About PepNet
The SOTA de novo sequencing model.
- High accuracy sequencing.
- Support multiple charges.
The SOTA de novo sequencing model.
The state of the art Deep CNN neural network forde novo sequencing of tandem mass spectra, currently works on unmodified HCD spectra of charges 1+ to 4+.
Also, Visithttps://www.predfull.com/ to check our previous project on full spectrum prediction
Based on the structure of the residual convolutional networks. Current precision (bin size): 0.1 Th.
After clone this project, you should download the pre-trained model (model.h5) fromzenodo.org and place it into PepNet's folder.
Recommend to install dependency viaAnaconda
Sample output looks like:
| TITLE | DENOVO | Score | PPM Difference | Positional Score |
|---|---|---|---|---|
| spectra 1 | LALYCHQLNLCSK | 1.0000 | -3.8919184 | [1.0, 0.9999956, 1.0, 1.0, 1.0, 1.0, 0.99999976, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0] |
| spectra 2 | HEELMLGDPCLK | 1.0000 | 4.207922 | [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.99999976, 1.0] |
| spectra 3 | AGLVGPEFHEK | 1.0000 | 0.54602236 | [1.0, 1.0, 1.0, 1.0, 1.0, 0.99999917, 1.0, 1.0, 1.0, 1.0, 1.0] |
Simply run:
python denovo.py --input example.mgf --model model.h5 --output example_prediction.tsv
The output file is in MGF format
We provide sample data onzenodo for you to evaluate the sequencing performance. Theexample.mgf file on google drive contains ground truth spectra (randomly sampled fromNIST Human Synthetic Peptide Spectral Library), while theexample.tsv file contains pre-run predictions.
WE ARE EXPLORERS. EXPLORERATION ARE OUR SUBJECTS.