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Protein Digestion Simulator specifications


Unique identifier OMICS_14945
Name Protein Digestion Simulator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein or peptide sequences.
Input format FASTA, TXT
Output data Create a new text file with the protein name, description, and sequence separated by tabs.
Operating system Windows
License Apache License version 2.0
Computer skills Advanced
Version 2.2.6138
Stability Stable
Maintained Yes




No version available


  • person_outline Protein Digestion Simulator Team

Protein Digestion Simulator citations


Rational engineering of a virulence gene from Mycobacterium tuberculosis facilitates proteomic analysis of a natural protein N terminus

Sci Rep
PMCID: 5021934
PMID: 27625110
DOI: 10.1038/srep33265

[…] For the data presented in , in silico digest of the M. tuberculosis Erdman strain proteome acquired from Uniprot ( was produced using the Pacific Northwest National Laboratories Protein Digestion Simulator ( v2.2.5679; July 20, 2015. Digestion settings were set to full tryptic (KR not P) normal output with one missed cleavage allowed and a minimum fragment mass […]


Proteomic analysis of Plasmodium falciparum parasites from patients with cerebral and uncomplicated malaria

Sci Rep
PMCID: 4887788
PMID: 27245217
DOI: 10.1038/srep26773

[…] e determined according to. The exponentially modified Protein Abundance Index (emPAI) was calculated by the following formula: The number of «observable» peptides per protein was calculated by the Protein Digestion Simulator program. To facilitate visualization and comparison, samples with missing emPAI values for a particular protein were assigned half the minimum emPAI value for that protein […]


Improvement of Shotgun Proteomics in the Negative Mode by Carbamylation of Peptides and Ultraviolet Photodissociation Mass Spectrometry

Anal Chem
PMCID: 4270407
PMID: 25420043
DOI: 10.1021/ac5035314

[…] In silico digests were performed using freely available software ( FASTA files containing the proteomes for H. sapiens, S. cerevisiae, E. coli, and H. salinarum were downloaded from the Swiss-prot database ( […]


Revealing the amino acid composition of proteins within an expanded genetic code

Nucleic Acids Res
PMCID: 4333366
PMID: 25378305
DOI: 10.1093/nar/gku1087

[…] (PSM) with a filter list containing all possible tryptic peptides from the TAG = X database. To generate the filter list, we first performed in silico digestion of the TAG = X protein database using Protein Digestion Simulator software v.2.2.5053 (retrieved from Up to five missed cleavages were considered and all fully tryptic peptides i […]


Two birds with one stone: Doing metabolomics with your proteomics kit

PMCID: 4265265
PMID: 24155035
DOI: 10.1002/pmic.201300192

[…] ensitive analysis by MS , proteins are proteolytically cleaved for most analyses, breaking the proteome down into much more complex enzyme-specific peptide pools (shotgun proteomics and PMF). We used Protein Digestion Simulator v2.2.3992.29199 by Matthew Monroe ( to generate an in silico digest of the human proteome with the commonly used […]


The Genome Organization of Thermotoga maritima Reflects Its Lifestyle

PLoS Genet
PMCID: 3636130
PMID: 23637642
DOI: 10.1371/journal.pgen.1003485

[…] e normalized the observed spectral counts for each ORF by the number of possible fully tryptic peptides in the ORF. The number of possible fully tryptic peptides for each ORF was determined using the Protein Digestion Simulator ( Default settings were used, except the parameter “Max Missed Cleavages” was set to 0 and “Minimum Residue Cou […]

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