Generate Mass and Inclusion Lists

Purpose

The purpose of the script is to generate a mass lists, which can be imported into Compound Discoverer. It also creates inclusion lists for positive and negative mode with predicted NCE for the use on a QExactivePlus. The script uses the PubChem database and for every compound a request is sent, thus the code can run for some time.

Input

The scripts needs one txt file as input that contains the SMILES of compounds (one string per line).

Output

Mass and two inclusion lists as well as an overview with SMILES, Name, CAS, Formula, monoisotopic mass and InchiKey as csv file. Additionally, a txt file is created containing the maximal element count of C, H, O, N, S, P, Cl, Br an I (useful for Compound Discoverer workflow). The output paths are per default the same folder as the script.

Installation

Step by step guide for non-python users:

1. Download Anaconda and install it, then run Anaconda Navigator
2. create new environment under the Environment tab, select python version 3.6.13
3. go to environments, click play button on newly created environment, open Terminal
4. run following lines individually (need to confirm: type y and press enter)(might take a while): conda install -c rdkit rdkit and pip install pubchempy
5. check if pandas is installed and active according to this Tutorial
6. open Anaconda Navigator, go to Home tab, check if Applications on is set to the new environment
7. click gear icon on Spyder > install specific version > 5.0.5 and wait for installation to finish
8. click launch button below Spyder
9. open the script: smiles_to_mass_and_inclusion_list.py
10. change the pathway of the input files according to the filepath on your harddrive
11. click somewhere in the left window and press F5 or click Run File, if Run settings windows appears, click Run
12. wait for the script to finish running (may take a while, Script finished successfully marks end of script)