Release 2019.02.20

MSGFPlus_v20190220.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:

• When reading settings from a configuration file, store custom amino acid definitions first

Release 2019.02.14

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:

• Add support for reading settings from a configuration file
  • Use the -conf switch at the command line
  • Example parameter file: https://github.com/MSGFPlus/msgfplus/blob/master/docs/examples/MSGFPlus_Params.txt

Release 2019.02.05

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

Release 2019.02.01

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
  • Warn if the mass is more than 0.01 Da larger or smaller than the default
  • Common modifications tracked via array defaultModList in file Modification.java

Release 2019.01.22

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
  • RawTools creates .mgf files that are Unicode with a byte order mark
• 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

Release 2018.10.15

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"/>

Release v2018.09.12

• 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)

Release v2018.07.17

• 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)

IMS CV RC2

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

IMS CV RC

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