using Knime 4.1.4 and OpenMS 2.6. with this simple workflow
but for example it works only with these two mzml files:
while not with these two:
The error message is that “The input file does not contain any spectra”. All the files contain centroided data and they are definitely not corrupted as they work perfectly fine with FeatureFinderMetabo and AccurateMassSearch.
Any ideas why this is not working? Does the MetaboliteSpectralMatcher accept specific files originating from specific experimental sources?