Protein Digestion Simulator Change Log Version 2.2.3603; November 12, 2009 - Updated to Visual Studio 2008 - Updated to new version of NETPrediction.dll - Added a splash screen that informs the user that the Kangas/Petritis retention time prediction algorithm is protected by patent 7,136,759 and pending patent 2005-0267688A1 - The splash screen will be shown every 6 months - You can also see this information by choosing About from the Help menu - Changed normalized elution time (NET) column header from GANET to NET - This value is computed for peptides when using the Parse and Digest mode - Updated to new version of ValidateFastaFile.dll Version 2.1.3336; February 18, 2009 - New version of NETPredictionBasic.dll - Computes predicted SCX NET values for proteins and for in-silico digestion peptides Version 2.1.3238; November 12, 2008 - New version of NETPrediction.dll - Computes predicted SCX NET values for proteins and for in-silico digestion peptides - Now saving the Xml parameter file at C:\Documents and Settings\%User%\Application Data\PAST Toolkit instead of in the folder that contains ProteinDigestionSimulator.exe Version 2.1.3131; July 28, 2008 - New version of ValidateFastaFile.dll that includes option Save Basic Protein Hash Info File - When enabled, will create file _ProteinHashes.txt, which includes protein name, residue count, and a hash value for each protein sequence - If you enable "Save Basic Protein Hash Info File" but disable "Check for Duplicate Protein Names and protein Sequences", then the memory usage of the validator will be minimal, even with huge .Fasta files Version 2.1.3044; May 2, 2008 - New version of ValidateFastaFile.dll that has additional Fixed Fasta options - Ability to control whether or not long protein names are truncated - Added option WrapLongResidueLines - When true, then wraps residue lines to length MaximumResiduesPerLine (default is 120 characters) - Added option RemoveInvalidResidues - You can now define additional special character lists in the XML parameter file: - LongProteinNameSplitChars - ProteinNameInvalidCharsToRemove - ProteinNameFirstRefSepChars - ProteinNameSubsequentRefSepChars - Added new option for splitting out multiple references from protein names, whereby this process is only performed if the name matches a known pattern (IPI, gi, and jgi) Version 2.1.2952; January 31, 2008 - Added a new enzyme: "Acetic Acid Hydrolysis" cleaves after aspartic acid (D) - Note that Asp-N can be used for cleavage before aspartic acid Version 2.1.2896; December 6, 2007 - New version of ValidateFastaFile.dll that can consolidate proteins with duplicate sequences when a fixed fasta file is generated Version 2.1.2771; August 3, 2007 - New version of ValidateFastaFile.dll that creates a text file that lists the hash value for each unique sequence found in the input file - This file is created if a fixed fasta file is generated Version 2.1.2769; August 1, 2007 - New version of ValidateFastaFile.dll that allows for renaming proteins with duplicate names when generating a fixed .Fasta file Version 2.1.2767; July 30, 2007 - Added option to use average elemental masses in addition to monoisotopic masses - Customize on the "Parse and Digest File Options" tab Version 2.1.2684; May 8, 2007 - New version of ValidateFastaFile.dll that raises a warning if duplicate protein sequences are found Version 1.1.2659; April 13, 2007 - Added several additional enzymes for in-silico digestion, including some that cleave on the N-terminal side of the target residues (e.g. Asp-N) - New enzymes: Lys-C, Arg-C, Asp-N, Proteinase K, and 3 variants of Pepsin Version 2.1.2565; January 9, 2007 - Fixed a bug in the Uniqueness Stats algorithm that prevented the program from reading the protein input file - Now informing the user if any lines are skipped from a delimited text file (which will typically occur if the input file format defined by the user doesn't match the data in the protein input file) Version 2.1.2546; December 21, 2006 - Fixed a bug that failed to insert a period between the end of a sequence and the suffix residue when "Include prefix and suffix residues" is enabled during In Silico digestion of proteins Version 2.1.2508; November 13, 2006 - Updated clsInSilicoDigest.vb to support using "No Enzyme" for in-silico digestion - Defines the residues to cleavage after as all residues: ABCDEFGHIJKLMNOPQRSTUVWXYZ Version 2.1.2481; October 17, 2006 - Now including a header line when converting a .Fasta file to a text file - If "Look for addnl Ref in description" is enabled, then includes each of the