MSGFPlus_v20190214.zip has:

File Description Requirements
MSGFPlus.jar MS-GF+ search engine Java runtime, v1.8 or newer
MzidToTsvConverter.exe Converts .mzid files to a tab-delimited text file .NET Runtime 4.6.2 or newer
Documentation files HTML files explaining how to use the software n/a
Example files Example modification files and example results n/a

Changes in this release:

Assets 3

@alchemistmatt alchemistmatt released this Feb 5, 2019 · 97 commits to master since this release

MSGFPlus_v20190205.zip has:

File Description Requirements
MSGFPlus.jar MS-GF+ search engine Java runtime, v1.8 or newer
MzidToTsvConverter.exe Converts .mzid files to a tab-delimited text file .NET Runtime 4.6.2 or newer
Documentation files HTML files explaining how to use the software n/a
Example files Example modification files and example results n/a

Changes in this release:

  • Add option to use a custom prefix for decoy proteins (default is XXX_)
    • Both MSGFPlus.jar and BuildSA now support the -decoy switch
Assets 3

@alchemistmatt alchemistmatt released this Feb 2, 2019 · 114 commits to master since this release

MSGFPlus_v20190201.zip has:

File Description Requirements
MSGFPlus.jar MS-GF+ search engine Java runtime, v1.8 or newer
MzidToTsvConverter.exe Converts .mzid files to a tab-delimited text file .NET Runtime 4.6.2 or newer
Documentation files HTML files explaining how to use the software n/a
Example files Example modification files and example results n/a

Changes in this release:

  • Add validation of user-defined dynamic and static modifiations to check for duplicates (same name, different mass)
  • Add validation to check for the same dynamic or static modification being defined for the same residue (or N- or C- terminus)
  • Validate user-defined modification masses against default values for commonly used modifications
Assets 3

@alchemistmatt alchemistmatt released this Jan 22, 2019 · 125 commits to master since this release

MSGFPlus_v20190122.zip has:

File Description Requirements
MSGFPlus.jar MS-GF+ search engine Java runtime, v1.8 or newer
MzidToTsvConverter.exe Converts .mzid files to a tab-delimited text file .NET Runtime 4.6.2 or newer
Documentation files HTML files explaining how to use the software n/a
Example files Example modification files and example results n/a

Changes in this release:

  • Add support for .mgf files created using RawTools
  • Skip spectra with a 0 m/z precursor ion
    • RawTools sometimes includes spectra with PEPMASS=0
    • These spectra are now ignored since we cannot make a peptide identification without a precursor ion mass
Assets 3

@alchemistmatt alchemistmatt released this Oct 15, 2018 · 144 commits to master since this release

MSGFPlus_v20181015.zip has:

File Description Requirements
MSGFPlus.jar MS-GF+ search engine Java runtime
MzidToTsvConverter.exe Converts .mzid files to a tab-delimited text file .NET Runtime 4.6.2 or newer
Documentation files HTML files explaining how to use the software n/a
Example files Example modification files and example results n/a

Changes in this release:

  • Parse the elution time (retention time) from Mascot Generic Format (.mgf) files if defined using RTINSECONDS
  • Parse out scan numbers from the TITLE line of .mgf files created by msconvert (part of ProteoWizard)

These changes will result in .mzid files having two new entries for each spectrum, for example

  <cvParam cvRef="PSI-MS" accession="MS:1001115" name="scan number(s)" value="19446"/>
  <cvParam cvRef="PSI-MS" accession="MS:1000016" name="scan start time" value="3163.3267" unitAccession="UO:0000010" unitName="second" unitCvRef="UO"/>
Assets 3

@alchemistmatt alchemistmatt released this Sep 13, 2018 · 150 commits to master since this release

  • In BuildSA, validate that the output directory exists and is writable
  • Update BuildSA syntax to include -o and mention that -d can be a directory with several FASTA files (addresses Issue #47)
Assets 3

@FarmGeek4Life FarmGeek4Life released this Jul 17, 2018 · 160 commits to master since this release

  • Change how rank is set in mzid results to properly comply with the mzIdentML specification (noticed thanks to @adder in Issue #40)
  • Get the scan retention time (and other cvParams) from the mzML ScanList for non-Thermo instruments (removed a check for a userParam that would prevent accessing the cvParams)
  • Add support for newer nativeID formats (in part thanks to @chambm's pull request #41)
  • Read some additional CV Params from mzML and output them to mzIdentML (fixes Issue #32)
Assets 3
Pre-release

@FarmGeek4Life FarmGeek4Life released this Jul 12, 2018 · 162 commits to master since this release

Version for testing ability to copy certain IMS-related CV params from mzML to the mzid
Update the NativeId formats that are detected

Assets 3
Pre-release

@FarmGeek4Life FarmGeek4Life released this Jul 11, 2018 · 165 commits to master since this release

Version for testing ability to copy certain IMS-related CV params from mzML to the mzid

Assets 3

@alchemistmatt alchemistmatt released this Jun 28, 2018 · 167 commits to master since this release

  • Add option to specify the maximum number of missed cleavages (thanks to Sean at CWRU-CPB)
  • Make command line argument names case-insensitive
  • Add additional checks to prevent the output of duplicate peptide evidences (fixes Issue #24)
Assets 3