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comparison test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml @ 14:d90c8bc10a9c draft

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Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 19:55:19 -0400
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13:b793fe628648 14:d90c8bc10a9c
1 <?xml version="1.0" encoding="UTF-8"?>
2 <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="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml">
3 <protein_summary_header reference_database="/Users/icooke/Sources/protk/spec/data/AASequences.fasta" residue_substitution_list="I -> L" source_files="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph.pep.xml" source_files_alt="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph.pep.xml" min_peptide_probability="0.20" min_peptide_weight="0.50" num_predicted_correct_prots="14.1" num_input_1_spectra="0" num_input_2_spectra="34" num_input_3_spectra="0" num_input_4_spectra="0" num_input_5_spectra="0" initial_min_peptide_prob="0.05" total_no_spectrum_ids="21.1" sample_enzyme="trypsin">
4 <program_details analysis="proteinprophet" time="2014-06-24T07:06:03" version=" Insilicos_LabKey_C++ (TPP v4.7 POLAR VORTEX rev 0, Build 201405141111 (linux))">
5 <proteinprophet_details occam_flag="Y" groups_flag="Y" degen_flag="Y" nsp_flag="Y" fpkm_flag="N" initial_peptide_wt_iters="1" nsp_distribution_iters="2" final_peptide_wt_iters="0" run_options="NOPLOT">
6 <nsp_information neighboring_bin_smoothing="Y">
7 <nsp_distribution bin_no="0" nsp_lower_bound_incl="0.00" nsp_upper_bound_excl="0.10" pos_freq="0.293" neg_freq="0.305" pos_to_neg_ratio="0.96"/>
8 <nsp_distribution bin_no="1" nsp_lower_bound_incl="0.10" nsp_upper_bound_excl="0.25" pos_freq="0.108" neg_freq="0.108" pos_to_neg_ratio="0.99" alt_pos_to_neg_ratio="0.81"/>
9 <nsp_distribution bin_no="2" nsp_lower_bound_incl="0.25" nsp_upper_bound_excl="0.50" pos_freq="0.081" neg_freq="0.070" pos_to_neg_ratio="1.16" alt_pos_to_neg_ratio="0.81"/>
10 <nsp_distribution bin_no="3" nsp_lower_bound_incl="0.50" nsp_upper_bound_excl="1.00" pos_freq="0.138" neg_freq="0.118" pos_to_neg_ratio="1.17"/>
11 <nsp_distribution bin_no="4" nsp_lower_bound_incl="1.00" nsp_upper_bound_excl="2.00" pos_freq="0.184" neg_freq="0.176" pos_to_neg_ratio="1.05" alt_pos_to_neg_ratio="1.17"/>
12 <nsp_distribution bin_no="5" nsp_lower_bound_incl="2.00" nsp_upper_bound_excl="5.00" pos_freq="0.086" neg_freq="0.107" pos_to_neg_ratio="0.81" alt_pos_to_neg_ratio="1.17"/>
13 <nsp_distribution bin_no="6" nsp_lower_bound_incl="5.00" nsp_upper_bound_excl="15.00" pos_freq="0.055" neg_freq="0.061" pos_to_neg_ratio="0.90" alt_pos_to_neg_ratio="1.17"/>
14 <nsp_distribution bin_no="7" nsp_lower_bound_incl="15.00" nsp_upper_bound_excl="inf" pos_freq="0.054" neg_freq="0.054" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.17"/>
15 </nsp_information>
16 <fpkm_information neighboring_bin_smoothing="Y">
17 <fpkm_distribution bin_no="0" fpkm_lower_bound_excl="0.00" fpkm_upper_bound_incl="2.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00"/>
18 <fpkm_distribution bin_no="1" fpkm_lower_bound_excl="2.00" fpkm_upper_bound_incl="4.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/>
19 <fpkm_distribution bin_no="2" fpkm_lower_bound_excl="4.00" fpkm_upper_bound_incl="6.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/>
20 <fpkm_distribution bin_no="3" fpkm_lower_bound_excl="6.00" fpkm_upper_bound_incl="8.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/>
21 <fpkm_distribution bin_no="4" fpkm_lower_bound_excl="8.00" fpkm_upper_bound_incl="10.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/>
