module SRFHelper File_32 = { :header => { :params_filename => "C:\\Xcalibur\\sequest\\john\\sashimi7\\sashimi7.params", :model => "LCQ Deca XP", :dta_log_filename => "C:\\Xcalibur\\sequest\\john\\sashimi7\\7MIX_STD_110802_1_dta.log", :ion_series => "ion series nABY ABCDVWXYZ: 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0", :db_filename => "C:\\Xcalibur\\database\\mixed_db_human_ecoli_7prot_unique.fasta", :modifications => "", :enzyme => "Enzyme:Trypsin(KR/P) (2)", :sequest_log_filename => "C:\\Xcalibur\\sequest\\john\\sashimi7\\7MIX_STD_110802_1_sequest.log", :version => "3.2", :raw_filename => "C:\\Xcalibur\\data\\john\\sashimi7\\7MIX_STD_110802_1.RAW" }, :dta_gen => { :min_group_count => 1, :start_time => 1.39999997615814, :start_mass => 400.0, :end_scan => 7161, :group_scan => 1, :start_scan => 1, :num_dta_files => 6952, :min_ion_threshold => 15, :end_mass => 4500.0, }, :dta_files_first => { :mh => 1221.88989257812, :dta_tic => 7703132.0, :num_peaks => 74, :charge => 1, :ms_level => 2, :total_num_possible_charge_states => 0, :peaks => 592, }, :dta_files_last => { :mh => 2604.8360326775, :dta_tic => 31977.0, :num_peaks => 17, :charge => 3, :ms_level => 2, :total_num_possible_charge_states => 0, :peaks => 136, }, :out_files_first => { :num_hits => 10, :computer => 'VELA', :date_time => '05/12/2006, 10:58 AM,', :hits => 10 }, :out_files_last => { :num_hits => 10, :computer => 'VELA', :date_time => '05/12/2006, 11:11 AM,', :hits => 10 }, :out_files_first_last_pep => { :aaseq => 'QFSLSKSSLPK', :sequence => 'K.QFSLSKSSLPK.S', :mh => 1222.4156904522, :deltacn => 1.1, :sp => 57.4083709716797, :xcorr => 0.802009999752045, :id => 19977, :rsp => 60, :ions_matched => 7, :ions_total => 20, :prots => 1, :deltamass => 0.525797874074897, :ppm => 430.315265940608, :base_name => '7MIX_STD_110802_1', :first_scan => 2, :last_scan => 2, :charge => 1 }, :out_files_last_last_pep => { :aaseq => 'EAFLVNSDLTLRAQLTEFRDHK', :sequence => 'R.EAFLVNSDLTLRAQLTEFRDHK.L', :mh => 2604.9025174522, :deltacn => 1.1, :sp => 26.1511478424072, :xcorr => 0.634012818336487, :id => 8105, :rsp => 165, :ions_matched => 6, :ions_total => 84, :prots => 1, :deltamass => 0.0664847746993473, :ppm => 25.523592988311, :base_name => '7MIX_STD_110802_1', :first_scan => 7161, :last_scan => 7161, :charge => 3, }, :params => { "add_O_Ornithine"=>"0.0000", "add_F_Phenylalanine"=>"0.0000", "add_A_Alanine"=>"0.0000", "add_C_Cysteine"=>"0.0000", "add_Y_Tyrosine"=>"0.0000", "add_X_LorI"=>"0.0000", "add_J_user_amino_acid"=>"0.0000", "add_Cterm_peptide"=>"0.0000", "add_S_Serine"=>"0.0000", "add_Nterm_protein"=>"0.0000", "add_D_Aspartic_Acid"=>"0.0000", "add_Q_Glutamine"=>"0.0000", "add_K_Lysine"=>"0.0000", "add_R_Arginine"=>"0.0000", "add_W_Tryptophan"=>"0.0000", "add_Nterm_peptide"=>"0.0000", "add_H_Histidine"=>"0.0000", "add_L_Leucine"=>"0.0000", "add_I_Isoleucine"=>"0.0000", "add_N_Asparagine"=>"0.0000", "add_B_avg_NandD"=>"0.0000", "add_Z_avg_QandE"=>"0.0000", "add_E_Glutamic_Acid"=>"0.0000", "add_G_Glycine"=>"0.0000", "add_P_Proline"=>"0.0000", "add_M_Methionine"=>"0.0000", "add_Cterm_protein"=>"0.0000", "add_V_Valine"=>"0.0000", "add_T_Threonine"=>"0.0000", "add_U_user_amino_acid"=>"0.0000", "match_peak_tolerance"=>"1.0000", "match_peak_allowed_error"=>"1", "normalize_xcorr"=>"0", "nucleotide