Mercurial > repos > iracooke > protk_proteogenomics
view test-data/small.prot.xml @ 0:28067ed4ea0e draft
Docker support and update for protk 1.4
| author | iracooke |
|---|---|
| date | Thu, 26 Mar 2015 20:11:34 -0400 |
| parents | |
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<?xml version="1.0" encoding="UTF-8"?> <protein_summary xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v6.xsd" summary_xml="/home/iracooke/venturiapg/search_results/Pirina/Pirina_pproph.prot.xml"> <protein_summary_header reference_database="/home/iracooke/venturiapg/vpirina6frame_decoy.fasta" residue_substitution_list="I -> L" source_files="/home/iracooke/venturiapg/search_results/Pirina/Pirina_iproph.pep.xml" source_files_alt="/home/iracooke/venturiapg/search_results/Pirina/Pirina_iproph.pep.xml" min_peptide_probability="0.20" min_peptide_weight="0.50" num_predicted_correct_prots="1787.3" num_input_1_spectra="5700" num_input_2_spectra="24737" num_input_3_spectra="8680" num_input_4_spectra="714" num_input_5_spectra="124" initial_min_peptide_prob="0.05" total_no_spectrum_ids="28710.0" sample_enzyme="trypsin"> <program_details analysis="proteinprophet" time="2014-01-20T14:17:37" version=" Insilicos_LabKey_C++ (TPP v0.0 Development trunk rev 0, Build 201307090846 (linux))"> <proteinprophet_details occam_flag="Y" groups_flag="Y" degen_flag="Y" nsp_flag="Y" initial_peptide_wt_iters="2" nsp_distribution_iters="2" final_peptide_wt_iters="3"> <nsp_information neighboring_bin_smoothing="Y"> <nsp_distribution bin_no="0" nsp_lower_bound_incl="0.00" nsp_upper_bound_incl="0.00" pos_freq="0.057" neg_freq="0.625" pos_to_neg_ratio="0.09"/> <nsp_distribution bin_no="1" nsp_lower_bound_excl="0.00" nsp_upper_bound_incl="0.31" pos_freq="0.037" neg_freq="0.152" pos_to_neg_ratio="0.24"/> <nsp_distribution bin_no="2" nsp_lower_bound_excl="0.31" nsp_upper_bound_incl="1.00" pos_freq="0.077" neg_freq="0.032" pos_to_neg_ratio="2.42"/> <nsp_distribution bin_no="3" nsp_lower_bound_excl="1.00" nsp_upper_bound_incl="2.50" pos_freq="0.113" neg_freq="0.033" pos_to_neg_ratio="3.39"/> <nsp_distribution bin_no="4" nsp_lower_bound_excl="2.50" nsp_upper_bound_incl="4.63" pos_freq="0.123" neg_freq="0.032" pos_to_neg_ratio="3.91"/> <nsp_distribution bin_no="5" nsp_lower_bound_excl="4.63" nsp_upper_bound_incl="7.90" pos_freq="0.143" neg_freq="0.032" pos_to_neg_ratio="4.50"/> <nsp_distribution bin_no="6" nsp_lower_bound_excl="7.90" nsp_upper_bound_incl="14.92" pos_freq="0.196" neg_freq="0.041" pos_to_neg_ratio="4.78"/> <nsp_distribution bin_no="7" nsp_lower_bound_excl="14.92" nsp_upper_bound_excl="inf" pos_freq="0.254" neg_freq="0.054" pos_to_neg_ratio="4.72" alt_pos_to_neg_ratio="4.78"/> </nsp_information> <ni_information> </ni_information> <protein_summary_data_filter min_probability="0.00" sensitivity="1.000" false_positive_error_rate="0.835" predicted_num_correct="1787" predicted_num_incorrect="9044"/> <protein_summary_data_filter min_probability="0.10" sensitivity="1.000" false_positive_error_rate="0.235" predicted_num_correct="1787" predicted_num_incorrect="548"/> <protein_summary_data_filter min_probability="0.20" sensitivity="1.000" false_positive_error_rate="0.235" predicted_num_correct="1787" predicted_num_incorrect="548"/> <protein_summary_data_filter min_probability="0.30" sensitivity="0.956" false_positive_error_rate="0.151" predicted_num_correct="1709" predicted_num_incorrect="305"/> <protein_summary_data_filter min_probability="0.40" sensitivity="0.916" false_positive_error_rate="0.095" predicted_num_correct="1638" predicted_num_incorrect="171"/> <protein_summary_data_filter min_probability="0.50" sensitivity="0.887" false_positive_error_rate="0.063" predicted_num_correct="1585" predicted_num_incorrect="106"/> <protein_summary_data_filter min_probability="0.60" sensitivity="0.853" false_positive_error_rate="0.036" predicted_num_correct="1525" predicted_num_incorrect="58"/> <protein_summary_data_filter