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DeepLC ThermoRawFileParser ThermoRawFileParserGUI colims compomics-utilities dbtoolkit denovogui fragmentation-analyzer iceLogo jsparklines jtraml mappi-dat mascotdatfile meta-proteome-analyzer ms-lims ms2pip ms2rescore omssa-parser pepshell peptide-shaker pladipus pride-asa-pipeline reporter search-all-assess-subset searchgui thermo-msf-parser xtandem-parser