22 <fpkm_distribution bin_no="5" fpkm_lower_bound_excl="10.00" fpkm_upper_bound_incl="12.50" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/>
23 <fpkm_distribution bin_no="6" fpkm_lower_bound_excl="12.50" fpkm_upper_bound_incl="15.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/>
24 <fpkm_distribution bin_no="7" fpkm_lower_bound_excl="15.00" fpkm_upper_bound_incl="17.50" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/>
25 <fpkm_distribution bin_no="8" fpkm_lower_bound_excl="17.50" fpkm_upper_bound_incl="20.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/>
26 <fpkm_distribution bin_no="9" fpkm_lower_bound_excl="20.00" fpkm_upper_bound_excl="inf" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/>
27 </fpkm_information>
28 <ni_information>
29 </ni_information>
30 <protein_summary_data_filter min_probability="0.00" sensitivity="1.000" false_positive_error_rate="0.327" predicted_num_correct="14" predicted_num_incorrect="7" />
31 <protein_summary_data_filter min_probability="0.10" sensitivity="1.000" false_positive_error_rate="0.169" predicted_num_correct="14" predicted_num_incorrect="3" />
32 <protein_summary_data_filter min_probability="0.20" sensitivity="1.000" false_positive_error_rate="0.169" predicted_num_correct="14" predicted_num_incorrect="3" />
33 <protein_summary_data_filter min_probability="0.30" sensitivity="0.983" false_positive_error_rate="0.132" predicted_num_correct="14" predicted_num_incorrect="2" />
34 <protein_summary_data_filter min_probability="0.40" sensitivity="0.983" false_positive_error_rate="0.132" predicted_num_correct="14" predicted_num_incorrect="2" />
35 <protein_summary_data_filter min_probability="0.50" sensitivity="0.949" false_positive_error_rate="0.107" predicted_num_correct="13" predicted_num_incorrect="2" />
36 <protein_summary_data_filter min_probability="0.60" sensitivity="0.949" false_positive_error_rate="0.107" predicted_num_correct="13" predicted_num_incorrect="2" />
37 <protein_summary_data_filter min_probability="0.70" sensitivity="0.901" false_positive_error_rate="0.090" predicted_num_correct="13" predicted_num_incorrect="1" />
38 <protein_summary_data_filter min_probability="0.80" sensitivity="0.795" false_positive_error_rate="0.064" predicted_num_correct="11" predicted_num_incorrect="1" />
39 <protein_summary_data_filter min_probability="0.90" sensitivity="0.622" false_positive_error_rate="0.024" predicted_num_correct="9" predicted_num_incorrect="0" />
40 <protein_summary_data_filter min_probability="0.95" sensitivity="0.556" false_positive_error_rate="0.018" predicted_num_correct="8" predicted_num_incorrect="0" />
41 <protein_summary_data_filter min_probability="0.96" sensitivity="0.421" false_positive_error_rate="0.009" predicted_num_correct="6" predicted_num_incorrect="0" />
42 <protein_summary_data_filter min_probability="0.97" sensitivity="0.352" false_positive_error_rate="0.004" predicted_num_correct="5" predicted_num_incorrect="0" />
43 <protein_summary_data_filter min_probability="0.98" sensitivity="0.352" false_positive_error_rate="0.004" predicted_num_correct="5" predicted_num_incorrect="0" />
44 <protein_summary_data_filter min_probability="0.99" sensitivity="0.352" false_positive_error_rate="0.004" predicted_num_correct="5" predicted_num_incorrect="0" />
45 <protein_summary_data_filter min_probability="1.00" sensitivity="0.000" false_positive_error_rate="0.000" predicted_num_correct="0" predicted_num_incorrect="0" />
46 </proteinprophet_details>
47 </program_details>
48 </protein_summary_header>
49 <dataset_derivation generation_no="0">
50 </dataset_derivation>