min_probability="0.70" sensitivity="0.826" false_positive_error_rate="0.020" predicted_num_correct="1477" predicted_num_incorrect="31"/> <protein_summary_data_filter min_probability="0.80" sensitivity="0.805" false_positive_error_rate="0.012" predicted_num_correct="1438" predicted_num_incorrect="18"/> <protein_summary_data_filter min_probability="0.90" sensitivity="0.773" false_positive_error_rate="0.006" predicted_num_correct="1381" predicted_num_incorrect="8"/> <protein_summary_data_filter min_probability="0.95" sensitivity="0.749" false_positive_error_rate="0.004" predicted_num_correct="1339" predicted_num_incorrect="5"/> <protein_summary_data_filter min_probability="0.96" sensitivity="0.738" false_positive_error_rate="0.003" predicted_num_correct="1318" predicted_num_incorrect="4"/> <protein_summary_data_filter min_probability="0.97" sensitivity="0.728" false_positive_error_rate="0.002" predicted_num_correct="1302" predicted_num_incorrect="3"/> <protein_summary_data_filter min_probability="0.98" sensitivity="0.711" false_positive_error_rate="0.002" predicted_num_correct="1272" predicted_num_incorrect="2"/> <protein_summary_data_filter min_probability="0.99" sensitivity="0.609" false_positive_error_rate="0.000" predicted_num_correct="1088" predicted_num_incorrect="0"/> <protein_summary_data_filter min_probability="1.00" sensitivity="0.164" false_positive_error_rate="0.000" predicted_num_correct="294" predicted_num_incorrect="0"/> </proteinprophet_details> </program_details> </protein_summary_header> <dataset_derivation generation_no="0"> </dataset_derivation> <protein_group group_number="3" probability="1.0000"> <protein protein_name="lcl|scaffold10_frame_3_orf_6477" n_indistinguishable_proteins="2" probability="1.0000" percent_coverage="33.3" unique_stripped_peptides="AGFHVTSVGINLK+EVAGPMLSPEVLKG+LIPDTTHLPSEPTTDILILPGGGPGAAAFVSSNSVQHLVR" group_sibling_id="a" total_number_peptides="5" pct_spectrum_ids="0.013" confidence="0.518"> <parameter name="prot_length" value="217"/> <annotation protein_description="513537 514187"/> <indistinguishable_protein protein_name="lcl|scaffold10_fwd_g553.t1"> <annotation protein_description="513490 514190"/> </indistinguishable_protein> <peptide peptide_sequence="EVAGPMLSPEVLKG" charge="2" initial_probability="0.9990" nsp_adjusted_probability="0.9997" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.38" n_sibling_peptides_bin="3" n_instances="2" exp_tot_instances="2.00" is_contributing_evidence="Y" calc_neutral_pep_mass="1425.7549"> </peptide> <peptide peptide_sequence="AGFHVTSVGINLK" charge="3" initial_probability="0.8377" nsp_adjusted_probability="0.9460" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.54" n_sibling_peptides_bin="3" n_instances="1" exp_tot_instances="0.84" is_contributing_evidence="Y" calc_neutral_pep_mass="1341.7405"> </peptide> <peptide peptide_sequence="LIPDTTHLPSEPTTDILILPGGGPGAAAFVSSNSVQHLVR" charge="4" initial_probability="0.5417" nsp_adjusted_probability="0.8004" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.84" n_sibling_peptides_bin="3" n_instances="2" exp_tot_instances="0.81" is_contributing_evidence="Y" calc_neutral_pep_mass="4077.1555"> </peptide> </protein> </protein_group> <protein_group group_number="7" probability="1.0000"> <protein protein_name="lcl|g447.t1" n_indistinguishable_proteins="1" probability="1.0000" percent_coverage="5.0" unique_stripped_peptides="LVPISDEELDPLTALPVYSR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.006" confidence="0.007"> <parameter name="prot_length" value="402"/> <annotation protein_description="195564 196835"/> <peptide peptide_sequence="LVPISDEELDPLTALPVYSR" charge="2" initial_probability="0.9990" nsp_adjusted_probability="0.9996" peptide_group_designator="a" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.75" n_sibling_peptides_bin="2" n_instances="1" exp_tot_instances="1.00" is_contributing_evidence="Y" calc_neutral_pep_mass="2226.1793"> </peptide> <peptide