Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network
Kaiyuan Liu, Sujun Li, Lei Wang, Yuzhen Ye, Haixu Tang
Based on the structure of the residual convolutional networks. Current precision: 0.1 Th.
Recommend to install dependency via Anaconda
The required input format is TSV, with following columns:
Peptide | Charge | Type | NCE ------- | ------ | ---- | --- AAAAAAAAAVSR | 2 | HCD | 25 AAGAAESEEDFLR | 2 | HCD | 25 AAPAPTASSTININTSTSK | 2 | HCD | 25
Apparently, 'Peptide' and 'Charge' columns mean what it says. The 'Type' must be HCD or ETD (in uppercase). NCE means normalized collision energy, set to 25 or 30 if you don't care. Check
example.tsv for examples.
python predfull.py --input .\example.tsv --weights pm.hdf5 --output .\example.mgf
The output file is in MGF format