51 <protein_group group_number="1" probability="0.9996">
52 <protein protein_name="sp|P22807|SLOU_DROME" n_indistinguishable_proteins="1" probability="0.9996" percent_coverage="8.3" unique_stripped_peptides="FIISANGAAVAGKQE+FKTTRYLSVCER+LVAAVAARTTQASST+SDIDDPSSETDSK" group_sibling_id="a" total_number_peptides="5" pct_spectrum_ids="17.10" confidence="0.87">
53 <parameter name="prot_length" value="659"/>
54 <annotation protein_description="Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1"/>
55 <peptide peptide_sequence="LVAAVAARTTQASST" charge="2" initial_probability="0.9740" nsp_adjusted_probability="0.9776" fpkm_adjusted_probability="0.9776" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.83" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="2" exp_tot_instances="1.30" is_contributing_evidence="Y" calc_neutral_pep_mass="1427.7737">
56 </peptide>
57 <peptide peptide_sequence="FIISANGAAVAGKQE" charge="2" initial_probability="0.8584" nsp_adjusted_probability="0.8760" fpkm_adjusted_probability="0.8760" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.95" n_sibling_peptides_bin="4" max_fpkm="-2.00" fpkm_bin="1588330504" n_instances="1" exp_tot_instances="0.86" is_contributing_evidence="Y" calc_neutral_pep_mass="1456.7677">
58 </peptide>
59 <peptide peptide_sequence="SDIDDPSSETDSK" charge="2" initial_probability="0.8343" nsp_adjusted_probability="0.8543" fpkm_adjusted_probability="0.8543" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.97" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="2" exp_tot_instances="1.31" is_contributing_evidence="Y" calc_neutral_pep_mass="1376.5577">
60 </peptide>
61 <peptide peptide_sequence="FKTTRYLSVCER" charge="2" initial_probability="0.1399" nsp_adjusted_probability="0.1399" fpkm_adjusted_probability="0.1399" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="2.67" n_sibling_peptides_bin="5" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.14" is_contributing_evidence="N" calc_neutral_pep_mass="1483.7607">
62 </peptide>
63 </protein>
64 </protein_group>
65 <protein_group group_number="2" probability="0.9990">
66 <protein protein_name="sp|Q04787|BSH_DROME" n_indistinguishable_proteins="1" probability="0.9990" percent_coverage="3.5" unique_stripped_peptides="SEPGKQPGEATSSSG" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="9.45" confidence="0.23">
67 <parameter name="prot_length" value="429"/>
68 <annotation protein_description="Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5"/>
69 <peptide peptide_sequence="SEPGKQPGEATSSSG" charge="2" initial_probability="0.9990" nsp_adjusted_probability="0.9990" fpkm_adjusted_probability="0.9990" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="2" exp_tot_instances="2.00" is_contributing_evidence="Y" calc_neutral_pep_mass="1399.6217">
70 </peptide>
71 </protein>
72 </protein_group>
73 <protein_group group_number="3" probability="0.9939">
74 <protein protein_name="sp|P28468|HOX1_HALRO" n_indistinguishable_proteins="1" probability="0.9939" percent_coverage="4.7" unique_stripped_peptides="EERTNNITTMAMK+NRAVFSLMQRR+NSGMSFDFPPK" group_sibling_id="a" total_number_peptides="3" pct_spectrum_ids="10.06" confidence="0.54">
75 <parameter name="prot_length" value="741"/>
76 <annotation protein_description="Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1"/>
77 <peptide peptide_sequence="NSGMSFDFPPK" charge="2" initial_probability="0.9488" nsp_adjusted_probability="0.9557" fpkm_adjusted_probability="0.9557" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.18" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.95" is_contributing_evidence="Y" calc_neutral_pep_mass="1207.5327">
