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Noble-Lab / casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
https://casanovo.readthedocs.io
Apache License 2.0
90 stars 31 forks source link

add additional inputs to encoder and decoder #318

Open wsnoble opened 3 months ago

wsnoble commented 3 months ago

Following NovoB, modify the encoder to take several additional inputs, including the precursor mass, charge, m/z, and intensity. Also, modify the decoder to take one additional input, which is an explicit representation of the residual mass.

wsnoble commented 3 months ago

Also consider Contranovo, which provides additional inputs to the decoder, including the masses of the previously predicted amino acids, the total mass of the remaining, uninferred peptide, and the masses of individual amino acids.