Slider is machine-learning-based peptide-spectrum-matching scoring method for spectrum identification in tandem mass spectrometry, shotgun proteomics.
Authors: Polina Kudriavtseva, Matvey Kashkinov, and Attila Kertesz-Farkas from HSE University, Moscow, Russia
Download the code.
Slider was tested with Python (3.7 ) Pytorch (1.5.1) Matplotlib (2.0) pyteomics (3.4) BioPython (1.75)
and other standard python toolboxes such as: argparse, time, numpy, seaborn, pandas, etc.
To see whether all components are installed properly, first unzip the test data.zip file in the ./data folder locally.
Then run:
$./RUN_TEST.sh
This script runs Slider on a small data. It should run not longer than 1-2 minutes. If this terminates without error, you are all set.
The python scripts will produce a transformed spectrum data file in .ms2 format. You can use standard database searching methods to search the transformed .ms2 data file.
The ./source/parameters.py file contains all the parameters, including to the path to the data files. You need to modify the path to your data files in own system.
akerteszfarkas at hse . r u