Thanks David, There weren't any errors, the search seemed to go OK - it's from an IP and I am seeing peptides in the pep.xml from the target protein among the top XCORR scores.
The end of the file says this: </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> For the sake of completeness and maybe some insight, here is the first portion of the pep.xml: <?xml version="1.0" encoding="UTF-8"?> <msms_pipeline_analysis date="2015-01-15T12:16:05" xmlns="http://regis-web.systemsbiology.net/pepXML"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd"; summary_xml="c:\Inetpub\wwwroot\ISB\data\parameters\1hour_Set4_C.pep.xml"> <msms_run_summary base_name="c:\Inetpub\wwwroot\ISB\data\Data\SarahParker\1hour_Set4_C" msManufacturer="" msModel="" raw_data_type="raw" raw_data=".mzXML"> <sample_enzyme name="Trypsin"> <specificity cut="KR" no_cut="P" sense="C"/> </sample_enzyme> <search_summary base_name="c:\Inetpub\wwwroot\ISB\data\parameters\1hour_Set4_C" search_engine="Comet" search_engine_version="2014.02 rev. 2" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1"> <search_database local_path="c:/Inetpub/wwwroot/ISB/data/Databases/uniprot_mouse_reviewed_canonical_Nov2014_iRT_DECOY.fasta" type="AA"/> <enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="2" min_number_termini="2"/> <aminoacid_modification aminoacid="M" massdiff="15.994900" mass="147.035385" variable="Y" symbol="*"/> <aminoacid_modification aminoacid="S" massdiff="79.966331" mass="166.998359" variable="Y" symbol="#"/> <aminoacid_modification aminoacid="T" massdiff="79.966331" mass="181.014010" variable="Y" symbol="#"/> <aminoacid_modification aminoacid="Y" massdiff="79.966331" mass="243.029660" variable="Y" symbol="#"/> <aminoacid_modification aminoacid="C" massdiff="57.021464" mass="160.030649" variable="N"/> <parameter name="# comet_version " value="2014.02"/> <parameter name="activation_method" value="ALL"/> <parameter name="add_A_alanine" value="0.000000"/> <parameter name="add_B_user_amino_acid" value="0.000000"/> <parameter name="add_C_cysteine" value="57.021464"/> <parameter name="add_Cterm_peptide" value="0.000000"/> <parameter name="add_Cterm_protein" value="0.000000"/> <parameter name="add_D_aspartic_acid" value="0.000000"/> <parameter name="add_E_glutamic_acid" value="0.000000"/> <parameter name="add_F_phenylalanine" value="0.000000"/> <parameter name="add_G_glycine" value="0.000000"/> <parameter name="add_H_histidine" value="0.000000"/> <parameter name="add_I_isoleucine" value="0.000000"/> <parameter name="add_J_user_amino_acid" value="0.000000"/> <parameter name="add_K_lysine" value="0.000000"/> <parameter name="add_L_leucine" value="0.000000"/> <parameter name="add_M_methionine" value="0.000000"/> <parameter name="add_N_asparagine" value="0.000000"/> <parameter name="add_Nterm_peptide" value="0.000000"/> <parameter name="add_Nterm_protein" value="0.000000"/> <parameter name="add_O_ornithine" value="0.000000"/> <parameter name="add_P_proline" value="0.000000"/> <parameter name="add_Q_glutamine" value="0.000000"/> <parameter name="add_R_arginine" value="0.000000"/> <parameter name="add_S_serine" value="0.000000"/> <parameter name="add_T_threonine" value="0.000000"/> <parameter name="add_U_user_amino_acid" value="0.000000"/> <parameter name="add_V_valine" value="0.000000"/> <parameter name="add_W_tryptophan" value="0.000000"/> <parameter name="add_X_user_amino_acid" value="0.000000"/> <parameter name="add_Y_tyrosine" value="0.000000"/> <parameter name="add_Z_user_amino_acid" value="0.000000"/> <parameter name="allowed_missed_cleavage" value="2"/> <parameter name="clear_mz_range" value="0.000000 0.000000"/> <parameter name="clip_nterm_methionine" value="0"/> <parameter name="database_name" value="c:/Inetpub/wwwroot/ISB/data/Databases/uniprot_mouse_reviewed_canonical_Nov2014_iRT_DECOY.fasta"/> <parameter name="decoy_prefix" value="DECOY_"/> <parameter name="decoy_search" value="1"/> <parameter name="digest_mass_range" value="600.000000 5000.000000"/> <parameter name="fragment_bin_offset" value="0.000000"/> <parameter name="fragment_bin_tol" value="0.020000"/> <parameter name="isotope_error" value="1"/> <parameter name="mass_type_fragment" value="1"/> <parameter name="mass_type_parent" value="1"/> <parameter