Mercurial > repos > galaxyp > idpquery
view test-data/201208-378803-cm.pep.xml @ 7:51d54a9c9283 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 3cc1eda0c28ff138ac19c103c9fbb2a4841beed9"
| author | galaxyp |
|---|---|
| date | Wed, 26 May 2021 19:58:12 +0000 |
| parents | 032c02d10694 |
| children |
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<?xml version="1.0" encoding="UTF-8"?> <msms_pipeline_analysis date="2014-09-19T11:13:55" 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:\idpicker\branches\IDPicker-3\TestData\201208-378803.pep.xml"> <msms_run_summary base_name="C:\idpicker\branches\IDPicker-3\TestData\201208-378803" msManufacturer="unknown" msModel="unknown" raw_data_type="raw" raw_data=".mzML"> <sample_enzyme name="Trypsin/P"> <specificity cut="KR" no_cut="-" sense="C"/> </sample_enzyme> <search_summary base_name="C:\idpicker\branches\IDPicker-3\TestData\201208-378803" search_engine="Comet" search_engine_version="2014.02 rev. 0" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1"> <search_database local_path="cow.protein.PRG2012-subset.fasta" type="AA"/> <enzymatic_search_constraint enzyme="Trypsin/P" max_num_internal_cleavages="2" min_number_termini="1"/> <aminoacid_modification aminoacid="M" massdiff="15.994900" mass="147.035385" variable="Y" symbol="*"/> <aminoacid_modification aminoacid="Q" massdiff="-17.026000" mass="111.032578" variable="Y" symbol="#"/> <aminoacid_modification aminoacid="Q" massdiff="0.984016" mass="129.042594" variable="Y" symbol="@"/> <aminoacid_modification aminoacid="N" massdiff="0.984016" mass="115.026943" variable="Y" symbol="@"/> <aminoacid_modification aminoacid="C" massdiff="58.005480" mass="161.014665" 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="58.005480"/> <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="1"/> <parameter name="database_name" value="cow.protein.PRG2012-subset.fasta"/> <parameter name="decoy_prefix" value="XXX_"/> <parameter name="decoy_search" value="1"/> <parameter name="digest_mass_range" value="600.000000 5000.000000"/> <parameter name="fragment_bin_offset" value="0.020000"/> <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="1"/> <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="-cm"/> <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="1 5"/> <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="2"/> <parameter name="scan_range" value="0 0"/> <parameter name="search_enzyme_number" value="2"/> <parameter name="show_fragment_ions" value="0"/> <parameter name="skip_researching" value="1"/> <parameter name="spectrum_batch_size" value="0"/> <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="0"/> <parameter name="variable_mod01" value="15.994900 M 0 3 -1 0"/> <parameter 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<modification_info modified_peptide="ASQGM[147]TPFR"> <mod_aminoacid_mass position="5" mass="147.035385"/> </modification_info> <search_score name="xcorr" value="0.473"/> <search_score name="deltacn" value="0.043"/> <search_score name="deltacnstar" value="0.000"/> <search_score name="spscore" value="0.0"/> <search_score name="sprank" value="7"/> <search_score name="expect" value="9.74E+000"/> </search_hit> <search_hit hit_rank="3" peptide="NESLDLYR" peptide_prev_aa="L" peptide_next_aa="L" protein="XXX_gi|528921178|ref|XP_592304.7|" num_tot_proteins="2" num_matched_ions="1" tot_num_ions="14" calc_neutral_pep_mass="1009.471640" massdiff="2.003266" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="622"> <modification_info modified_peptide="N[115]ESLDLYR"> <mod_aminoacid_mass position="1" mass="115.026943"/> </modification_info> <search_score name="xcorr" value="0.453"/> <search_score name="deltacn" value="0.208"/> <search_score name="deltacnstar" value="0.000"/> 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