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RevisionHistory.txt
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RevisionHistory.txt
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Peptide Hit Results Processor Runner Revision History
Version 3.1.8791; January 26, 2024
- Add support for MaxQuant modifications that specify modification composition using amino acids
Version 3.1.8503; April 13, 2023
- Add support for DIA-NN
Version 3.1.8290; September 12, 2022
- Add support for new columns in the TopPIC v1.5 results file
Version 3.1.8056; January 22, 2022
- Updated ProteinFileReader that uses a new version of CsvHelper
Version 3.1.8049; January 14, 2022
- Add support for MSFragger
Version 3.1.7997; November 23, 2021
- Add support for the _PepToProtMap.txt file having a header line and having more than two columns
Version 3.1.7983; November 9, 2021
- Change the parameter file format from an XML file to a Key=Value parameter file
- Parse command line arguments using CommandLineParser instead of clsParseCommandLine
Version 3.0.7972; October 29, 2021
- Read column UniMod_Mod_Name from _ModDefs.txt files
Version 3.0.7937; September 24, 2021
- Add support for a header line in Mass_Correction_Tags and _ModDefs.txt files
- If the MaxQuant modifications.xml file was not loaded, look for the MaxQuant mod in data loaded from the _ModDefs.txt file
Version 3.0.7825; June 4, 2021
- For MaxQuant results, only call ComputeDelMCorrectedPPM if the mass error is less than 15 Da
- Show a warning when the computed monoisotopic mass of a MaxQuant result is more than 3x larger than the precursor match tolerance
Version 3.0.7824; June 3, 2021
- When an isobaric mod is present, use the peptide mass computed by PHRP instead of the mass computed by MaxQuant
- When reading a MaxQuant synopsis file, add the Razor Protein to the protein list (if empty)
- Look for precursor info files in the current directory, subdirectories of the current directory, the parent directory, and subdirectories of the parent directory
Version 3.0.7803; May 13, 2021
- Read static MaxQuant modifications from the parameters.txt file instead of an XML-based parameter file
Version 3.0.7797; May 7, 2021
- Add class for loading precursor m/z values from either a _PrecursorInfo.txt file or MASIC files
- Add readers for _SICStats.txt and _ReporterIons.txt files
Version 3.0.7789; April 29, 2021
- Read precursor m/z values from _PrecursorInfo.txt files
Version 3.0.7780; April 20, 2021
- Read peptides from the MaxQuant peptides.txt file
Version 3.0.7766; April 6, 2021
- Add support for MaxQuant results
Version 3.0.7763; April 3, 2021
- Move enums into Data\Enums.cs
Version 3.0.7755; May 26, 2021
- Rename methods and variables to switch from Parser to Reader
- Remove obsolete enums
Version 3.0.7752; May 23, 2021
- Rename classes and enums
- Reorganize classes
Version 2.0.7724; February 23, 2021
- Convert to C#
Version 2.0.7704; February 3, 2021
- Add support for new TopPIC column names
- Rename constants and methods to use MSGFPlus instead of MSGFDB
- Rename properties
Version 1.5.7692; January 22, 2021
- Rename enum ePeptideHitResultType to PeptideHitResultType
- Remove unused code
Version 1.5.7458; June 2, 2020
- Update to .NET 4.7.2
Version 1.5.7130; July 10, 2019
- Allow the MS-GF+ input file to be named Dataset.tsv instead of Dataset_msgfplus.tsv
Version 1.5.7037; April 8, 2019
- Add support for TopPIC results
Version 1.5.6871; October 24, 2018
- Replace HashTables with a SortedSet or Dictionary
- Code cleanup
Version 1.5.6583; January 9, 2018
- Use FileProcessor.ProcessFilesBase in PRISM.dll
Version 1.5.6502; October 20, 2017
- Fix bug finding a matching mass correction tag based on mass
Version 1.5.6501; October 19, 2017
- Extensive code cleanup, including using clsEventNotifier in PRISM.dll
Version 1.5.6487; October 5, 2017
- Convert to C#
Version 1.5.6274; March 6, 2017
- Replace ToLower and ToUpper-based string comparisons with StringComparison.InvariantCultureIgnoreCase
Version 1.5.6128; November 22, 2016
- PHRPReader now supports MSGF+ results files named _msgfplus in addition to _msgfdb
Version 1.5.6128; October 11, 2016
- Filter MSGF+ results while reading the .TSV file to create synopsis and first hits files
- Greatly reduces memory usage for result files that have a large number of low scoring peptides and/or peptides with a large number of parent proteins
- Add support for option ChargeCarrierMass in the MSGF+ parameter file
Version 1.5.6125; October 8, 2016
- Check for a dynamic or static mod specification having an unrecognized keyword before the equals sign
- Update GetEmpiricalFormulaComponents to allow for duplicate elements in the empirical formula
Version 1.5.6124; October 7, 2016
