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. Author manuscript; available in PMC: 2022 Apr 2.
Published in final edited form as: J Proteome Res. 2021 Mar 4;20(4):1936–1942. doi: 10.1021/acs.jproteome.0c00954

Table 2:

Comparison of in silico Digestion Tool Features

Tool Name Digests Whole Proteome User Supplied Database(s) Can Digest Multiple Databases Runs Parallel Protease Digestions Enables Custom Protease Generation Determines Uniqueness of Peptides Provides Data Visualization Includes PTM Annotations Cross- Platform Web Interface Provides Theoretical Peptide Fragmentation Data
ProteaseGuru Yes Yes Yes Yes Yes Yes Yes Yes No (C# GUI) No
iHPDM24 Yes No No Yes No Yes Yes Yes Yes No
IPEP25 No No No Yes No No Yes No Yes No
MS-Digest No No No No No No No Yes Yes Yes
pepServe26 No No No No No Yes No Yes Yes No
PeptideCutter27 No No No No No No No No Yes No
 PeptideManager10 Yes Yes Yes (max:2) No No Yes No Yes No (C# GUI) No
PeptideMass28 No No No No No No No Yes Yes No
Protein Digest No No No No No No No No Yes No
Proteogest29 Yes Yes No No Yes Yes No Yes No (Perl application) No
Rapid Peptides Generator30 Yes Yes No Yes Yes No No No No (Python tool) No