I am working with v22.2.0.351 and trying to run a MSGF+ search.

However, when running the searches, I got multiple errors related to my digest and modification settings.

Digestion: I had made a customized trypsin with proline digestion, and that was not recognized. I had to revert back to the default Trypsin digest setting (no cut when Pro follows KR). Once I did that, that error went away. My customized digest setting was "-1", which was out of the expected range of 0-9.

Modifications: I got multiple errors for modifications that were defined by their chemical formula in my Peptide Settings. It did not like "H3N" that was defined for pyroGluQ. It did not like "H2O" defined for pyroGluE. It also did not like "O - HN" that was defined for deamidation. I tried clearing all modifications from my Peptide Settings, and re-entering all the default modifications that had these chemical formula definitions, but that did not help. I ended up deleting all the chemical formulas from the modifications, just leaving the numerical values in there, and now the searches run as expected.

Below is the error information I got for the deamidation and pyroGluQ chemical formula instances:

MS-GF+ Release (v2021.09.06) (06 September 2021)
Java 17.0.1 (Oracle Corporation)
Windows 10 (amd64, version 10.0)
java.lang.NumberFormatException: For input string: "O - HN"
at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.base/java.lang.Double.parseDouble(Double.java:651)
at edu.ucsd.msjava.msutil.AminoAcidSet.parseConfigEntry(AminoAcidSet.java:930)
at edu.ucsd.msjava.msutil.AminoAcidSet.getAminoAcidSetFromModFile(AminoAcidSet.java:797)
at edu.ucsd.msjava.msdbsearch.SearchParams.parse(SearchParams.java:337)
at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:77)
at edu.ucsd.msjava.ui.MSGFPlus.main(MSGFPlus.java:61)
Search canceled.

MS-GF+ Release (v2021.09.06) (06 September 2021)
Java 17.0.1 (Oracle Corporation)
Windows 10 (amd64, version 10.0)
java.lang.NumberFormatException: For input string: "-H3N"
at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.base/java.lang.Double.parseDouble(Double.java:651)
at edu.ucsd.msjava.msutil.AminoAcidSet.parseConfigEntry(AminoAcidSet.java:930)
at edu.ucsd.msjava.msutil.AminoAcidSet.getAminoAcidSetFromModFile(AminoAcidSet.java:797)
at edu.ucsd.msjava.msdbsearch.SearchParams.parse(SearchParams.java:337)
at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:77)
at edu.ucsd.msjava.ui.MSGFPlus.main(MSGFPlus.java:61)
Search canceled.