It's about 100MB...I tried to attach it but got an error. Do you have an FTP somewhere I could upload it to?
Would love a hand with this. I've stumbled my way through plenty of TPP operations but this is my first time with Comet. I'm not sure if that's the issue or something else. Thanks! On Thursday, January 15, 2015 at 3:13:43 PM UTC-6, Sarah Parker wrote: > > 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]> 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]. >>> To post to this group, send email to [email protected]. >>> 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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