Tandem mass spectra prediction

This guide explains how to use 3DMolMS for tandem mass spectra (MS/MS) prediction.

Setup

Please set up the environment as shown in the Source code setup page.

Step 1: Input preparation

Prepare the test set. The following formats are supported: csv, mgf, or customed pkl.

CSV Format Example

Here is an input example from MoNA of csv format:

ID,SMILES,Precursor_Type,Collision_Energy
demo_0,C/C(=C\CNc1nc[nH]c2ncnc1-2)CO,[M+H]+,40 V
demo_1,C/C(=C\CNc1nc[nH]c2ncnc1-2)CO,[M+H]+,20 V
demo_2,C/C(=C\CNc1nc[nH]c2ncnc1-2)CO,[M+H]+,10 V

MGF Format Example

Here is an input example from MoNA of mgf format:

BEGIN IONS
TITLE=demo_0
CHARGE=1+
PRECURSOR_TYPE=[M+H]+
PRECURSOR_MZ=220.1193
MOLMASS=219.11201003600002
MS_LEVEL=MS2
IONMODE=P
SOURCE_INSTRUMENT=Agilent 6530 Q-TOF
INSTRUMENT_TYPE=LC-ESI-QTOF
COLLISION_ENERGY=40 V
SMILES=C/C(=C\CNc1nc[nH]c2ncnc1-2)CO
INCHI_KEY=UZKQTCBAMSWPJD-FARCUNLSSA-N
41.0399 6.207207
43.0192 49.711712
43.0766 1.986987
...

Supported inputs

The unsupported input will be filtered out automatically when loading the dataset. The supported inputs are:

Item	Supported input
Atom number	≤300
Atom types	‘C’, ‘O’, ‘N’, ‘H’, ‘P’, ‘S’, ‘F’, ‘Cl’, ‘B’, ‘Br’, ‘I’, ‘Na’
Precursor types	‘[M+H]+’, ‘[M-H]-’, ‘[M+H-H2O]+’, ‘[M+Na]+’
Collision energy	any number

Step 2: Running prediction

Predict the MS/MS spectra using the following command:

python scripts/predict.py --task msms \
--test_data ./examples/demo_input.csv \
--model_config_path ./molnetpack/config/molnet.yml \
--data_config_path ./molnetpack/config/preprocess_etkdgv3.yml \
--resume_path ./check_point/molnet_qtof_etkdgv3.pt \
--result_path ./examples/demo_output.mgf

Arguments

--resume_path: Path of model’s checkpoint. In the first running, the checkpoint (./checkpoint/molnet_qtof_etkdgv3.pt) will be downloaded from Google Drive. You can also set the resume path to your own model.
--result_path: Path to save the predicted MS/MS. It should end with .mgf or .csv. We recommend using .mgf because MGF is a more common format for MS/MS.