Bimodal Peptide Collision Cross Section Distributions Reflect Two Stable Conformations in the Gas Phase

Repsitory containing the trained models and the code for the paper mentioned on the title.

Data Availability

Download the concatenated MaxQuant output file evidence-03122024.csv from here and place it under anew folder /data. In the same repository you can find the aligned train and test sets, i.e., the files evidence_aligned_trainv2660.csv and evidence_test_fromRawFiles_2pop_v2660.csv. Place them as well under /data if you dont want to do the alignment following K0_alignment.ipynb.

Merging of multiple runs

Because we are integrating results from different MaxQuant runs we need to allign them. This is done in the notebook K0_alignment.ipynb.

Paper Figures

• The figures of the section Bi-modality of peptide collision cross section distribution are in the notebook section_1.ipynb
• The development and plots for the geometric scattering fit are in the notebook fit_geometric_scaterring.ipynb
• The development and plots for the geometric fit are in the notebook fit_geometric.ipynb
• The development and plots for the empirical fit are in the notebook fit_empirical.ipynb
• The Machine Learning Regressor is trained in the notebook training-prediction.ipynb
• The MaxDIA analysis is in the notebook maxdia.ipynb