Tool Name Tool Use Tool Version ThermoRawFileParser [12] Conversion from Thermo Raw files to mzML v1.4.2 FLASHDeconv [13] Deconvolution v3-pre.51bcc6e TopPIC-suite [14] Deconvolution & Identification v1.5.3 Nextflow [11] Workflow management system v22.10.4 Panel (Python) [15] Graphical User Interface v0.14.4 Pyteomics [16] Computational access to mzML v4.5.6 Table 1: Tools in use with the current version (May 2023) of TopDownApp. See the code repository for details about the most recent versions (if applicable). Table 1: Tools in use with the current version (May 2023) of TopDownApp. See the code repository for details about the most recent versions (if applicable). Table 1: Tools in use with the current version (May 2023) of TopDownApp. See the code repository for details about the most recent versions (if applicable).