- Add properties MsgfPlusSpecEValueThreshold and MsgfPlusEValueThreshold to clsPeptideHitResultsProcRunner
- When running the executable, customize the filter thresholds using /MSGFPlusSpecEValue and /MSGFPlusEValue
- Use stricter data filters when creating synopsis files from MSGF+ and MSPathFinder results
- SpecEValue threshold changed from 1E-4 to 5E-7
- EValue threshold changed from 0.95 to 0.75
- Store results in the MSGF+ synopsis file if QValue is less than 1%, regardless of SpecEValue or EValue
Version 1.5.6008; June 13, 2016
- Remove the dependency on ThermoRawFileReader in PHRPReader
- Added function ExtractParentIonMzFromFilterText
Version 1.5.5981; May 17, 2016
- Return a non-zero error code if processing an MSGF+ results file and the ModDefs file does not have a definition for a given dynamic mod
Version 1.5.5978; May 14, 2016
- Improved support for custom amino acid definitions in MSGF+ parameter files
Version 1.5.5973; May 9, 2016
- Added support for custom amino acid definitions in MSGF+ parameter files
Version 1.5.5959; April 25, 2016
- Updated to System.Data.SQLite v1.0.97
- Updated to .NET 4.5.1
Version 1.5.5813; December 1, 2015
- Fixed a bug that affected modification parsing when the same modification is defined in the MSGF+ search parameters as both a static and a dynamic modification (but for different target residues)
Version 1.5.5800; November 18, 2015
- PHRP now recognizes that HexNAc is Hexosam, which is 203.079376 Da
Version 1.5.5792; November 10, 2015
- Updated clsParseCommandLine, clsProcessFilesOrFoldersBase, and clsXmlSettingsFileAccessor
Version 1.5.5717; August 27, 2015
- When filtering MSPathFinder results, test for SpecEValue < 0.0001 or QValue < 5%
- Now considering QValue for sorting (in case SpecEValue is not defined)
Version 1.5.5714; August 24, 2015
- Add columns SpecEValue and EValue for MSPathfinder
Version 1.5.5696; August 6, 2015
- Now assuring that the protein name shown in MSGF+ result files is the first protein that appears in the FASTA file
- Applies to peptides that are present in multiple proteins
Version 1.5.5683; July 24, 2015
- Added support for MSPathFinder
Version 1.5.5620; May 22, 2015
- Now sorting MODPlus results by descending score instead of descending probability
Version 1.5.5617; May 19, 2015
- Added switch /SynProb
- Added QValue column to MODPlus result files
Version 1.5.5616; May 18, 2015
- Added support for MODPlus
Version 1.5.5553; March 16, 2015
- New version of PHRPReader.dll
Version 1.5.5359; September 3, 2014
- Now ignoring charge state when ranking peptides in a scan by score
- Applies to MSGF+, MSAlign, and MODa
Version 1.5.5329; August 4, 2014
- When parsing MSGF+ results, now treating static N- and C-terminal mods that only target certain residues as dynamic mods
Version 1.5.5303; July 9, 2014
- Updated to System.Data.SQLite v1.0.93 (used by PeptideToProteinMapEngine.dll)
Version 1.5.5276; June 12, 2014
- Now computing QValues for MODa results
Version 1.5.5255; May 22, 2014
- Fixed bug tracking NTerm and CTerm mod masses from MODa parameter files
Version 1.5.5225; April 23, 2014
- Added support for results from MODa
Version 1.5.5198; March 26, 2014
- New versions of dependent DLLs, including PHRPReader.dll
- Added MSGFPlus_Example_Data.zip to the installer
Version 1.5.5168; February 24, 2014
- New version of PeptideHitResultsProcessor.dll
Version 1.5.5150; February 6, 2014
- New version of PHRPReader.dll
Version 1.5.5142; January 29, 2014
- Added 64-bit version
- New version of PHRPReader.dll
- Resharper code cleanup
Version 1.5.5072; November 20, 2013
- New versions of PHRPReader.dll, ProteinCoverageSummarizer.dll, and PeptideToProteinMapEngine.dll
Version 1.5.5050; October 29, 2013
- New version of ThermoRawFileReaderDLL
Version 1.5.4927; June 28, 2013
- Now using String.IsNullOrWhiteSpace
Version 1.5.4926; June 27, 2013
- Updated default Mass Correction Tags
- Now comparing DelM_PPM value computed by MSGF+ with the search tolerances used
- If the computed value is more than 1.5 fold larger than the search tolerances, then a new DelM_PPM value is computed
- This change was prompted by Analysis Job 957459
Version 1.5.4841; April 3, 2013
- Added MSAlign columns Species_ID and FragMethod
Version 1.5.4821; March 14, 2013
- Updated modMain to latest standard format
Version 1.5.4734; December 17, 2012
- MSGF+ static mod bug fix
Version 1.5.4730; December 13, 2012
- Now skipping the ProteinMods step if the FASTA file contains nucleic acids instead of amino acids
Version 1.5.4727; December 10, 2012
- Replaced Char.IsLetter() calls with a RegEx that matches [A-Za-z]
Version 1.5.4723; December 6, 2012
- Now naming new, unknown modifications using the modification mass instead of using UnkMod01, UnkMod02, etc.
