MSCI: an open-source Python package for information content assessment of peptide fragmentation spectra.

Motivation: In mass spectrometry-based proteomics, the availability of peptide prior knowledge has improved our ability to assign fragmentation spectra to specific peptide sequences. However, some peptides exhibit similar analytical values and fragmentation patterns, which makes them nearly indistinguishable with current data analysis tools.

Results: Here we developed the Mass Spectrometry Content Information (MSCI) Python package to tackle the challenges of peptide identification in mass spectrometry-based proteomics, particularly regarding indistinguishable peptides. MSCI provides a comprehensive toolset that streamlines the workflow from data import to spectral analysis, enabling researchers to effectively evaluate fragmentation similarity scores among peptide sequences and pinpoint indistinguishable peptide pairs in a given proteome.

Availability and implementation: MSCI is implemented in Python and it is released under a permissive MIT license. The source code and the installers are available on GitHub at https://github.com/proteomicsunitcrg/MSCI.