Release 2.4.8937

Installation

File ProteinDigestionSimulator_Installer.zip includes the installer for the Protein Digestion Simulator

Use shortcut "PAST Toolkit, Protein Digestion Simulator" to start the program, or navigate to
C:\Program Files\ProteinDigestionSimulator
and double click ProteinDigestionSimulator.exe

Alternatively, download ProteinDigestionSimulator_Program.zip which includes the executable and required DLLs.

Usage Options

Running the executable without any command line arguments will show the GUI

• Alternatively, run with command line arguments, as shown in the Readme
• The program can be run on Linux using Mono
  • For example, mono ProteinDigestionSimulator.exe QC_Standards_2004-01-21.fasta /Q

Changes

• Updated PRISM DLLs

Release 2.4.7993

Installation

File ProteinDigestionSimulator_Installer.zip includes the installer for the Protein Digestion Simulator

Use shortcut "PAST Toolkit, Protein Digestion Simulator" to start the program, or navigate to
C:\Program Files\ProteinDigestionSimulator
and double click ProteinDigestionSimulator.exe

Alternatively, download ProteinDigestionSimulator_Program.zip which includes the executable and required DLLs.

Usage Options

Running the executable without any command line arguments will show the GUI

• Alternatively, run with command line arguments, as shown in the Readme
• The program can be run on Linux using Mono
  • For example, mono ProteinDigestionSimulator.exe QC_Standards_2004-01-21.fasta /Q

Changes

• Updated FASTA file validator that checks for a Unicode replacement character after the protein name
• Updated ProteinFileReader DLL
  • Looks for a non-breaking space and a Unicode replacement character after protein names
• Add option to create a decoy FASTA file
  • Includes both forward and reverse protein sequences
• Warn the user if protein sequences appear to have DNA sequences instead of amino acids
• Assure that the output file extension is .fasta, .txt, or .tsv
• Parameter files for use with the console version of the program are now Key=Value parameter files
  • Previous versions used an XML-based parameter file
  • An example parameter file is in the Documentation directory on GitHub
• Each of the options in the Key=Value parameter file are accessible using command line arguments

Release 2.4.7992

Installation

File ProteinDigestionSimulator_Installer.zip includes the installer for the Protein Digestion Simulator

Use shortcut "PAST Toolkit, Protein Digestion Simulator" to start the program, or navigate to
C:\Program Files\ProteinDigestionSimulator
and double click ProteinDigestionSimulator.exe

Alternatively, download ProteinDigestionSimulator_Program.zip which includes the executable and required DLLs.

Usage Options

Running the executable without any command line arguments will show the GUI

• Alternatively, run with command line arguments, as shown in the Readme
• The program can be run on Linux using Mono
  • For example, mono ProteinDigestionSimulator.exe QC_Standards_2004-01-21.fasta /Q

Changes

• Add option to create a decoy FASTA file
  • Includes both forward and reverse protein sequences
• Warn the user if protein sequences appear to have DNA sequences instead of amino acids
• Assure that the output file extension is .fasta, .txt, or .tsv
• Parameter files for use with the console version of the program are now Key=Value parameter files
  • Previous versions used an XML-based parameter file
  • An example parameter file is in the Documentation directory on GitHub
• Each of the options in the Key=Value parameter file are accessible using command line arguments

Release 2.4.7991

Installation

File ProteinDigestionSimulator_Installer.zip includes the installer for the Protein Digestion Simulator

Use shortcut "PAST Toolkit, Protein Digestion Simulator" to start the program, or navigate to
C:\Program Files\ProteinDigestionSimulator
and double click ProteinDigestionSimulator.exe

Alternatively, download ProteinDigestionSimulator_Program.zip which includes the executable and required DLLs.

