MS2CNN

Predicting MS/MS spectrum based on protein sequence using Deep Convolutional Neural Networks (Under construction, we will update it soon).

Prerequisites

MS2CNN compilation requires the following tools installed on your system:

• Python
• Keras v2.0.4
• Tensorflow v1.1.0.

Compile/Installation

Download the git repository on your computer with the following command:

git clone git@github.com:jmchanglab/MS2CNN.git MS2CNN

Make sure you have installed the required dependencies listed above. When done, move in the project root folder named MS2CNN and enter the following commands:

$ cd src
$ make

Usage

We provide prediction models for length 15 to 19 in peptide charge 2 or 3.

python predict.py -l length -c charge
	length: 15~19
	chareg: 2|3

An example commend for a charge 2 peptide with lentgh 19.

python predict.py -l 19 -c 2

Input

format

Output

format

Reference

Lin YM, Chen CT, Chang JM. MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks. BMC Genomics. 2019;20(Suppl 9):906.