Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectral Alignment For Discovery of Structurally Related Molecules

Spectral libraries and analysis results of the evaluation between the cosine similarity, modified cosine similarity, and neutral loss matching for the discovery of structurally related molecules.

Spectral libraries used as input:
- MassIVE-KB peptide spectral library (version 2018/06/15): LIBRARY_CREATION_AUGMENT_LIBRARY_TEST-82c0124b-download_filtered_mgf_library-main.mgf
- GNPS community spectral libraries (downloaded on 2022/05/12): ALL_GNPS_NO_PROPOGATED.mgf
- GNPS bile acids spectral library (downloaded on 2022/05/12): BILELIB19.mgf

Analysis output results:
- massivekb_peptide_mods.csv: 955,228 peptide MS/MS spectrum pairs from MassIVE-KB
- gnps_libraries.csv: 10 million small molecule MS/MS spectrum pairs from the GNPS community spectral libraries
- gnps_libraries_metadata.csv: structural (InChI, SMILES) and class information (computed using Classyfire) for 58,165 small molecule spectra from the GNPS community spectral libraries
- gnps_bilelib.csv: 340,637 bile acids MS/MS spectrum pairs from the GNPS bile acids spectral library

For more information, see: https://github.com/bittremieux/cosine_neutral_loss/