Release 1.1.8305

Changes:

• New version of PSI_Interface that supports peptides with C-terminal modifications

The .zip file includes PbfGen.exe, ProMex.exe, ProMexAlign.exe, and MSPathFinderT.exe, plus example input files.

Alternatively, use Informed-Proteomics_Installer.exe to install to C:\Program Files\Informed-Proteomics

Release 1.1.8082

Changes:

• Update PbfGen to look for .mzML files in the specified input directory

The .zip file includes PbfGen.exe, ProMex.exe, ProMexAlign.exe, and MSPathFinderT.exe, plus example input files.

Alternatively, use Informed-Proteomics_Installer.exe to install to C:\Program Files\Informed-Proteomics

Release 1.1.8066

Changes:

• Update PbfGen to look for .mzML files in the specified input directory

The .zip file includes PbfGen.exe, ProMex.exe, ProMexAlign.exe, and MSPathFinderT.exe, plus example input files.

Alternatively, use Informed-Proteomics_Installer.exe to install to C:\Program Files\Informed-Proteomics

Release 1.1.7867

Changes:

• Update ProMexAligner to add error handling and to allow for missing PBF files

The .zip file includes PbfGen.exe, ProMex.exe, ProMexAlign.exe, and MSPathFinderT.exe, plus example input files.

Alternatively, use Informed-Proteomics_Installer.exe to install to C:\Program Files\Informed-Proteomics

Release 1.1.7844

Changes:

• Add parameter BinningResolutionPPM to ProMex (use -BinResPPM at the command line)
  • Allows for customizing the bin size used when creating LC-MS features

The .zip file includes PbfGen.exe, ProMex.exe, and MSPathFinderT.exe, plus example input files.

Alternatively, use Informed-Proteomics_Installer.exe to install to C:\Program Files\Informed-Proteomics

Release 1.1.7811

Changes:

• When multiple proteoforms have the same score for a given scan, include each of them in the .tsv file
• Fix logic to avoid reporting duplicate proteoforms when NumMatchesPerSpec is greater than 1
• Add parameter MatchesPerSpectrumToKeepInMemory (-memMatches at the command line)

The .zip file includes PbfGen.exe, ProMex.exe, and MSPathFinderT.exe, plus example input files.

Alternatively, use Informed-Proteomics_Installer.exe to install to C:\Program Files\Informed-Proteomics

Release 1.1.7761

Changes:

• When creating a .pbf file, switch to virtual scan numbers if a duplicate scan number is encountered
  • This can occur for Waters .raw datasets

Release 1.1.7709

Changes

• Fix the version number listed in .mzid files created by MSPathFinder
• PbfGen, ProMex, and MSPathFinderT can now be run on Linux using mono
  • Supported input file formats are Thermo .raw files, .mzML files, and .mzML.gz files
  • See file Example_CommandLineArguments.txt for examples

Release 1.1.7707

Changes:

• Add support for using wildcards to specify input files

Release 1.0.7569

• Change .NET version requirement from 4.6.2 to 4.7.2
• Add support for loading options from a parameter file
  • For example parameter files, see the Example_Files subdirectory (below in the directory with MSPathFinderT.exe)
• Optionally include decoy hits in the _IcTda.tsv file
  • Enable this by providing a parameter file with IncludeDecoyResults=true or by using -IncludeDecoy at the command line
• Optionally include more than one PSM for each scan, both in the _IcTda.tsv file and in the .mzid file
  • Enable this by providing a parameter file with NumMatchesPerSpec=2 or NumMatchesPerSpec=3 or by using -n at the command line
  • QValue and PepQValue are reported as 10 for rank 2 and higher PSMs since QValue is only computed using the top hit for each scan

The zip file includes the PromexAlign application, which is not included in the installer.