peptide_sequence="LVPISDEELDPLTALPVYSR" charge="3" initial_probability="0.7530" nsp_adjusted_probability="0.8805" peptide_group_designator="a" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.00" n_sibling_peptides_bin="2" n_instances="1" exp_tot_instances="0.75" is_contributing_evidence="Y" calc_neutral_pep_mass="2226.1798"> </peptide> </protein> </protein_group> <protein_group group_number="322" pseudo_name="29" probability="1.0000"> <protein protein_name="lcl|scaffold10_frame_6_orf_3129" n_indistinguishable_proteins="1" probability="1.0000" percent_coverage="30.9" unique_stripped_peptides="ALLDDLPK+DREGLDAAAVVDR+EIQQYLAQFSSVSSPQFAVIK+ELFTDTGAGTLIR+LFLHENLK+LLEDAGVEPEYEEGIR+MFGDINLESQLK+NAVLGVLNQISSK+QLYDMGLYPVIVHGGGPQLNK+SSSVAIIHPDHLQR+VGGAILTDYLDSLVEALK+YATEENNQR" group_sibling_id="b" total_number_peptides="16" pct_spectrum_ids="0.095" confidence="1.000"> <parameter name="prot_length" value="538"/> <annotation protein_description="346373 347986"/> <peptide peptide_sequence="EIQQYLAQFSSVSSPQFAVIK" charge="1" initial_probability="0.9990" nsp_adjusted_probability="0.9998" peptide_group_designator="a" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="10.66" n_sibling_peptides_bin="6" n_instances="2" exp_tot_instances="1.98" is_contributing_evidence="Y" calc_neutral_pep_mass="2369.2267"> </peptide> <peptide peptide_sequence="DREGLDAAAVVDR" charge="2" initial_probability="0.9990" nsp_adjusted_probability="0.9998" peptide_group_designator="d" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.16" n_sibling_peptides_bin="6" n_instances="1" exp_tot_instances="1.00" is_contributing_evidence="N" calc_neutral_pep_mass="1385.6910"> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t1"/> <peptide_parent_protein 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<peptide peptide_sequence="VGGAILTDYLDSLVEALK" charge="2" initial_probability="0.9990" nsp_adjusted_probability="0.9998" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.16" n_sibling_peptides_bin="6" n_instances="2" exp_tot_instances="1.77" is_contributing_evidence="Y" calc_neutral_pep_mass="1876.0272"> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t3"/> </peptide> <peptide peptide_sequence="LLEDAGVEPEYEEGIR" charge="2" initial_probability="0.9987" nsp_adjusted_probability="0.9997" peptide_group_designator="b" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.16" n_sibling_peptides_bin="6" n_instances="7" exp_tot_instances="6.96" is_contributing_evidence="N" calc_neutral_pep_mass="1817.8695"> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t1"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t3"/> </peptide> <peptide peptide_sequence="QLYDMGLYPVIVHGGGPQLNK" charge="2" initial_probability="0.9981" nsp_adjusted_probability="0.9996" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.16" n_sibling_peptides_bin="6" n_instances="1" exp_tot_instances="1.00" is_contributing_evidence="Y" calc_neutral_pep_mass="2281.1565"> <modification_info modified_peptide="Q[111]LYDMGLYPVIVHGGGPQLNK"> <mod_aminoacid_mass position="1" mass="111.032100"/> </modification_info> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t3"/> </peptide> <peptide peptide_sequence="QLYDMGLYPVIVHGGGPQLNK" charge="2" initial_probability="0.9972" nsp_adjusted_probability="0.9994" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.16" n_sibling_peptides_bin="6" n_instances="1" exp_tot_instances="1.00" is_contributing_evidence="Y" calc_neutral_pep_mass="2297.1514"> <modification_info modified_peptide="Q[111]LYDM[147]GLYPVIVHGGGPQLNK"> <mod_aminoacid_mass position="1" mass="111.032100"/> <mod_aminoacid_mass position="5" mass="147.035400"/> </modification_info> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t3"/> </peptide> <peptide