Version 1.5.4721; December 4, 2012
- Now assuring that the various Count columns in MSAlign results contain integers
Version 1.5.4720; December 3, 2012
- Added support for results from MSAlign v0.5
Version 1.5.4716; November 29, 2012
- Added support for MSGF+ results with semicolon-separated protein names
- Now supports adding over 100 unknown mods
Version 1.5.4715; November 28, 2012
- Added support for MSAlign results
Version 1.5.4714; November 27, 2012
- Added support for MSGF+ results
- New versions of PeptideToProteinMapEngine.DLL, PHRPReader.DLL, and ProteinCoverageSummarizer.DLL to support MSGF+ column names
Version 1.5.4681; October 25, 2012
- Added several new switches to support creating a _ProteinMods.txt file with details on modified residues for each protein
Version 1.4.4619; August 24, 2012
- Added support for columns IMS_Scan and IMS_Drift_Time in MSGFDB search results
- New version of PHRPReader
Version 1.4.4512; May 9, 2012
- Now posting error messages to the error stream
Version 1.4.4511; May 8, 2012
- New version of PeptideHitResultsProcessor that adds support for the EFDR column in MSGFDB results
- This column is included if a target/decoy search is not run and if MSGFDB is instructed to just write out the top hit for each spectrum
- Reported in the _msgfdb_syn.txt file under the FDR column (the PepFDR column will show 1 for every record in this case)
Version 1.4.4504; May 1, 2012
- Now looking for the search engine parameter file and ModDefs file in the same folder as the input folder if not found in the working directory
- New version of PeptideHitResultsProcessor
Version 1.4.4500; April 27, 2012
- Removed duplicated classes from PeptideHitResultsProcessor
- Now skipping synopsis-specific SeqInfo files when parsing a first-hits file with the PHRPReader
Version 1.4.4499; April 26, 2012
- New version of PHRPReader.dll that uses ThermoRawFileReaderDLL.dll
Version 1.4.4497; April 24, 2012
- Updated NumToString to correctly handle intDigitsOfPrecision
- PeptideHitResultsProcessor now depends on PHRPReader
Version 1.4.4496; April 23, 2012
- New version of PeptideHitResultsProcessor
Version 1.4.4349; November 28, 2011
- Now writing out a separate entry to the synopsis or first-hits file for each scan involved in a merged result reported by MSGFDB
- Now creating a ScanGroupInfo.txt file when MSGFDB merged spectra are processed
Version 1.4.4342; November 21, 2011
- Updated to support MSGFDB search results with merged spectra (scan numbers of the form 3010/3011/3012)
Version 1.4.4293; October 3, 2011
- New version of PeptideHitResultsProcessor.dll
- Fixes bug that incorrectly computed Rank_MSGFDB_SpecProb as 2 for the final entry in the MSGFDB results file
Version 1.4.4286; September 26, 2011
- Updated program syntax
Version 1.4.4268; September 8, 2011
- Fixed tryptic state computation bug when processing MSGFDB results
Version 1.4.4267; September 7, 2011
- Renamed column headers in the MSGFDB synopsis and first-hits file
Version 1.4.4257; August 29, 2011
- New version of PeptideHitResultsProcessor.dll
- Fixed mass computation bug for MSGFDB results with static mods
Version 1.4.4252; August 23, 2011
- New version of PeptideHitResultsProcessor.dll
- Now reads/writes columns FDR and pepFDR for MSGFDB results
Version 1.4.4247; August 18, 2011
- New version of PeptideHitResultsProcessor.dll
- Added support for MSGFDB results
- Now reading the column headers from Sequest and Inspect _syn.txt files
- X!Tandem _xt.txt files and Inspect _syn.txt and _fht.txt files now have column DelM_PPM
- The MH column in Inspect _syn.txt and _fht.txt files is now (M+H)+ instead of uncharged monoisotopic mass
Version 1.4.4239; August 10, 2011
- Updated to Visual Studio 2010
- Added command line switches /InsFHT and /InsSyn
Version 1.3.3855; July 22, 2010
- New version of PeptideHitResultsProcessor.dll
- Removed dependence on AnalysisManagerProg.exe
Version 1.3.3841; July 8, 2010
- Now supports specifying the input filename without using /I:
Version 1.3.3827; June 24, 2010
- Added support for specifying the log file name when using /L
Version 1.3.3597; November 6, 2009
- New version of PeptideHitResultsProcessor.dll
Version 1.3.3562; October 2, 2009
- Now returning False if unknown modification symbols are found when processing Sequest results
