Alpha-XIC

Alpha-XIC is a deep neural network to score the coelution of peak groups which improves the identification of DIA data by DIA-NN.

Hardware

A GPU with CUDA support

Package

• PyTorch 1.0.0+
• Pyteomics
• numba

Tutorial

1. Compile the modified DIA-NN:

   cd 'Alpha-XIC/diann_1.7.16_plus_alpha/mstoolkit'
   make

2. Make a workspace folder containing:

   • diann-alpha-xic.exe compiled by step 1
   • *.mzML,
   • lib.tsv (the spectral library)

3. Run DIA-NN:

   cd workspace
   ./diann-alpha-xic.exe --f *.mzML --lib lib.tsv --out diann_out.tsv --threads 4 --qvalue 0.01

   Meanwhile, the modified DIA-NN will generate the scores file in workspace.

4. Run Alpha-xic:

   cd 'Alpha-XIC' project
   python main_alpha workspace_dir