OpenMS - MetaboliteSpectralMatcher - Error: The input file does not contain any spectra.


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?


What do you use as database? I don’t think it expects a certain schema. But correct MS level annotation and centroiding annotation will probably be crucial.

I do not have access to those GDrive files.

There was an error in the tool, such that it would only read MS2 spectra:

Apparently, the second set only contained MS1 Spectra?

But do you really want to compare Ms1 spectra?

Actually we are probably going to consider this as intended. Unless there are good reasons to compare MS1 spectra

Thank you very much for your answers! You are right, it works only with ms/ms data indeed. The truth is comparing MS1 spectra would not be as accurate as MS2.

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