Version 1.3.3561; October 1, 2009
- New version of PeptideHitResultsProcessor.dll
Version 1.3.3455; June 17, 2009
- New version of PeptideHitResultsProcessor.dll that uses AnalysisManagerProg.exe instead of PRISM.Dll
Version 1.2.3295; January 8, 2009
- PeptideHitResultsProcessor.dll has updated Inspect support
Version 1.2.3294; January 7, 2009
- PeptideHitResultsProcessor.dll has updated Inspect support and additional debugging
Version 1.2.3265; December 9, 2008
- Improved support for N-terminal and C-terminal Inspect modifications
Version 1.2.3264; December 8, 2008
- Added support for Inspect modifications starting with a plus sign followed by the modification mass, for example: S.SPATLNSR+14.V
Version 1.2.3261; December 5, 2008
- Updated PeptideHitResultsProcessor.dll that includes event ErrorOccured
- Added switch /L which enables logging to a file
- will log any errors raised by PeptideHitResultsProcessor.dll
Version 1.2.3219; October 24, 2008
- Updated PeptideHitResultsProcessor.dll to compute DeltaNormMQScore and DeltaNormTotalPRMScore for Inspect (these values are similar to DelCn2 for Sequest)
Version 1.2.3212; October 17, 2008
- Additional Inspect processing updates to PeptideHitResultsProcessor.dll
Version 1.2.3202; October 7, 2008
- New version of PeptideHitResultsProcessor.dll with expanded Inspect support
Version 1.2.3199; October 4, 2008
- Expanded support for Inspect results files
- Now reads the parameter file provided to Inspect so that the modification names and masses can be determined
- Now reads the _PeptideToProteinMapping.txt file so that the PHRP files can include all of the proteins for each peptide
Version 1.2.3191; September 26, 2008
- Converted solution to VB .NET 2008
- Added support for Inspect results files
Version 1.1.3006; March 25, 2008
- Updates to PeptideHitResultsProcessor.dll:
- Added support for scan numbers specified by "MyDataset.300.300.2.dta" where "300" is the scan number
Version 1.1.2991; March 10, 2008
- Removed SharedVBNetRoutines.dll
Version 1.1.2673; April 27, 2007
- Updates to PeptideHitResultsProcessor.dll:
- Added support for scan numbers specified by "scan 1234" instead of "scan=1234" in the "description" note of the "fragment ion mass spectrum" element
- Now looking for the text ":reversed" in the protein description, in addition to the protein label; if found, the protein name will end in :reversed
Version 1.1.2494; October 30, 2006
- Updated to inform user when unable to auto-determine the format of the input file
Version 1.1.2364; June 26, 2006
- No longer saving negative numbers in the _ModDetails.txt file or _SeqInfo.txt file for Peptide and Protein terminus static modifications
Version 1.1.2322; May 11, 2006
- Updated the routine that parses out the scan number from the "description" note of the "fragment ion mass spectrum" element to look for the first number present if "scan=" is not present
Version 1.1.2256; March 6, 2006
- Updated modification definition parsing routines to group modifications with the same modification mass together
Version 1.1.2249; February 27, 2006
- Updated the default mass correction tag list
Version 1.1.2245; February 23, 2006
- Fixed bug that failed to label reversed sequence proteins with the ":reverse" tag in the _SeqToProteinMap.txt file
Version 1.1.2244; February 22, 2006
- Now updating static XTandem mods to dynamic XTandem mods if a dynamic mod with an identical mass is found or if the directive <note type="input" label="refine, modification mass">none</note> is present in the XTandem parameters
Version 1.1.2237; February 15, 2006
- Updated to new version of PeptideHitResultsProcessor.dll
- The _SeqInfo.txt file no longer contains cleavage state and terminus state information
- The new version now creates files _ResultToSeqMap.txt and _SeqToProteinMap.txt in addition to _SeqInfo.txt and _ModDetails.txt
- The _xt.txt file no longer contains the protein name, protein expectation value, or protein intensity
- The _xt.txt file now includes the Multiple_Protein_Count value for each search result (0 if the peptide is in one protein, 1 if in two proteins, etc.)
Version 1.0.2207; January 16, 2006
- Initial stable release version
- Supports XTandem _xt.txt files and Sequest _syn.txt and _fht.txt files