﻿<?xml version="1.0" encoding="utf-8"?>
<srm_settings format_version="20.1" software_version="Skyline (64-bit) 20.1.0.31 (f09d9bed5)">
  <settings_summary name="デフォルト">
    <peptide_settings>
      <enzyme name="LysC" cut="K" no_cut="P" sense="C" />
      <digest_settings max_missed_cleavages="0" />
      <peptide_prediction use_measured_rts="true" measured_rt_window="2" use_spectral_library_drift_times="false" spectral_library_drift_times_peak_width_calc_type="resolving_power" spectral_library_drift_times_resolving_power="0" spectral_library_drift_times_width_at_dt_zero="0" spectral_library_drift_times_width_at_dt_max="0" />
      <peptide_filter start="0" min_length="6" max_length="25" auto_select="true">
        <peptide_exclusions>
          <exclusion name="Met" regex="[M]" />
        </peptide_exclusions>
      </peptide_filter>
      <peptide_libraries pick="library" />
      <peptide_modifications max_variable_mods="3" max_neutral_losses="1">
        <static_modifications>
          <static_modification name="Carbamidomethyl (C)" aminoacid="C" variable="true" formula="H3C2NO" />
        </static_modifications>
        <heavy_modifications />
      </peptide_modifications>
    </peptide_settings>
    <transition_settings>
      <transition_prediction precursor_mass_type="Monoisotopic" fragment_mass_type="Monoisotopic" optimize_by="None">
        <predict_collision_energy name="Shimadzu QQQ" step_size="1" step_count="5">
          <regression_ce charge="2" slope="0.04" intercept="-0.5082" />
          <regression_ce charge="3" slope="0.037" intercept="-0.8368" />
        </predict_collision_energy>
      </transition_prediction>
      <transition_filter precursor_charges="2,3" product_charges="1,2" precursor_adducts="[M-3H],[M-2H],[M-H],[M-],[M+H],[M+],[M+2H],[M+3H]" product_adducts="[M-3],[M-2],[M-],[M+],[M+2],[M+3]" fragment_types="b,y" small_molecule_fragment_types="f" fragment_range_first="ion 2" fragment_range_last="last ion" precursor_mz_window="0" auto_select="true">
        <measured_ion name="N-terminal to Proline" cut="P" sense="N" min_length="3" />
      </transition_filter>
      <transition_libraries ion_match_tolerance="0.5" min_ion_count="0" ion_count="3" pick_from="all" />
      <transition_integration />
      <transition_instrument min_mz="50" max_mz="1500" mz_match_tolerance="0.055" />
    </transition_settings>
    <data_settings document_guid="42375253-04f2-4d41-8554-9cd5b95cd766" />
    <measured_results time_normal_area="true">
      <replicate name="purified_r-protein_Lys-C_N=3_0.01">
        <sample_file id="purified_r-protein_Lys-C_N-3_0.01_f0" file_path="D:\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190301\48_lysC ribosome 0.01 3.lcd" sample_name="48_lysC ribosome 0.01 3" modified_time="2019-03-02T13:40:54">
          <instrument_info_list>
            <instrument_info>
              <model>Shimadzu instrument model</model>
              <ionsource>electrospray ionization</ionsource>
              <analyzer>quadrupole/quadrupole/quadrupole</analyzer>
              <detector>conversion dynode electron multiplier</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="purified_r-protein_Lys-C_N=3_0.1">
        <sample_file id="purified_r-protein_Lys-C_N-3_0.1_f0" file_path="D:\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190301\50_lysC ribosome 0.1 3.lcd" sample_name="50_lysC ribosome 0.1 3" modified_time="2019-03-02T15:33:59">
          <instrument_info_list>
            <instrument_info>
              <model>Shimadzu instrument model</model>
              <ionsource>electrospray ionization</ionsource>
              <analyzer>quadrupole/quadrupole/quadrupole</analyzer>
              <detector>conversion dynode electron multiplier</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="purified_r-protein_Lys-C_N=3_0.25">
        <sample_file id="purified_r-protein_Lys-C_N-3_0.25_f0" file_path="D:\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190301\52_lysC ribosome 0.25.lcd" sample_name="52_lysC ribosome 0.25" modified_time="2019-03-02T17:27:04">
          <instrument_info_list>
            <instrument_info>
              <model>Shimadzu instrument model</model>
              <ionsource>electrospray ionization</ionsource>
              <analyzer>quadrupole/quadrupole/quadrupole</analyzer>
              <detector>conversion dynode electron multiplier</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="purified_r-protein_Lys-C_N=3_0.5">
        <sample_file id="purified_r-protein_Lys-C_N-3_0.5_f0" file_path="D:\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190301\34_lysC ribosome 0.5 3.lcd" sample_name="34_lysC ribosome 0.5 3" modified_time="2019-03-02T00:29:14">
          <instrument_info_list>
            <instrument_info>
              <model>Shimadzu instrument model</model>
              <ionsource>electrospray ionization</ionsource>
              <analyzer>quadrupole/quadrupole/quadrupole</analyzer>
              <detector>conversion dynode electron multiplier</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="purified_r-protein_Lys-C_N=3_1">
        <sample_file id="purified_r-protein_Lys-C_N-3_1_f0" file_path="D:\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190301\28_lysC ribosome 1 2.lcd" sample_name="28_lysC ribosome 1 2" modified_time="2019-03-01T18:49:51">
          <instrument_info_list>
            <instrument_info>
              <model>Shimadzu instrument model</model>
              <ionsource>electrospray ionization</ionsource>
              <analyzer>quadrupole/quadrupole/quadrupole</analyzer>
