| spectra (full pathname to spectrum file or folder of spectrum files) | Specify the full path to a single mzXML/Mascot generic format (MGF) file or the full path to the folder containing mzXML and/or MGF file(s) to be searched |
| protease (trypsin or other protease used) | Specify the protease used to digest the sample (e.g., trypsin; see ‘Input.txt’ in IGAP download for list of supported options) |
| db (protein sequence database) | Specify the name of the protein sequence database in FASTA format |
| refinedb (refinement protein database) | Specify the name of the refinement protein database created as described in Step 25. |
| organism (sample’s organism type) | Specify the sample’s organism (valid options are human, mouse, all) |
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