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Predicting Complete Tandem Mass Spectra
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README.md

PredFull

Visit http://predfull.com/ to try online prediction

Model for Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network

Kaiyuan Liu, Sujun Li, Lei Wang, Yuzhen Ye, Haixu Tang

Method

Based on the structure of the residual convolutional networks. Current precision: 0.1 Th.

model

How to use

Required Packages

Recommend to install dependency via Anaconda

  • Keras >= 2.2.4
  • Tensorflow >= 1.12
  • Pandas >= 0.20
  • pyteomics
  • lxml

Input format

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.

Usage

Simply run:

python predfull.py --input .\example.tsv --weights pm.hdf5 --output .\example.mgf

The output file is in MGF format

  • --input : the input file
  • --weights : the weight file
  • --output : the output path

Prediction Examples

example 1

example 2

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