Usage Options

Running the executable without any command line arguments will show the GUI

• Alternatively, run with command line arguments, as shown in the Readme
• The program can be run on Linux using Mono
  • For example, mono ProteinDigestionSimulator.exe QC_Standards_2004-01-21.fasta /Q

Changes

• Warn the user if protein sequences appear to be DNA
• Assure that the output file extension is .fasta, .txt, or .tsv
• Parameter files for use with the console version of the program are now Key=Value parameter files
  • Previous versions used an XML-based parameter file
  • An example parameter file is in the Documentation directory on GitHub
• Each of the options in the Key=Value parameter file are accessible using command line arguments

Release 2.4.7969

Installation

File ProteinDigestionSimulator_Installer.zip includes the installer for the Protein Digestion Simulator

Use shortcut "PAST Toolkit, Protein Digestion Simulator" to start the program, or navigate to
C:\Program Files\ProteinDigestionSimulator
and double click ProteinDigestionSimulator.exe

Alternatively, download ProteinDigestionSimulator_Program.zip which includes the executable and required DLLs.

Usage Options

Running the executable without any command line arguments will show the GUI

• Alternatively, run with command line arguments, as shown in the Readme
• The program can be run on Linux using Mono
  • For example, mono ProteinDigestionSimulator.exe QC_Standards_2004-01-21.fasta /Q

Changes

• Converted to C#
• Parameter files for use with the console version of the program are now Key=Value parameter files
  • Previous versions used an XML-based parameter file
  • An example parameter file is in the Documentation directory on GitHub
• Each of the options in the Key=Value parameter file are accessible using command line arguments

Release 2.3.7794

Installation

File ProteinDigestionSimulator_Installer.zip includes the installer for the Protein Digestion Simulator

Use shortcut "PAST Toolkit, Protein Digestion Simulator" to start the program, or navigate to
C:\Program Files\ProteinDigestionSimulator
and double click ProteinDigestionSimulator.exe

Alternatively, download ProteinDigestionSimulator_Program.zip which includes the executable and required DLLs.

Changes

• When validating FASTA files, check for non-breaking spaces after protein names

Updates

A newer version of the executable may be available on the on the AppVeyor CI server

Release 2.3.7745

Installation

File ProteinDigestionSimulator_Installer.zip includes the installer for the Protein Digestion Simulator

Use shortcut "PAST Toolkit, Protein Digestion Simulator" to start the program, or navigate to
C:\Program Files\ProteinDigestionSimulator
and double click ProteinDigestionSimulator.exe

Alternatively, download ProteinDigestionSimulator_Program.zip which includes the executable and required DLLs.

Changes

• Increase the maximum protein name length to 512 characters (applies when creating a reversed FASTA file)

Updates

A newer version of the executable may be available on the on the AppVeyor CI server

Release 2.3.7713

Installation

File ProteinDigestionSimulator_Installer.zip includes the installer for the Protein Digestion Simulator

Use shortcut "PAST Toolkit, Protein Digestion Simulator" to start the program, or navigate to
C:\Program Files\ProteinDigestionSimulator
and double click ProteinDigestionSimulator.exe

Alternatively, download ProteinDigestionSimulator_Program.zip which includes the executable and required DLLs.

Changes

• Add support for .fasta.gz files

Updates

A newer version of the executable may be available on the on the AppVeyor CI server

Release 2.3.7494

Installation

File ProteinDigestionSimulator_Installer.zip includes the installer for the Protein Digestion Simulator

Use shortcut "PAST Toolkit, Protein Digestion Simulator" to start the program, or navigate to
C:\Program Files\ProteinDigestionSimulator
and double click ProteinDigestionSimulator.exe

Alternatively, download ProteinDigestionSimulator_Program.zip which includes the executable and required DLLs.

Changes

• Update the default parameter file to include ComputeNET and ComputeSCX

Updates

A newer version of the executable may be available on the on the AppVeyor CI server

Release 2.3.7426

Installation

File ProteinDigestionSimulator_Installer.zip includes the installer for the Protein Digestion Simulator

Use shortcut "PAST Toolkit, Protein Digestion Simulator" to start the program, or navigate to
C:\Program Files\ProteinDigestionSimulator
and double click ProteinDigestionSimulator.exe

Alternatively, download ProteinDigestionSimulator_Program.zip which includes the executable and required DLLs.

Changes

• Fix bug displaying FASTA file validation results

Updates

A newer version of the executable may be available on the on the AppVeyor CI server