name="max_fragment_charge" value="3"/> <parameter name="max_precursor_charge" value="6"/> <parameter name="max_variable_mods_in_peptide" value="5"/> <parameter name="minimum_intensity" value="0"/> <parameter name="minimum_peaks" value="10"/> <parameter name="ms_level" value="2"/> <parameter name="nucleotide_reading_frame" value="0"/> <parameter name="num_enzyme_termini" value="2"/> <parameter name="num_output_lines" value="5"/> <parameter name="num_results" value="50"/> <parameter name="num_threads" value="0"/> <parameter name="output_outfiles" value="0"/> <parameter name="output_pepxmlfile" value="1"/> <parameter name="output_percolatorfile" value="0"/> <parameter name="output_sqtfile" value="0"/> <parameter name="output_sqtstream" value="0"/> <parameter name="output_suffix" value=""/> <parameter name="output_txtfile" value="0"/> <parameter name="override_charge" value="0"/> <parameter name="peptide_mass_tolerance" value="20.000000"/> <parameter name="peptide_mass_units" value="2"/> <parameter name="precursor_charge" value="0 0"/> <parameter name="print_expect_score" value="1"/> <parameter name="remove_precursor_peak" value="0"/> <parameter name="remove_precursor_tolerance" value="1.500000"/> <parameter name="sample_enzyme_number" value="1"/> <parameter name="scan_range" value="0 0"/> <parameter name="search_enzyme_number" value="1"/> <parameter name="show_fragment_ions" value="0"/> <parameter name="skip_researching" value="1"/> <parameter name="spectrum_batch_size" value="5000"/> <parameter name="theoretical_fragment_ions" value="0"/> <parameter name="use_A_ions" value="0"/> <parameter name="use_B_ions" value="1"/> <parameter name="use_C_ions" value="0"/> <parameter name="use_NL_ions" value="1"/> <parameter name="use_X_ions" value="0"/> <parameter name="use_Y_ions" value="1"/> <parameter name="use_Z_ions" value="0"/> <parameter name="use_sparse_matrix" value="1"/> <parameter name="variable_mod01" value="15.994900 M 0 3 -1 0"/> <parameter name="variable_mod02" value="79.966331 STY 0 3 -1 0"/> <parameter name="variable_mod03" value="0.000000 X 0 3 -1 0"/> <parameter name="variable_mod04" value="0.000000 X 0 3 -1 0"/> <parameter name="variable_mod05" value="0.000000 X 0 3 -1 0"/> <parameter name="variable_mod06" value="0.000000 X 0 3 -1 0"/> <parameter name="variable_mod07" value="0.000000 X 0 3 -1 0"/> <parameter name="variable_mod08" value="0.000000 X 0 3 -1 0"/> <parameter name="variable_mod09" value="0.000000 X 0 3 -1 0"/> </search_summary> On Thursday, January 15, 2015 at 1:30:25 PM UTC-6, David Shteynberg wrote: > > Hello Sarah, > > Is your pepXML file 1hour_Set4_C.pep.xml complete? Did you observe any > errors during the search? Can you look at the last few lines of that file, > they should contain something like this: > > ... > </analysis_result> </search_hit> </search_result> </spectrum_query> > </msms_run_summary> </msms_pipeline_analysis> > > > -David > > > > On Thu, Jan 15, 2015 at 10:30 AM, Sarah Parker <[email protected] > <javascript:>> wrote: > >> Hello, >> >> Trying to run xinteract on comet search results (obtained via TPP). >> >> >> >> *EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/parameters& >> c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM -OARP >> -dDECOY 1hour_Set4_C.pep.xml *Getting this error: >> >> c:\Inetpub\tpp-bin\xinteract (TPP v4.8.0 PHILAE, Build 201411201551-6764 >> (mingw-i686)) >> PPM mode in Accurate Mass Model ... >> >> running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" >> "1hour_Set4_C.pep.xml" -L"7"" >> file 1: 1hour_Set4_C.pep.xml >> SUCCESS: CORRECTED data file >> c:\Inetpub\wwwroot\ISB\data\Data\SarahParker\1hour_Set4_C.mzXML in >> msms_run_summary tag ... >> >> This application has requested the Runtime to terminate it in an unusual way. >> Please contact the application's support team for more information. >> >> command "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" >> "1hour_Set4_C.pep.xml" -L"7"" failed: Unknown error >> >> command "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" >> "1hour_Set4_C.pep.xml" -L"7"" exited with non-zero exit code: 255 >> QUIT - the job is incomplete >> >> I can't figure out what's wrong, can anyone help? >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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