Search engine is X! Tandem in the output pepXML

[zhuchcn]

In the output pepXML file of MSFragger, the search_engine attribute is 'X! Tandem'. Is it done on purpose?

<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="pepXML_std.xsl"?>
<msms_pipeline_analysis date="2022-02-27T22:45:48" xmlns="http://regis-web.systemsbiology.net/pepXML" summary_xml="13CPTAC_LUAD_W_BI_20180629_KR_f04_indexed_centroid.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="13CPTAC_LUAD_W_BI_20180629_KR_f04_indexed_centroid" raw_data_type="mzML" raw_data="mzML">
<sample_enzyme name="Trypsin">
<specificity cut="KR" no_cut="P" sense="C"/>
</sample_enzyme>
<search_summary base_name="13CPTAC_LUAD_W_BI_20180629_KR_f04_indexed_centroid" precursor_mass_type="monoisotopic" search_engine="X! Tandem" search_engine_version="MSFragger-3.3" fragment_mass_type="monoisotopic" search_id="1">
<search_database local_path="/hot/users/czhu/pipeline-validate-ProteomicPSM/sandbox/genome/gencode_37_chr21_proteins_decoy.fasta" type="AA"/>
<enzymatic_search_constraint enzyme="default" min_number_termini="2" max_num_internal_cleavages="2"/>

Also when running PeptideProphet, it says it's using Tandem's expectation score for modeling. Not sure if it is going to be an issue.

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "DECOY_".
Decoy Probabilities will be reported.
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
init with X! Tandem trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

Just realized that I probably should post it on the MSFragger repo. Let me know if that's more appropriate and I'll repost it over there!

[anesvi]

This is for some compatibility reasons (so that MSFragger output can be used with PeptideProphet). You can ignore it. At some point we should fix it, but it does not affect anything. Alexey Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: Chenghao Zhu ***@***.***> Sent: Thursday, March 31, 2022 7:11:09 AM To: Nesvilab/philosopher ***@***.***> Cc: Subscribed ***@***.***> Subject: [Nesvilab/philosopher] Search engine is X! Tandem in the output pepXML (Discussion #333) External Email - Use Caution In the output pepXML file, the search_engine attribute is 'X! Tandem'. Is it done on purpose? <?xml version="1.0" encoding="UTF-8"?> <?xml-stylesheet type="text/xsl" href="pepXML_std.xsl"?> <msms_pipeline_analysis date="2022-02-27T22:45:48" xmlns="http://regis-web.systemsbiology.net/pepXML" summary_xml="13CPTAC_LUAD_W_BI_20180629_KR_f04_indexed_centroid.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="13CPTAC_LUAD_W_BI_20180629_KR_f04_indexed_centroid" raw_data_type="mzML" raw_data="mzML"> <sample_enzyme name="Trypsin"> <specificity cut="KR" no_cut="P" sense="C"/> </sample_enzyme> <search_summary base_name="13CPTAC_LUAD_W_BI_20180629_KR_f04_indexed_centroid" precursor_mass_type="monoisotopic" search_engine="X! Tandem" search_engine_version="MSFragger-3.3" fragment_mass_type="monoisotopic" search_id="1"> <search_database local_path="/hot/users/czhu/pipeline-validate-ProteomicPSM/sandbox/genome/gencode_37_chr21_proteins_decoy.fasta" type="AA"/> <enzymatic_search_constraint enzyme="default" min_number_termini="2" max_num_internal_cleavages="2"/> Also when running PeptideProphet, it says it's using Tandem's expectation score for modeling. Not sure if it is going to be an issue. using Accurate Mass Bins using PPM mass difference Using Decoy Label "DECOY_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution init with X! Tandem trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN — Reply to this email directly, view it on GitHub<#333>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM66B2XGPVWHYEKGWF7TVCTNQ3ANCNFSM5SDOBWYA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[zhuchcn]

Got it! Thanks!