78 </peptide>
79 <peptide peptide_sequence="EERTNNITTMAMK" charge="2" initial_probability="0.6481" nsp_adjusted_probability="0.6821" fpkm_adjusted_probability="0.6821" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.48" n_sibling_peptides_bin="4" max_fpkm="108106074808565001639284951201340339017093864540219515696523998091203710034133539363830907323547648.00" fpkm_bin="1296125268" n_instances="1" exp_tot_instances="0.65" is_contributing_evidence="Y" calc_neutral_pep_mass="1501.7017">
80 <modification_info modified_peptide="E[111]ERTNNITTMAMK">
81 <mod_aminoacid_mass position="1" mass="111.032000"/>
82 </modification_info>
83 </peptide>
84 <peptide peptide_sequence="NRAVFSLMQRR" charge="2" initial_probability="0.5301" nsp_adjusted_probability="0.5679" fpkm_adjusted_probability="0.5679" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.60" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.53" is_contributing_evidence="Y" calc_neutral_pep_mass="1374.7307">
85 <modification_info modified_peptide="NRAVFSLM[147]QRR">
86 <mod_aminoacid_mass position="8" mass="147.035400"/>
87 </modification_info>
88 </peptide>
89 </protein>
90 </protein_group>
91 <protein_group group_number="4" probability="0.9938">
92 <protein protein_name="sp|O35767|NKX25_RAT" n_indistinguishable_proteins="1" probability="0.9938" percent_coverage="10.7" unique_stripped_peptides="PDPAKDPRADK+QDQTLELLGPPP+SLAAGDLSARL" group_sibling_id="a" total_number_peptides="3" pct_spectrum_ids="8.52" confidence="0.76">
93 <parameter name="prot_length" value="318"/>
94 <annotation protein_description="Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1"/>
95 <peptide peptide_sequence="PDPAKDPRADK" charge="2" initial_probability="0.9741" nsp_adjusted_probability="0.9777" fpkm_adjusted_probability="0.9777" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.83" n_sibling_peptides_bin="3" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.97" is_contributing_evidence="Y" calc_neutral_pep_mass="1190.6047">
96 </peptide>
97 <peptide peptide_sequence="SLAAGDLSARL" charge="2" initial_probability="0.6075" nsp_adjusted_probability="0.6433" fpkm_adjusted_probability="0.6433" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.19" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.61" is_contributing_evidence="Y" calc_neutral_pep_mass="1054.5767">
98 </peptide>
99 <peptide peptide_sequence="QDQTLELLGPPP" charge="2" initial_probability="0.2197" nsp_adjusted_probability="0.2197" fpkm_adjusted_probability="0.2197" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.58" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.22" is_contributing_evidence="Y" calc_neutral_pep_mass="1271.6397">
100 <modification_info modified_peptide="Q[111]DQTLELLGPPP">
101 <mod_aminoacid_mass position="1" mass="111.032100"/>
102 </modification_info>
103 </peptide>
104 </protein>
105 </protein_group>
106 <protein_group group_number="5" probability="0.9918">
107 <protein protein_name="tr|O35455|O35455_MOUSE" n_indistinguishable_proteins="1" probability="0.9918" percent_coverage="13.1" unique_stripped_peptides="ALPTTLAMRAAAPAPAPAP+QPLPGSDVAAFLVPT" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="7.38" confidence="0.70">
108 <parameter name="prot_length" value="260"/>
109 <annotation protein_description="Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1"/>
110 <peptide peptide_sequence="ALPTTLAMRAAAPAPAPAP" charge="2" initial_probability="0.9747" nsp_adjusted_probability="0.9782" fpkm_adjusted_probability="0.9782" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.59" n_sibling_peptides_bin="3" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.97" is_contributing_evidence="Y" calc_neutral_pep_mass="1768.9657">