_reading_frame"=>"0", "num_results"=>"250", "sequence_header_filter"=>"", "diff_search_options"=>"0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y", "partial_sequence"=>"", "max_num_internal_cleavage_sites"=>"2", "search_engine"=>"SEQUEST", "print_duplicate_references"=>"40", "ion_series"=>"0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0", "remove_precursor_peak"=>"0", "num_output_lines"=>"10", "second_database_name"=>"", "first_database_name"=>"C:\\Xcalibur\\database\\mixed_db_human_ecoli_7prot_unique.fasta", "peptide_mass_tolerance"=>"1.4000", "digest_mass_range"=>"600.0 3500.0", "enzyme_info"=>"Trypsin(KR/P) 1 1 KR P", "show_fragment_ions"=>"0", "protein_mass_filter"=>"0 0", "term_diff_search_options"=>"0.000000 0.000000", "num_description_lines"=>"5", "fragment_ion_tolerance"=>"1.0000", "peptide_mass_units"=>"0", "mass_type_parent"=>"0", "match_peak_count"=>"0", "max_num_differential_per_peptide"=>"1", "ion_cutoff_percentage"=>"0.0000", "mass_type_fragment"=>"0"}, } File_35 = {} File_32.each {|k,v| File_35[k] = v.dup } File_35[:header].merge!( { :sequest_log_filename => "C:\\Xcalibur\\sequest\\7MIX_STD_110802_1_sequest.log", :raw_filename => "C:\\Xcalibur\\data\\john\\sash7\\7MIX_STD_110802_1.RAW", :params_filename => "C:\\Xcalibur\\sequest\\john\\bioworks331\\sashimi7.params", :dta_log_filename => "C:\\Xcalibur\\sequest\\7MIX_STD_110802_1_dta.log", :version=>"3.5" } ) File_35[:params].merge!( { "add_O_Ornithine"=>"0.00000", "add_F_Phenylalanine"=>"0.00000", "add_A_Alanine"=>"0.00000", "add_C_Cysteine"=>"0.00000", "add_Y_Tyrosine"=>"0.00000", "add_X_LorI"=>"0.00000", "add_J_user_amino_acid"=>"0.00000", "add_Cterm_peptide"=>"0.00000", "add_S_Serine"=>"0.00000", "add_Nterm_protein"=>"0.00000", "add_D_Aspartic_Acid"=>"0.00000", "add_Q_Glutamine"=>"0.00000", "add_K_Lysine"=>"0.00000", "add_R_Arginine"=>"0.00000", "add_W_Tryptophan"=>"0.00000", "add_Nterm_peptide"=>"0.00000", "add_H_Histidine"=>"0.00000", "add_L_Leucine"=>"0.00000", "add_I_Isoleucine"=>"0.00000", "add_N_Asparagine"=>"0.00000", "add_B_avg_NandD"=>"0.00000", "add_Z_avg_QandE"=>"0.00000", "add_E_Glutamic_Acid"=>"0.00000", "add_G_Glycine"=>"0.00000", "add_P_Proline"=>"0.00000", "add_M_Methionine"=>"0.00000", "add_Cterm_protein"=>"0.00000", "add_V_Valine"=>"0.00000", "add_T_Threonine"=>"0.00000", "add_U_user_amino_acid"=>"0.00000", "match_peak_tolerance"=>"1.00000", "match_peak_allowed_error"=>"1", "normalize_xcorr"=>"0", "nucleotide_reading_frame"=>"0", "num_results"=>"250", "sequence_header_filter"=>"", "diff_search_options"=>"0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y", "partial_sequence"=>"", "max_num_internal_cleavage_sites"=>"2", "search_engine"=>"SEQUEST", "print_duplicate_references"=>"40", "ion_series"=>"0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0", "remove_precursor_peak"=>"0", "num_output_lines"=>"10", "second_database_name"=>"", "first_database_name"=>"C:\\Xcalibur\\database\\mixed_db_human_ecoli_7prot_unique.fasta", "peptide_mass_tolerance"=>"1.40000", "digest_mass_range"=>"400.0000 4500.0000", "enzyme_info"=>"Trypsin(KR/P) 1 1 KR P", "show_fragment_ions"=>"0", "protein_mass_filter"=>"0 0", "term_diff_search_options"=>"0.000000 0.000000", "num_description_lines"=>"5", "fragment_ion_tolerance"=>"1.00000", "peptide_mass_units"=>"0", "mass_type_parent"=>"0", "match_peak_count"=>"0", "max_num_differential_per_peptide"=>"1", "fragment_ion_units"=>"0", "ion_cutoff_percentage"=>"0.00000", "mass_type_fragment"=>"0"} ) File_35[:out_files_first].merge!