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When importing an mzTab file to MassIVE search, the code currently parses modifications from each PSM row and uses them to build a "variant" or modified peptide string to write to the database. When doing so, it handles "neutral loss" CV terms (e.g. MS:1001524 - "fragment neutral loss") by simply parsing the numeric value of the CV tuple and adding it to the mass at the indicated peptide position.

However, this is semantically inappropriate for such CV terms, as their intention is obviously to encode a negative mass (hence "loss"). The negativity of the numeric CV value is implied even if not explicitly written. The code must be updated to always interpret these terms as negative mass offsets, whether the negative sign is explicitly written into the value or not.

My MS/MS runs are giving this error (below) yet I can run them on my lap top with MS-GF+ (MSGFPlus_v20190122) and they run without errors plus they parse to TSV files just fine.

MS-GF+ support said it was a bug with MzTabUtils. Can you help with this Pls.

These are Agilent QTof LC-MS/MS runs that have been converted to mzML format using msconvert (default parameters:proteowizered:pwiz-setup-3.0.19014.f9d5b8a3b-x86_64). The mzML files are still on the server.

---------- createConvertConfig command: [java -Xmx512M -cp /data/ccms-proteomics/tools/MzTabUtils/2016.0517/MzTabUtils.jar edu.ucsd.mztab.TSVToMzTabParamGenerator -tsv 'tsvResult/TEST_NUMBER_3_9c18a21f2401465d87e5d4d72ae3df78.tsv' -params 'parameters/params.xml' -output 'convertParameters/TEST_NUMBER_3_9c18a21f2401465d87e5d4d72ae3df78.properties' -header_line 'true' -filename '#SpecFile' -modified_sequence 'Peptide' -mod_pattern '#' -fixed_mods_reported 'true' -match_mass_precision '3' -scan 'ScanNum' -index 'SpecID' -accession 'Protein' -charge 'Charge'] ---------- Reading input TSV file [TEST_NUMBER_3_9c18a21f2401465d87e5d4d72ae3df78.tsv]... Exception in thread "main" java.lang.RuntimeException: There was an error parsing the input tab-delimited result file, line 2: Could not determine the spectrum ID type of the input TSV file, since the values of neither the scan column [-1] nor the index column [scanId=277467] in the first data row were valid for their type. at edu.ucsd.mztab.TSVToMzTabParamGenerator.(TSVToMzTabParamGenerator.java:321) at edu.ucsd.mztab.TSVToMzTabParamGenerator.extractArguments(TSVToMzTabParamGenerator.java:981) at edu.ucsd.mztab.TSVToMzTabParamGenerator.main(TSVToMzTabParamGenerator.java:901) Caused by: java.lang.IllegalArgumentException: Could not determine the spectrum ID type of the input TSV file, since the values of neither the scan column [-1] nor the index column [scanId=277467] in the first data row were valid for their type. at edu.ucsd.mztab.TSVToMzTabParamGenerator.determineSpectrumIDType(TSVToMzTabParamGenerator.java:650) at edu.ucsd.mztab.TSVToMzTabParamGenerator.(TSVToMzTabParamGenerator.java:293) ... 2 more createConvertConfig command failed with exit code [1]. Tool execution terminates abnormally with exit code [1]