ProteoformDB: A Built-in Application to Generate Proteoform Database (Processing Data)

Processing data from MSFragger includes: 1. Traditional search in Global mode (labeled as "Global" in the manuscript): 9_26_2024_Traditional_search_global_abundance_peptide_MD.tsv 2. Traditional search in Phospho mode (labeled as "Uniprot vP" in the manuscript): 1_22_2025_Traditional_search_phospho_abundance_peptide_MD.tsv 1_22_2025_Traditional_search_phospho_abundance_multi-site_MD.tsv 3. ProteoformDB search with the proteoform database (labeled as "ProteoformDB" in the manuscript): 9_26_2024_ProteformDB_search_method_abundance_peptide_MD.tsv