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

Processing data from MSFragger includes: 1. Phosphoproteome dataset (PDC000313): - Traditional search in Phospho mode (build proteoform database): Traditional_phosphoproteome_phospho_config_builddb_psm.tsv 2. Proteome data (PDC000311): - Traditional search in Global mode (labeled as "Global" in the manuscript): Traditional_proteome_global_config_abundance_peptide_MD.tsv - Traditional search in Phospho mode (labeled as "Uniprot vP" in the manuscript): Traditional_proteome_phospho_config_abundance_multi-site_MD.tsv Traditional_proteome_phospho_config_abundance_peptide_MD.tsv - ProteoformDB search with the proteoform database (labeled as "ProteoformDB" in the manuscript): ProteformDB_proteome_abundance_peptide_MD.tsv