111 </peptide>
112 <peptide peptide_sequence="QPLPGSDVAAFLVPT" charge="2" initial_probability="0.5852" nsp_adjusted_probability="0.6217" fpkm_adjusted_probability="0.6217" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.97" n_sibling_peptides_bin="3" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.59" is_contributing_evidence="Y" calc_neutral_pep_mass="1492.7927">
113 </peptide>
114 </protein>
115 </protein_group>
116 <protein_group group_number="6" probability="0.9671">
117 <protein protein_name="tr|Q90853|Q90853_CHICK" n_indistinguishable_proteins="1" probability="0.9671" percent_coverage="4.3" unique_stripped_peptides="TSRCGPHSPLRLGASG" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="4.58" confidence="0.25">
118 <parameter name="prot_length" value="368"/>
119 <annotation protein_description="Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1"/>
120 <peptide peptide_sequence="TSRCGPHSPLRLGASG" charge="2" initial_probability="0.9683" nsp_adjusted_probability="0.9671" fpkm_adjusted_probability="0.9671" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.97" is_contributing_evidence="Y" calc_neutral_pep_mass="1576.7897">
121 </peptide>
122 </protein>
123 </protein_group>
124 <protein_group group_number="7" probability="0.9582">
125 <protein protein_name="sp|P22711|TIN_DROME" n_indistinguishable_proteins="1" probability="0.9582" percent_coverage="2.4" unique_stripped_peptides="KLNLSATQVK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="4.54" confidence="0.22">
126 <parameter name="prot_length" value="416"/>
127 <annotation protein_description="Muscle-specific homeobox protein tinman OS=Drosophila melanogaster GN=tin PE=2 SV=2"/>
128 <peptide peptide_sequence="KLNLSATQVK" charge="2" initial_probability="0.9597" nsp_adjusted_probability="0.9582" fpkm_adjusted_probability="0.9582" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.96" is_contributing_evidence="Y" calc_neutral_pep_mass="1082.6447">
129 </peptide>
130 </protein>
131 </protein_group>
132 <protein_group group_number="8" probability="0.9558">
133 <protein protein_name="sp|Q26604|SMOX5_SCHMA" n_indistinguishable_proteins="1" probability="0.9558" percent_coverage="5.3" unique_stripped_peptides="TQPPSISNILPSSLK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="4.53" confidence="0.31">
134 <parameter name="prot_length" value="284"/>
135 <annotation protein_description="Homeobox protein SMOX-5 OS=Schistosoma mansoni GN=SMOX-5 PE=2 SV=1"/>
136 <peptide peptide_sequence="TQPPSISNILPSSLK" charge="2" initial_probability="0.9574" nsp_adjusted_probability="0.9558" fpkm_adjusted_probability="0.9558" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="-2.00" fpkm_bin="1588330504" n_instances="1" exp_tot_instances="0.96" is_contributing_evidence="Y" calc_neutral_pep_mass="1562.8667">
137 </peptide>
138 </protein>
139 </protein_group>
140 <protein_group group_number="9" probability="0.9265">
141 <protein protein_name="sp|Q01702|DLX3B_DANRE" n_indistinguishable_proteins="1" probability="0.9265" percent_coverage="3.3" unique_stripped_peptides="EEPETEVRM" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="4.39" confidence="0.31">
142 <parameter name="prot_length" value="269"/>
143 <annotation protein_description="Homeobox protein Dlx3b OS=Danio rerio GN=dlx3b PE=2 SV=1"/>
144 <peptide peptide_sequence="EEPETEVRM" charge="2" initial_probability="0.9292" nsp_adjusted_probability="0.9265" fpkm_adjusted_probability="0.9265" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.93" is_contributing_evidence="Y" calc_neutral_pep_mass="1100.4807">
