ProteoSim

ProteoSim is a Python library for simulating a bottom-up mass-spectrometry proteomics workflow. It walks through key stages of the experiment, starting with protein FASTA inputs and peptide digestion to LC separation, MS1 ionization, and MS2 fragmentation.

Installation

Clone the repository, install Proteosim and its dependencies in your active environment:

git clone https://github.com/UKHD-NP/proteosim.git
cd proteosim
pip install .

or for an editable installation

git clone https://github.com/UKHD-NP/proteosim.git
cd proteosim
pip install -e .

This will install NumPy, pandas, Pyteomics, and Matplotlib, which are used across the simulation steps.

Provided Functionality

Proteosim exposes functions and variables to run the full proteomics pipeline which consists of four main steps:

• fasta file handling: read_fasta
• protein digestion: digest_protein_sequence, digest_protein_collection, compute_sequence_coverage and the variable enzyme_cleavage_patterns
• liquid chromatography: predict_lc_retention_times, plot_retention_time
• mass spectrometry simulation: select_retention_time_window, calculate_mol_mass, calculate_mol_mass_collection, calculate_mz, calculate_mz_collection, plot_spectrum, fragment_peptide, plus the variable amino_acid_mass_dalton

Together, these pieces let you:

1. Load proteins from FASTA files.
2. Simulate enzymatic digestion with common proteases.
3. Predict peptide retention on LC gradients and visualize chromatograms.
4. Compute peptide masses, convert them to m/z values under typical charge states, and render MS1-like spectra.
5. Fragment peptides into theoretical b/y ions for MS2 reasoning.

Getting Started

Check the tutorials/ms_simulation.ipynb notebook for an end-to-end walkthrough that wires the modules together. You can adapt the steps to your own FASTA inputs or integrate the functions into teaching material and demos.

License

Released under the MIT License. See LICENSE for details.