MSCI: Mass Spectrometry Content Information Python Library

MSCI is a Python package designed for the assessment of peptide fragmentation spectra information content. It helps researchers identify indistinguishable peptides in a given proteome by analyzing spectral similarity scores.

Contents

• Installation Guide
  • Installing MSCI via pip
  • Clone the Repository
  • Conclusion
• Example of usage
  • Import
  • Generate predicted dataset
  • Parse fasta file
  • Load dataset
  • Group within MS1 tolerance
  • Calculate similarity within fragment tolerance
  • Plot results
• MSCI Documentation
  • Functions
  • generate_variable_length_peptides(protein_sequence, min_length=8, max_length=11)
  • extract_peptides_from_fasta(fasta_path, min_length=8, max_length=11)
  • keep_top_n_peaks(spectrum, n)
  • filter_spectra_by_top_peaks(input_file_path, output_file_path, n_peaks)
  • reading MS spectra
  • read_msp_file
  • read_mgf_file
  • read_mzml_file
  • read_ms_file
  • Grouping MS1 Module
  • make_data_compatible(index_df)
  • within_ppm(pair, ppm_tolerance1, ppm_tolerance2)
  • within_tolerance(pair, tolerance1, tolerance2)
  • find_combinations_kdtree(data, tolerance1, tolerance2, use_ppm=True)
  • Similarity Module
  • ndotproduct(x, y, m=0, n=0.5, na_rm=True)
  • nspectraangle(x, y, m=0, n=0.5, na_rm=True)
  • joinPeaks(tolerance=0, ppm=0)
  • Mutation Module
  • ProteinMutator
  • tryptic_digest(sequence)
• Contributing
  • Types of Contributions

API

The MSCI package offers functionalities for:

• Data Import: Load proteomes and spectral libraries.

• Spectra Prediction & Processing: Predict peptide spectra and filter fragments.

• Spectra Grouping: Group peptides based on m/z and iRT values.

• Similarity Measurement: Compute spectral similarity using different scoring functions.

• Output & Visualization: Export similarity results and generate fragmentation plots.

For full API documentation, see MSCI Documentation.

Usage

Example workflow: Visit https://msci.readthedocs.io/en/latest/tutorial.html

For a full tutorial, visit our Colab notebook: https://colab.research.google.com/drive/1ny97RNgvnpD7ZrHW8TTRXWCAQvIcavkk

For Code and datasets visit https://github.com/proteomicsunitcrg/MSCI

Graphical User Interface (GUI)

MSCI includes a web-based GUI for non-programmers, accessible at: https://msci–proteomicsunit.streamlit.app/

License

MSCI is released under the MIT License.