145 </peptide>
146 </protein>
147 </protein_group>
148 <protein_group group_number="10" probability="0.8221">
149 <protein protein_name="sp|P34663|HM23_CAEEL" n_indistinguishable_proteins="1" probability="0.8221" percent_coverage="3.9" unique_stripped_peptides="SPNLPFSATIPR" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="3.91" confidence="0.23">
150 <parameter name="prot_length" value="305"/>
151 <annotation protein_description="Homeobox protein ceh-23 OS=Caenorhabditis elegans GN=ceh-23 PE=2 SV=1"/>
152 <peptide peptide_sequence="SPNLPFSATIPR" charge="2" initial_probability="0.8278" nsp_adjusted_probability="0.8221" fpkm_adjusted_probability="0.8221" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.83" is_contributing_evidence="Y" calc_neutral_pep_mass="1280.6877">
153 </peptide>
154 </protein>
155 </protein_group>
156 <protein_group group_number="11" probability="0.8155">
157 <protein protein_name="tr|Q23819|Q23819_HYDVD" n_indistinguishable_proteins="1" probability="0.8155" percent_coverage="12.1" unique_stripped_peptides="LQLKQNNAKGSGIK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="3.88" confidence="0.45">
158 <parameter name="prot_length" value="116"/>
159 <annotation protein_description="Cnox3 protein (Fragment) OS=Hydra viridissima GN=cnox3 PE=2 SV=1"/>
160 <peptide peptide_sequence="LQLKQNNAKGSGIK" charge="2" initial_probability="0.8214" nsp_adjusted_probability="0.8155" fpkm_adjusted_probability="0.8155" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="-2.00" fpkm_bin="1588330504" n_instances="1" exp_tot_instances="0.82" is_contributing_evidence="Y" calc_neutral_pep_mass="1479.8517">
161 </peptide>
162 </protein>
163 </protein_group>
164 <protein_group group_number="12" probability="0.8110">
165 <protein protein_name="tr|Q9YHC2|Q9YHC2_CHICK" n_indistinguishable_proteins="1" probability="0.8110" percent_coverage="14.4" unique_stripped_peptides="IAQLLKKHKPGAG+KHKPGAGGLLPHPAEG" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="4.97" confidence="0.55">
166 <parameter name="prot_length" value="153"/>
167 <annotation protein_description="Homeodomain protein (Fragment) OS=Gallus gallus GN=Nkx-6.1 PE=2 SV=1"/>
168 <peptide peptide_sequence="KHKPGAGGLLPHPAEG" charge="2" initial_probability="0.7800" nsp_adjusted_probability="0.7409" fpkm_adjusted_probability="0.7409" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.27" n_sibling_peptides_bin="2" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.78" is_contributing_evidence="Y" calc_neutral_pep_mass="1546.8367">
169 </peptide>
170 <peptide peptide_sequence="IAQLLKKHKPGAG" charge="2" initial_probability="0.2705" nsp_adjusted_probability="0.2705" fpkm_adjusted_probability="0.2705" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.78" n_sibling_peptides_bin="3" max_fpkm="179430918457452872074560764997795840.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.27" is_contributing_evidence="Y" calc_neutral_pep_mass="1341.8247">
171 </peptide>
172 </protein>
173 </protein_group>
174 <protein_group group_number="13" probability="0.7912">
175 <protein protein_name="tr|Q24785|Q24785_9METZ" n_indistinguishable_proteins="1" probability="0.7912" percent_coverage="5.7" unique_stripped_peptides="TQLIALERK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="3.77" confidence="0.36">
176 <parameter name="prot_length" value="157"/>
177 <annotation protein_description="Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox3 PE=3 SV=1"/>
