IonQuant returns ambiguous error with our pepxml file

[kiahalespractice]

Hello,

We want to use IonQuant alone, without the whole MSFragger pipeline. When I feed IonQuant our pepxml file like this: java -jar IonQuant-1.5.5.jar --specdir /path/to/spectral-directory/ my.pepXML It returns the following error: Please specify the directory containing the spectral file corresponding to /path/to/my.pepXML

When I feed IonQuant a pepXML file generated by MSFragger on the same original spectral file, the same command works. This makes me think the problem is an incompatibility between IonQuant and my.pepXML, not the directory containing the spectral file fed to IonQuant, and not the IonQuant execution itself. I would appreciate any help with pointing out where that incompatibility may be. I have included a portion of the relevant header of my.pepXML here:

<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="pepXML_std.xsl"?>
<msms_pipeline_analysis date="2021-04-30T10:27:13" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML /usr/local/tpp/schema/pepXML_v110.xsd" summary_xml="/path/to/Pf_C10-600_MixES-Sol_SG-1_rKCTi_VO2_101.pepXML">
<msms_run_summary base_name="/path/to/spectral-directory/Pf_C10-600_MixES-Sol_SG-1_rKCTi_VO2_101" raw_data_type="mzML" raw_data="mzML" >
<sample_enzyme name="trypsin">
</sample_enzyme>
<search_summary base_name="/path/to/spectral-directory/Pf_C10-600_MixES-Sol_SG-1_rKCTi_VO2_101" search_engine="Crux" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" out_data_type="NA" out_data="NA" search_id="1" >
<search_database local_path="/path/to/fastas/pfal_human.fasta" type="AA" />
<enzymatic_search_constraint enzyme="trypsin" max_num_internal_cleavages="0" min_number_termini="2"/>
<aminoacid_modification aminoacid="C" mass="160.0307" massdiff="57.02" variable="N" />
<aminoacid_modification aminoacid="M" mass="147.0354" massdiff="15.99" variable="Y" />

I have also included a portion of the relevant header for the MSFragger pepXML file here:

<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="pepXML_std.xsl"?>
<msms_pipeline_analysis date="2021-04-30T11:14:27" xmlns="http://regis-web.systemsbiology.net/pepXML" summary_xml="/path/to/spectral-directory/Pf_C10-600_MixES-Sol_SG-1_rKCTi_VO2_101.pepXML" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v122.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<msms_run_summary base_name="/path/to/spectral-directory/Pf_C10-600_MixES-Sol_SG-1_rKCTi_VO2_101" raw_data_type="mzML" raw_data="mzML">
<sample_enzyme name="stricttrypsin">
<specificity cut="KR" no_cut="" sense="C"/>
</sample_enzyme>
<search_summary base_name="/path/to/spectral-directory/Pf_C10-600_MixES-Sol_SG-1_rKCTi_VO2_101" precursor_mass_type="monoisotopic" search_engine="X! Tandem" search_engine_version="MSFragger-3.2" fragment_mass_type="monoisotopic" search_id="1">
<search_database local_path="/path/to/fastas/pfal_human.fasta" type="AA"/>
<enzymatic_search_constraint enzyme="default" min_number_termini="2" max_num_internal_cleavages="2"/>
<aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0307" variable="N"/>
<aminoacid_modification aminoacid="M" massdiff="15.9949" mass="147.0354" variable="Y"/>
<terminal_modification massdiff="42.0106" protein_terminus="Y" mass="43.0184" terminus="N" variable="Y"/>
<parameter name="# MSFragger.build" value="MSFragger-3.2"/>
<parameter name="database_name" value="/path/to/fastas/pfal_human.fasta"/>

[fcyu]

Can you send us your log files, including the command line, first?

You can also send us all of your files so that I can troubleshoot from my side.

Best,

Fengchao

[fcyu]

No response.