peptide_sequence="ALLDDLPK" charge="2" initial_probability="0.9953" nsp_adjusted_probability="0.9990" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.16" n_sibling_peptides_bin="6" n_instances="2" exp_tot_instances="1.71" is_contributing_evidence="N" calc_neutral_pep_mass="883.5025"> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t1"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t3"/> </peptide> <peptide peptide_sequence="LLEDAGVEPEYEEGIR" charge="1" initial_probability="0.9870" nsp_adjusted_probability="0.9973" peptide_group_designator="b" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.16" n_sibling_peptides_bin="6" n_instances="2" exp_tot_instances="1.97" is_contributing_evidence="N" calc_neutral_pep_mass="1817.8683"> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t1"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t3"/> </peptide> <peptide peptide_sequence="ELFTDTGAGTLIR" charge="1" initial_probability="0.9692" nsp_adjusted_probability="0.9934" peptide_group_designator="c" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.17" n_sibling_peptides_bin="6" n_instances="2" exp_tot_instances="1.16" is_contributing_evidence="N" calc_neutral_pep_mass="1392.7249"> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t1"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t3"/> </peptide> <peptide peptide_sequence="EIQQYLAQFSSVSSPQFAVIK" charge="3" initial_probability="0.9491" nsp_adjusted_probability="0.9889" peptide_group_designator="a" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="10.71" n_sibling_peptides_bin="6" n_instances="4" exp_tot_instances="3.02" is_contributing_evidence="Y" calc_neutral_pep_mass="2369.2282"> </peptide> <peptide peptide_sequence="YATEENNQR" charge="1" initial_probability="0.9281" nsp_adjusted_probability="0.9840" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="10.73" n_sibling_peptides_bin="6" n_instances="1" exp_tot_instances="0.93" is_contributing_evidence="Y" calc_neutral_pep_mass="1123.4897"> </peptide> <peptide peptide_sequence="DREGLDAAAVVDR" charge="3" initial_probability="0.8384" nsp_adjusted_probability="0.9612" peptide_group_designator="d" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.24" n_sibling_peptides_bin="6" n_instances="1" exp_tot_instances="0.84" is_contributing_evidence="N" calc_neutral_pep_mass="1385.6977"> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t1"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t3"/> </peptide> <peptide peptide_sequence="SSSVAIIHPDHLQR" charge="3" initial_probability="0.7666" nsp_adjusted_probability="0.9401" peptide_group_designator="e" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.27" n_sibling_peptides_bin="6" n_instances="1" exp_tot_instances="0.77" is_contributing_evidence="N" calc_neutral_pep_mass="1558.8233"> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t1"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t3"/> </peptide> <peptide peptide_sequence="LFLHENLK" charge="2" initial_probability="0.6685" nsp_adjusted_probability="0.9060" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.32" n_sibling_peptides_bin="6" n_instances="1" exp_tot_instances="0.67" is_contributing_evidence="N" calc_neutral_pep_mass="1012.5716"> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t1"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t3"/> </peptide> <peptide peptide_sequence="MFGDINLESQLK" charge="2" initial_probability="0.3764" nsp_adjusted_probability="0.3764" weight="0.50" group_weight="1.00" is_nondegenerate_evidence="N" n_enzymatic_termini="2" n_sibling_peptides="11.47" n_sibling_peptides_bin="6" n_instances="1" exp_tot_instances="0.38" is_contributing_evidence="N" calc_neutral_pep_mass="1409.6939"> <modification_info modified_peptide="M[147]FGDINLESQLK"> <mod_aminoacid_mass position="1" mass="147.035400"/> </modification_info> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t1"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t2"/> <peptide_parent_protein protein_name="lcl|scaffold10_rev_g496.t3"/> </peptide> </protein> </protein_group> </protein_summary>