178 <peptide peptide_sequence="TQLIALERK" charge="2" initial_probability="0.7977" nsp_adjusted_probability="0.7912" fpkm_adjusted_probability="0.7912" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.80" is_contributing_evidence="Y" calc_neutral_pep_mass="1052.6347">
179 </peptide>
180 </protein>
181 </protein_group>
182 <protein_group group_number="14" probability="0.7078">
183 <protein protein_name="tr|Q24786|Q24786_9METZ" n_indistinguishable_proteins="1" probability="0.7078" percent_coverage="11.0" unique_stripped_peptides="AVQKYLTAHEQSK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="3.38" confidence="0.37">
184 <parameter name="prot_length" value="118"/>
185 <annotation protein_description="Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox1 PE=3 SV=1"/>
186 <peptide peptide_sequence="AVQKYLTAHEQSK" charge="2" initial_probability="0.7159" nsp_adjusted_probability="0.7078" fpkm_adjusted_probability="0.7078" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.72" is_contributing_evidence="Y" calc_neutral_pep_mass="1483.7787">
187 </peptide>
188 </protein>
189 </protein_group>
190 <protein_group group_number="15" probability="0.6690">
191 <protein protein_name="tr|O16132|O16132_HYDVU" n_indistinguishable_proteins="1" probability="0.6690" percent_coverage="4.6" unique_stripped_peptides="MNDKNITETERDFNK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="3.20" confidence="0.17">
192 <parameter name="prot_length" value="328"/>
193 <annotation protein_description="NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1"/>
194 <peptide peptide_sequence="MNDKNITETERDFNK" charge="2" initial_probability="0.6777" nsp_adjusted_probability="0.6690" fpkm_adjusted_probability="0.6690" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="-2.00" fpkm_bin="1588330504" n_instances="1" exp_tot_instances="0.68" is_contributing_evidence="Y" calc_neutral_pep_mass="1835.8467">
195 </peptide>
196 </protein>
197 </protein_group>
198 <protein_group group_number="16" probability="0.4795">
199 <protein protein_name="sp|O88181|BARH2_RAT" n_indistinguishable_proteins="2" probability="0.4795" percent_coverage="2.3" unique_stripped_peptides="RQTAVGLEL" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="2.31" confidence="0.11">
200 <parameter name="prot_length" value="384"/>
201 <annotation protein_description="BarH-like 2 homeobox protein OS=Rattus norvegicus GN=Barhl2 PE=2 SV=1"/>
202 <indistinguishable_protein protein_name="sp|Q24255|BARH1_DROME">
203 <annotation protein_description="Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2"/>
204 </indistinguishable_protein>
205 <peptide peptide_sequence="RQTAVGLEL" charge="2" initial_probability="0.4894" nsp_adjusted_probability="0.4795" fpkm_adjusted_probability="0.4795" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.49" is_contributing_evidence="Y" calc_neutral_pep_mass="967.5447">
206 </peptide>
207 </protein>
208 </protein_group>
209 <protein_group group_number="17" probability="0.2438">
210 <protein protein_name="tr|Q90263|Q90263_DANRE" n_indistinguishable_proteins="1" probability="0.2438" percent_coverage="5.2" unique_stripped_peptides="PENLLLHGPFSR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="1.87" confidence="0.10">
211 <parameter name="prot_length" value="233"/>
212 <annotation protein_description="Empty spiracles homeobox 3 OS=Danio rerio GN=emx3 PE=2 SV=1"/>
213 <peptide peptide_sequence="PENLLLHGPFSR" charge="2" initial_probability="0.2511" nsp_adjusted_probability="0.2438" fpkm_adjusted_probability="0.2438" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="2" exp_tot_instances="0.40" is_contributing_evidence="Y" calc_neutral_pep_mass="1360.7247">
214 </peptide>
215 </protein>
216 </protein_group>
217 <protein_group group_number="18" probability="0.0000">
