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Protocols

Protein Digestion Simulator specifications

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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

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Protein Digestion Simulator citations

 (9)
library_books

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

2016
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 (www.uniprot.org) was produced using the Pacific Northwest National Laboratories Protein Digestion Simulator (omics.pnl.gov) 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 […]

library_books

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

2016
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 […]

library_books

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

2014
Anal Chem
PMCID: 4270407
PMID: 25420043
DOI: 10.1021/ac5035314

[…] In silico digests were performed using freely available software (http://omics.pnl.gov/software/protein-digestion-simulator). FASTA files containing the proteomes for H. sapiens, S. cerevisiae, E. coli, and H. salinarum were downloaded from the Swiss-prot database (http://beta.uniprot.org/unipro […]

library_books

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

2014
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 http://omics.pnl.gov/software/protein-digestion-simulator). Up to five missed cleavages were considered and all fully tryptic peptides i […]

library_books

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

2013
Proteomics
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 (http://omics.pnl.gov/software/ProteinDigestionSimulator.php) to generate an in silico digest of the human proteome with the commonly used […]

library_books

The Genome Organization of Thermotoga maritima Reflects Its Lifestyle

2013
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 (http://omics.pnl.gov/software/ProteinDigestionSimulator.php). Default settings were used, except the parameter “Max Missed Cleavages” was set to 0 and “Minimum Residue Cou […]


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