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volpato30 / DeepNovoV2

Pytorch implementation of DeepNovoV2, a state-of-the-art de novo peptide sequencing model.
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Pretrained Weights available? #1

Open mkdasso2 opened 4 years ago

mkdasso2 commented 4 years ago

Hi, I am hoping to use the pretrained DeepNovo model (V1) to generate feature embeddings for my data to benchmark. Is a pretrained model available to download? Alternatively, did you train your model from scratch or did you port the weights from the author's tensorflow github?

volpato30 commented 4 years ago

I trained weights from scratch. Due to the nature of this problem, it is hard to provide a pre-trained model that works well on MS/MS data generated under different settings (i.e. mass spectrometer, fragmentation method, PTMs settings.). The training process is fairly short since this is a small model, so the best practice is to find some data from ProteomeXchange that are generated in a similar setting with your test data. Then train your own model.