              <detector>conversion dynode electron multiplier</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
    </measured_results>
  </settings_summary>
  <protein name="sp|P0ADZ0|RL23_ECOLI" description="50S ribosomal protein L23 OS=Escherichia coli (strain K12) GN=rplW PE=1 SV=1" accession="P0ADZ0" gene="rplW" species="Escherichia coli (strain K12)" preferred_name="RL23_ECOLI" websearch_status="X" auto_manage_children="false">
    <sequence>
        MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL
        FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKEG QNLDFVGGAE</sequence>
    <peptide auto_manage_children="false" sequence="VLRAPHVSEK" modified_sequence="VLRAPHVSEK" start="9" end="19" prev_aa="K" next_aa="A" calc_neutral_pep_mass="1134.650942" num_missed_cleavages="0" avg_measured_retention_time="21.2592">
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        <peptide_result replicate="purified_r-protein_Lys-C_N=3_0.1" peak_count_ratio="1" retention_time="21.22" />
        <peptide_result replicate="purified_r-protein_Lys-C_N=3_0.25" peak_count_ratio="1" retention_time="21.1808" />
        <peptide_result replicate="purified_r-protein_Lys-C_N=3_0.5" peak_count_ratio="1" retention_time="21.2396" />
        <peptide_result replicate="purified_r-protein_Lys-C_N=3_1" peak_count_ratio="1" retention_time="21.22" />
      </peptide_results>
      <precursor charge="3" calc_neutral_mass="1134.650942" precursor_mz="379.224257" auto_manage_children="false" collision_energy="13.194497" modified_sequence="VLRAPHVSEK">
        <precursor_results>
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          <precursor_peak replicate="purified_r-protein_Lys-C_N=3_0.1" peak_count_ratio="1" retention_time="21.22" start_time="21.0044" end_time="21.6512" fwhm="0.10796462" area="1898049.25" background="76519.63" height="170767" truncated="0" identified="false" user_set="TRUE" />
          <precursor_peak replicate="purified_r-protein_Lys-C_N=3_0.25" peak_count_ratio="1" retention_time="21.1808" start_time="20.9456" end_time="21.514" fwhm="0.0750393" area="4153930.75" background="97513.5" height="375550" truncated="0" identified="false" user_set="FALSE" />
          <precursor_peak replicate="purified_r-protein_Lys-C_N=3_0.5" peak_count_ratio="1" retention_time="21.2396" start_time="21.0044" end_time="21.7296" fwhm="0.135939717" area="12198087" background="57435.59" height="759468" truncated="0" identified="false" user_set="TRUE" />
          <precursor_peak replicate="purified_r-protein_Lys-C_N=3_1" peak_count_ratio="1" retention_time="21.22" start_time="21.024" end_time="21.9844" fwhm="0.102781117" area="15986798" background="94502.95" height="865886" truncated="0" identified="false" user_set="TRUE" />
        </precursor_results>
        <transition fragment_type="b" fragment_ordinal="6" calc_neutral_mass="673.402379" product_charge="2" cleavage_aa="H" loss_neutral_mass="0">
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          <product_mz>337.708465</product_mz>
          <collision_energy>13.194497</collision_energy>
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        </transition>
        <transition fragment_type="y" fragment_ordinal="9" calc_neutral_mass="1035.582528" product_charge="2" cleavage_aa="L" loss_neutral_mass="0">
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          <product_mz>518.79854</product_mz>
          <collision_energy>13.194497</collision_energy>
          <transition_results>
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        </transition>
        <transition fragment_type="y" fragment_ordinal="8" calc_neutral_mass="922.498464" product_charge="2" cleavage_aa="R" loss_neutral_mass="0">
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          <product_mz>462.256508</product_mz>
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        </transition>
      </precursor>
    </peptide>
    <peptide auto_manage_children="false" sequence="SNTIVLK" modified_sequence="SNTIVLK" start="26" end="33" prev_aa="K" next_aa="V" calc_neutral_pep_mass="773.464704" num_missed_cleavages="0" avg_measured_retention_time="24.34464">
      <peptide_results>
        <peptide_result replicate="purified_r-protein_Lys-C_N=3_0.01" peak_count_ratio="1" retention_time="24.474" />
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        <peptide_result replicate="purified_r-protein_Lys-C_N=3_1" peak_count_ratio="1" retention_time="24.278" />
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      <precursor charge="2" calc_neutral_mass="773.464704" precursor_mz="387.739628" auto_manage_children="false" collision_energy="15.001385" modified_sequence="SNTIVLK">
        <precursor_results>
          <precursor_peak replicate="purified_r-protein_Lys-C_N=3_0.01" peak_count_ratio="1" retention_time="24.474" start_time="24.2388" end_time="24.9248" fwhm="0.114534609" area="592182.8" background="0" height="29260" truncated="0" identified="false" user_set="TRUE" />
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        <transition fragment_type="b" fragment_ordinal="2" calc_neutral_mass="201.074956" product_charge="1" cleavage_aa="N" loss_neutral_mass="0">
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          <product_mz>202.082232</product_mz>
          <collision_energy>15.001385</collision_energy>
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        </transition>
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        <transition fragment_type="y" fragment_ordinal="4" calc_neutral_mass="471.34207" product_charge="1" cleavage_aa="I" loss_neutral_mass="0">
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