accession names in the header line - When writing out the accession numbers, no longer includes the accession name in each data line, since the header line contains that information - Fixed a parsing bug that caused proteins with descriptions like the following to throw an error when splitting on | and : to find addnl Refs in protein descriptions - Tax_Id=9606 PREDICTED: hypothetical - Updated to new version of NETPrediction.dll (v 1.0.2481) Version 2.1.2419; August 16, 2006 - Added the ability to create multiple scrambled fasta files for a given input file using the Protein Scrambling Loop Count option - Fixed loading of options from a parameter file specified at the command line Version 2.1.2379; July 7, 2006 - Added option to filter digested peptides by pI Version 2.1.2369; June 27, 2006 - Added enzyme LysC, which cleaves after K - See http://ca.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html Version 2.1.2347; June 5, 2006 - Updated to new version of ValidateFastaFile.dll Version 2.1.2203; January 12, 2006 - Updated to new version of ValidateFastaFile.dll Version 2.1.2189; December 29, 2005 - Updated the copyright notice Version 2.1.2104.30263; October 5, 2005 - Updated to new version of ValidateFastaFile.dll - In ValidateFastaFile, updated the SaveSettingsToParameterFile function to re-open the .Xml file and replace instances of ">" with ">" to improve readability - Updated to new version of NETPrediction.dll/NETPredictionBasic.dll Version 2.1.2091.33214; September 22, 2005 - Now using the name Basic version instead of Lite version for the version that does not contain the Kangas prediction algorithm Version 2.1.2090.22113; September 21, 2005 - Updated to use new NETPrediction DLL - Added Help->About NET Prediction menu item - Displays information about the algorithm's developers, including a journal reference or website with additional information Version 2.1.2082.22601; September 13, 2005 - Updated to use SharedVBNetRoutines.dll instead of clsSharedADONetFunctions.vb and clsSharedVBNetFunctions.vb Version 2.1.2064.27890; August 26, 2005 - Added option to compute pI and hydrophobicity of proteins and peptides - Code provided by Gordon Anderson from ICR-2LS - There are 6 available hydrophobicity modes - GUI includes an interactive textbox where a peptide sequence can be pasted and the pI and hydrophobicity computed Version 2.1.2056.27567; August 18, 2005 - Updated to new version of ValidateFastaFile.dll; includes rule to check for escape characters in the protein description Version 2.1.2053.31162; August 15, 2005 - Updated the formula and mass of residues J and X to be the same as Leucine or Isoleucine (C6H11NO: 113.08 Da) - Previously, J and X had the same formula and mass as Lysine (C6H12N2O: 128.09) Version 2.1.2049.28765; August 11, 2005 - Fixed bug that caused the program to crash if an invalid file fasta path was present and the user clicked Validate Fasta File - Updated to a new version of ValidateFastaFile.dll which uses a VB.NET interface to define the functions and properties - Updated to a new version of SharedVBNetRoutines.dll Version 2.1.2008.27908; June 30, 2005 - Updated to use new ValidateFastaFile.dll which implements user-editable RegEx-based definitions for the validation rules Version 2.1.1992; June 15, 2005 - Updated to use new NETPrediction DLL with 1052 node prediction model May 6, 2005 - Added option to identify matching peaks (for uniqueness calculations) using a simple Ellipse search range rather than SLiC score May 2, 2005 - Added Fasta file validation option (utilizing ValidateFastaFile.dll) January 26, 2005 - Abandoned storing data in the Sql Server database since inefficient January 18, 2005 - Redesigned feature info, peptide info, and protein info classes to optionally store data in a Sql Server Database, thereby allowing signficant decreases in memory consumption (at the cost of execution speed) December 17, 2004 - Added option to write out a percentage of the residues from reversed protein sequences December 3, 2004 - Added option to output data as new fasta file; added saving/loading addition info from Xml settings file. November 22, 2004 - Switched to writing results by threshold as they are computed to decrease memory usage November 21, 2004 - Moved peak matching results into a class that uses a DataTable rather than a UDT October 18, 2004 - Improved GUI for peptide uniqueness module October 12, 2004 - Parse fasta/delimited protein file functionality is working; working on clsProteinDigestionSimulator October 4, 2004 - Started writing Protein Digestion Simulator