218 <protein protein_name="sp|Q22909|HM30_CAEEL" n_indistinguishable_proteins="1" probability="0.0000" unique_stripped_peptides="RQATSGMDLLS" group_sibling_id="a" total_number_peptides="0" confidence="0.0803">
219 <parameter name="prot_length" value="237"/>
220 <annotation protein_description="Homeobox protein ceh-30 OS=Caenorhabditis elegans GN=ceh-30 PE=2 SV=2"/>
221 <peptide peptide_sequence="RQATSGMDLLS" charge="2" initial_probability="0.1644" nsp_adjusted_probability="0.1591" fpkm_adjusted_probability="0.1591" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.16" is_contributing_evidence="N" calc_neutral_pep_mass="1175.5607">
222 <modification_info modified_peptide="RQATSGM[147]DLLS">
223 <mod_aminoacid_mass position="7" mass="147.035400"/>
224 </modification_info>
225 </peptide>
226 </protein>
227 </protein_group>
228 <protein_group group_number="19" probability="0.0000">
229 <protein protein_name="tr|O77024|O77024_EPHMU" n_indistinguishable_proteins="1" probability="0.0000" unique_stripped_peptides="ETEMEMK" group_sibling_id="a" total_number_peptides="0" confidence="0.0790">
230 <parameter name="prot_length" value="166"/>
231 <annotation protein_description="EmH-3 (Fragment) OS=Ephydatia muelleri GN=EmH-3 PE=3 SV=1"/>
232 <peptide peptide_sequence="ETEMEMK" charge="2" initial_probability="0.0906" nsp_adjusted_probability="0.0874" fpkm_adjusted_probability="0.0874" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.09" is_contributing_evidence="N" calc_neutral_pep_mass="892.3307">
233 <modification_info modified_peptide="E[111]TEM[147]EM[147]K">
234 <mod_aminoacid_mass position="1" mass="111.032000"/>
235 <mod_aminoacid_mass position="4" mass="147.035400"/>
236 <mod_aminoacid_mass position="6" mass="147.035400"/>
237 </modification_info>
238 </peptide>
239 </protein>
240 </protein_group>
241 <protein_group group_number="20" probability="0.0000">
242 <protein protein_name="tr|Q23824|Q23824_HYDVD" n_indistinguishable_proteins="1" probability="0.0000" unique_stripped_peptides="SKEAEIEESVR" group_sibling_id="a" total_number_peptides="0" confidence="0.0908">
243 <parameter name="prot_length" value="128"/>
244 <annotation protein_description="Msh protein (Fragment) OS=Hydra viridissima GN=msh PE=2 SV=1"/>
245 <peptide peptide_sequence="SKEAEIEESVR" charge="2" initial_probability="0.1145" nsp_adjusted_probability="0.1105" fpkm_adjusted_probability="0.1105" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.11" is_contributing_evidence="N" calc_neutral_pep_mass="1257.6197">
246 </peptide>
247 </protein>
248 </protein_group>
249 <protein_group group_number="21" probability="0.0000">
250 <protein protein_name="tr|Q9YH59|Q9YH59_CHICK" n_indistinguishable_proteins="1" probability="0.0000" unique_stripped_peptides="FMAPSSGMNMGGMGG" group_sibling_id="a" total_number_peptides="0" confidence="0.0611">
251 <parameter name="prot_length" value="344"/>
252 <annotation protein_description="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1"/>
253 <peptide peptide_sequence="FMAPSSGMNMGGMGG" charge="2" initial_probability="0.0864" nsp_adjusted_probability="0.0833" fpkm_adjusted_probability="0.0833" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.09" is_contributing_evidence="N" calc_neutral_pep_mass="1460.5197">
254 <modification_info modified_peptide="FM[147]APSSGMNM[147]GGM[147]GG">
255 <mod_aminoacid_mass position="2" mass="147.035400"/>
256 <mod_aminoacid_mass position="10" mass="147.035400"/>
257 <mod_aminoacid_mass position="13" mass="147.035400"/>
258 </modification_info>
259 </peptide>
260 </protein>
261 </protein_group>
262 </protein_summary>