Some suggestions (but not crucial to change if we want to send it out for review first):
In the DIA-NN files, since they are predicted spectra, the precursor m/z should probably be encoded as "MS:1003053|theoretical monoisotopic m/z" under Analyte instead of "experimental precursor monoisotopic m/z" under Spectrum. For "constituent spectrum file", should we try to set an example of using URI's (e.g. file://localhost/...), instead of a LINUX-style local path? Finally, I think the protein accession should be something like sp|P12345|ABC4_HUMAN, but now we are encoding P12345 as "protein accession" and "ABC4_HUMAN" as protein name.
For the NIST library, I noticed that the "Acetyl" modification was put on the first amino acid instead of the N-terminus. (It's not the converter's fault, as NIST's indexing seems to be zero-based, i.e. that "0" in the spectrum name means the first amino acid.) However, chemically speaking, the acetyl group should be considered an N-terminus modification and should be like [Acetyl]-APEPTIDEK in Proforma. For the "monoisotopic m/z deviation" field, the value is given as -0.2ppm, which should not be. The unit "ppm" should be separate.
For the Spectronaut file, the same comment about constituent file name (should be an URI?), and the protein accession/protein name (but may be too hard to fix for the converter?).
Some suggestions (but not crucial to change if we want to send it out for review first):
In the DIA-NN files, since they are predicted spectra, the precursor m/z should probably be encoded as "MS:1003053|theoretical monoisotopic m/z" under Analyte instead of "experimental precursor monoisotopic m/z" under Spectrum. For "constituent spectrum file", should we try to set an example of using URI's (e.g. file://localhost/...), instead of a LINUX-style local path? Finally, I think the protein accession should be something like sp|P12345|ABC4_HUMAN, but now we are encoding P12345 as "protein accession" and "ABC4_HUMAN" as protein name.
For the NIST library, I noticed that the "Acetyl" modification was put on the first amino acid instead of the N-terminus. (It's not the converter's fault, as NIST's indexing seems to be zero-based, i.e. that "0" in the spectrum name means the first amino acid.) However, chemically speaking, the acetyl group should be considered an N-terminus modification and should be like [Acetyl]-APEPTIDEK in Proforma. For the "monoisotopic m/z deviation" field, the value is given as -0.2ppm, which should not be. The unit "ppm" should be separate.
For the Spectronaut file, the same comment about constituent file name (should be an URI?), and the protein accession/protein name (but may be too hard to fix for the converter?).