DeepMASS2

DeepMASS2 is a cross-platform GUI software tool, which enables deep-learning based metabolite annotation via semantic similarity analysis of mass spectral language. This approach enables the prediction of structurally related metabolites for the unknown compounds. By considering the chemical space, these structurally related metabolites provide valuable information about the potential location of the unknown metabolites and assist in ranking candidates obtained from molecular structure databases.

Installation

Please follow the following installation steps:

Install Anaconda or Miniconda

Create a new conda environment and activate:

 conda create -n deepmass python=3.8.13
 conda activate deepmass

Clone the repository and enter:

 git clone https://github.com/hcji/DeepMASS2_GUI.git
 cd DeepMASS2_GUI

Install dependency (note, for MacOS some dependency may install with conda manually):
```
 pip install -r requirements.txt
 
```

Download the dependent data.

put the following files into data folder:

     DeepMassStructureDB-v1.0.csv
     references_index_negative_spec2vec.bin
     references_index_positive_spec2vec.bin
     references_spectrums_negative.pickle
     references_spectrums_positive.pickle

put the following files into model folder:

     Ms2Vec_allGNPSnegative.hdf5
     Ms2Vec_allGNPSnegative.hdf5.syn1neg.npy
     Ms2Vec_allGNPSnegative.hdf5.wv.vectors.npy
     Ms2Vec_allGNPSpositive.hdf5
     Ms2Vec_allGNPSpositive.hdf5.syn1neg.npy
     Ms2Vec_allGNPSpositive.hdf5.wv.vectors.npy

Run DeepMASS
```
 python DeepMASS2.py
```

Release

Version 0.99.0

Documentation

For the details on how to use DeepMASS, please check Ducomentation.

Citation

In preparation

Contact

Ji Hongchao
E-mail: ji.hongchao@foxmail.com

https://orcid.org/0000-0002-7364-0741

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