UniSpec is a comprehensive DL spectrum predictor that can predict the intensity of the entire HCD MS/MS fragment ion series, going beyond existing tools limited to b/y ion series. All datasets developed for UniSpec model are shared on Zenodo as part of the UniSpec publication, "UniSpec: Deep Learning for Predicting Comprehensive Peptide Fragment Ion Series to Improve Peptide-Spectrum Matches from Shotgun Proteomics Experiments". This includes UniSpec datasets, downstream evaluation and analysis, and application case studies. 1. pre-processed training, evaluation and testing data for machine learning; UniSpec-Datasets.7z, Readme_UniSpecDatasets.txt 2. Streamlined input datasets based on the fragmentation dictionary; Streamlined_inputdatasets.7z, Readme_Streamlined_inputdatasets.txt 3. Predictions on the validation and test sets; UniSpecPred_Validation-Test.7z, Readme_Predictons_ValidationTest.txt 4. Evaluation by comparison with Prosit; a. Predictions: prosit_and_unispec_predictions.7z, Readme_prosit_and_unispec_predictions.txt b. Cosine similarity scores: prosit_vs_unispec_CS.7z, Readme_prosit_vs_unispec_CS.txt 5. CSS for Different HCD Fragment Ion Series; CS_for_ion_splits.tsv 6. Application 1: PSM rescoring; PSM rescoring_zipfiles.7z, PSM rescoring_readme.txt 7. Application 2: In-silico spectral library search in-silico_librarysearch.7z, in-silico_librarysearch_readme.txt