( {:computer=>'TESLA', :date_time=>'09/17/2007, 03:11 PM,'} ) File_35[:out_files_last].merge!( {:computer=>'TESLA', :date_time=>'09/17/2007, 03:15 PM,'} ) # I'm assuming this difference is due to higher precision mass...? (not a # parsing error) File_35[:out_files_first_last_pep][:rsp] = 56 File_35[:out_files_last_last_pep][:rsp] = 125 Header = { :db_filename => "C:\\Xcalibur\\database\\mixed_db_human_ecoli_7prot_unique.fasta", :ion_series => "ion series nABY ABCDVWXYZ: 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0", :sequest_log_filename => "C:\\Xcalibur\\sequest\\john\\db_quest\\alone_new\\sash7\\7MIX_STD_110802_1_sequest.log", :raw_filename => "C:\\Xcalibur\\data\\john\\sashimi7\\7MIX_STD_110802_1.RAW", :enzyme => "Enzyme:Trypsin(KR/P) (2)", :params_filename => "C:\\Xcalibur\\sequest\\john\\db_quest\\alone_new\\sash7\\sash7.params", :modifications => "", :version => "3.2", :dta_log_filename => "C:\\Xcalibur\\sequest\\john\\db_quest\\alone_new\\sash7\\7MIX_STD_110802_1_dta.log", :model => "LCQ Deca XP", } ## DTA Gen Dta_gen = { :group_scan => 1, :start_time => 1.39999997615814, :start_scan => 1, :num_dta_files => 6952, :min_ion_threshold => 15, :end_mass => 4500.0, :min_group_count => 1, :start_mass => 400.0, :end_scan => 7161, } Dta_files_first = { :mh => 1221.88989257812, :dta_tic => 7703132.0, :num_peaks => 74, :charge => 1, :ms_level => 2, :total_num_possible_charge_states => 0, :peaks => "\346\214\271C\000p|F\340\016\335C\000D\fG\022l\335C\000\3604F\020\205\337C\000D~F\260\256\340C\000\020\347E\220\023\343C\000\220&F\020R\352C\000\244\313F\246\237\353C\000\360\032E\206\223\004D\000\204\030F\260\177\005D\000\346\220F \316\005D\000`\222F<\001\006D\000\356\217Fd\213\010D\000\336\tGr\314\vD\000\034}F\262\006\rD\000\026\221F\f\202!D\000\340\274E\302u#D\000\030\036Fl\275#D\000U\035G\254~&D\200\370\022H\364\315&D\000\346bGT\365&D\000\000\000@\300s5D\000`\307ET\2008D\000\3175G\310{:D\200\307\251G\230\311:D\000`5F\000\214\222D\000\264\213F\302\321\223D\000H\354Ed\275\230D\000-\fHv\332\230D@\313\tH\374\367\230D\000?\aG", } Dta_files_last = { :mh => 2604.8360326775, :dta_tic => 31977.0, :num_peaks => 17, :charge => 3, :ms_level => 2, :total_num_possible_charge_states => 0, :peaks => "4\n\216C\000`\305D\254\205\303C\000@;D\354\321\nD\000 \275D\232\243'D\000\020iE\350\2302D\000`\245D\f\3164D\000p@E\314JID\000\300\213D\264\002PD\000\260\016E\252\213[D\0000\eE\340NoD\000@\177D0\371xD\000@:Dd\f\205D\000\000yD\200\261\215D\000@\371D\210N\221D\000`\274D\034N\256D\000\020\032EN\372\266D\000\000\aD\356\223\322D\000\250\227E" } Out_files_first = { :num_hits => 10, :computer => "VELA", :date_time => "11/17/2006, 04:13 PM,", } Out_files_first_hit = { :mh => 1220.5128044522, :deltacn => 0.071944423019886, ## this is the modified version :sp => 96.5815887451172, :xcorr => 1.08377742767334, :id => 224, :rsp => 13, :ions_matched => 8, :ions_total => 20, :sequence => "K.LCPHLTLLPGR.F", :aaseq => "LCPHLTLLPGR", :reference => "gi|1786425|gb|AAC73335.1| damage-inducible protein P; putative tRNA synthetase", :first_scan => 2, :last_scan => 2, :base_name => '7MIX_STD_110802_1', :charge => 1, } Out_files_last = { :num_hits => 10, :computer => "VELA", :date_time => "11/17/2006, 04:25 PM," , } Out_files_last_first_hit = { :mh => 2605.9368784522, :deltacn => 0.03921128064394, :sp => 76.7447052001953, :xcorr => 0.915680646896362, :id => 13562, :rsp => 4, :ions_matched => 10, :ions_total => 84, :sequence => "K.HLEINPNHPIVETLRQKAETHK.N", :aaseq => "HLEINPNHPIVETLRQKAETHK", :reference => "gi|30149327|ref|XP_293672.2| similar to ebiP7687 [Homo sapiens]", :first_scan => 7161, :last_scan => 7161, :base_name => '7MIX_STD_110802_1', :deltamass => 2605.9368784522 - 2604.8360326775, :ppm => ((1.0e6 * (2605.9368784522 - 2604.8360326775)) / 2604.8360326775).abs, :charge => 3, } Out_files_last_last_hit = { :mh => 2604.9025174522, :deltacn => 1.1, :sp => 26.1511478424072, :xcorr => 0.634012818336487, :id => 8105, :rsp => 165, :ions_matched => 6, :ions_total => 84, :sequence => "R.EAFLVNSDLTLRAQLTEFRDHK.L", :aaseq => "EAFLVNSDLTLRAQLTEFRDHK", :reference => "gi|5453830|ref|NP_006181.1| origin recognition complex, subunit 2-like; origin", :first_scan => 7161, :last_scan => 7161, :base_name => '7MIX_STD_110802_1', :deltamass => 2604.9025174522 - 2604.8360326775, :ppm => ((1.0e6 * (2604.9025174522 - 2604.8360326775)) / 2604.8360326775).abs, :charge => 3, } Sequest_params = { "add_F_Phenylalanine"=>"0.0000", "add_O_Ornithine"=>"0.0000", "add_Y_Tyrosine"=>"0.0000", "add_C_Cysteine"=>"0.0000", "add_A_Alanine"=>"0.0000", "add_J_user_amino_acid"=>"0.0000", "add_X_LorI"=>"0.0000", "add_S_Serine"=>"0.0000", "add_Cterm_peptide"=>"0.0000", "add_Q_Glutamine"=>"0.0000", "add_D_Aspartic_Acid"=>"0.0000", "add_Nterm_protein"=>"0.0000", "add_W_Tryptophan"=>"0.0000", "add_R_Arginine"=>"0.0000", "add_K_Lysine"=>"0.0000", "add_H_Histidine"=>"0.0000", "add_Nterm_peptide"=>"0.0000", "add_E_Glutamic_Acid"=>"0.0000", "add_Z_avg_QandE"=>"0.0000", "add_B_avg_NandD"=>"0.0000", "add_N_Asparagine"=>"0.0000", "add_I_Isoleucine"=>"0.0000", "add_L_Leucine"=>"0.0000", "add_M_Methionine"=>"0.0000", "add_P_Proline"=>"0.0000", "add_G_Glycine"=>"0.0000", "add_U_user_amino_acid"=>"0.0000", "add_T_Threonine"=>"0.0000", "add_V_Valine"=>"0.0000", "add_Cterm_protein"=>"0.0000", "match_peak_tolerance"=>"1.0000", "match_peak_allowed_error"=>"1", "normalize_xcorr"=>"0", "nucleotide_reading_frame"=>"0", "num_results"=>"250", "sequence_header_filter"=>"", "diff_search_options"=>"0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y", "partial_sequence"=>"", "max_num_internal_cleavage_sites"=>"2", "search_engine"=>"SEQUEST", "print_duplicate_references"=>"40", "ion_series"=>"0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0", "remove_precursor_peak"=>"0", "num_output_lines"=>"10", "second_database_name"=>"", "first_database_name"=>"C:\\Xcalibur\\database\\mixed_db_human_ecoli_7prot_unique.fasta", "peptide_mass_tolerance"=>"1.4000", "digest_mass_range"=>"600.0 3500.0", "enzyme_info"=>"Trypsin(KR/P) 1 1 KR P", "show_fragment_ions"=>"0", "protein_mass_filter"=>"0 0", "term_diff_search_options"=>"0.000000 0.000000", "num_description_lines"=>"5", "fragment_ion_tolerance"=>"1.0000", "peptide_mass_units"=>"0", "mass_type_parent"=>"0", "match_peak_count"=>"0", "max_num_differential_per_peptide"=>"1", "ion_cutoff_percentage"=>"0.0000", "mass_type_fragment"=>"0" } end