Nic Bollis

This issue has been resolved with the most recent release of MetaMorpheus 1.0.0

Within Proteomics folder, it appears as through some things have specific namespaces while others do not: AminoAcidPolymer -> MassSpectrometry.Proteomics.AminoAcidPolymer Fragmentaiton -> MassSpectrometry.Proteomics.Fragmentation Modification -> MassSpectrometry.Proteomics Protein -> MassSpectrometry.Proteomics ProteolyticDigestion ->...

That is a good idea and maybe a good starter project. Our current tests only truly test b, y, and c ions

> is the top supposed to look like this?  This has been fixed

This is a great point and should be addressed. The original implementation did not account for us expanding to a dozen or more different files that all end with 'tsv'

> I'm not sure how the neutral mass spectra fit together with IsoDec. Does isodec return neutral mass spectra? Neutral mass spectrum does not fit with IsoDec. Isodec returns isotopic...

> Also, can't set assumed charge states to negative when no data is loaded in. It is set to positive mode. No negatives can be input. Once RNA is added,...

Thank you for this update. One simple troubleshooting step would be to delete the database index folder found in the same directory as your database.