﻿<?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="Trypsin" cut="KR" no_cut="P" sense="C" />
      <digest_settings max_missed_cleavages="0" />
      <peptide_prediction use_measured_rts="true" measured_rt_window="10" 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="label R 13C(6) 15N(4)" aminoacid="R" variable="true" formula="C'6N'4-C6N4" />
          <static_modification name="label K 13C(6) 15N(2)" aminoacid="K" variable="true" formula="C'6N'2-C6N2" />
          <static_modification name="Carbamidomethyl (C)" aminoacid="C" formula="H3C2NO" unimod_id="4" short_name="CAM" />
        </static_modifications>
        <heavy_modifications>
          <static_modification name="Label:13C(6)15N(4) (C-term R)" aminoacid="R" terminus="C" label_13C="true" label_15N="true" />
          <static_modification name="Label:13C(6)15N(2) (C-term K)" aminoacid="K" terminus="C" label_13C="true" label_15N="true" />
        </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="09117109-1320-4fa0-8460-b2056daa0edc" />
    <measured_results time_normal_area="true">
      <replicate name="rpmE_13C">
        <sample_file id="rpmE_13C_f0" file_path="C:\Users\81809\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190228\1_rpmE.lcd" sample_name="1_rpmE" modified_time="2019-02-27T18:16:11">
          <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|P0A7M9|RL31_ECOLI" description="50S ribosomal protein L31 OS=Escherichia coli (strain K12) GN=rpmE PE=1 SV=1" accession="P0A7M9" gene="rpmE" species="Escherichia coli (strain K12)" preferred_name="RL31_ECOLI" websearch_status="X" auto_manage_children="false">
    <sequence>
        MKKDIHPKYE EITASCSCGN VMKIRSTVGH DLNLDVCSKC HPFFTGKQRD
        VATGGRVDRF NKRFNIPGS</sequence>
    <peptide auto_manage_children="false" sequence="STVGHDLNLDVCSK" modified_sequence="STVGHDLNLDVC[+57.021464]SK" start="25" end="39" prev_aa="R" next_aa="C" calc_neutral_pep_mass="1543.730057" num_missed_cleavages="0" avg_measured_retention_time="25.9266663">
      <implicit_modifications>
        <implicit_static_modifications>
          <implicit_modification index_aa="11" modification_name="Carbamidomethyl (C)" mass_diff="+57" />
        </implicit_static_modifications>
        <implicit_heavy_modifications>
          <implicit_modification index_aa="13" modification_name="Label:13C(6)15N(2) (C-term K)" mass_diff="+8" />
        </implicit_heavy_modifications>
      </implicit_modifications>
      <peptide_results>
        <peptide_result replicate="rpmE_13C" peak_count_ratio="1" retention_time="25.9266663" />
      </peptide_results>
      <precursor charge="3" calc_neutral_mass="1543.730057" precursor_mz="515.583962" auto_manage_children="false" collision_energy="18.239807" modified_sequence="STVGHDLNLDVC[+57.0]SK">
        <precursor_results>
          <precursor_peak replicate="rpmE_13C" peak_count_ratio="1" retention_time="25.9133339" start_time="25.7866669" end_time="26.26" fwhm="0.07517475" area="259240.766" background="32217.4941" height="47018.97" truncated="0" identified="false" user_set="TRUE" />
        </precursor_results>
        <transition fragment_type="b" fragment_ordinal="2" calc_neutral_mass="188.079707" product_charge="1" cleavage_aa="T" loss_neutral_mass="0">
          <precursor_mz>515.583962</precursor_mz>
          <product_mz>189.086983</product_mz>
          <collision_energy>18.239807</collision_energy>
          <transition_results>
            <transition_peak replicate="rpmE_13C" retention_time="25.9133339" start_time="25.7866669" end_time="26.26" area="259240.766" background="32217.4941" height="47018.97" fwhm="0.07517475" truncated="false" identified="false" rank="1" points_across="198" user_set="TRUE" />
          </transition_results>
        </transition>
      </precursor>
      <precursor charge="3" isotope_label="heavy" calc_neutral_mass="1551.744256" precursor_mz="518.255361" auto_manage_children="false" collision_energy="18.239807" modified_sequence="STVGHDLNLDVC[+57.0]SK[+8.0]">
        <precursor_results>
          <precursor_peak replicate="rpmE_13C" peak_count_ratio="1" retention_time="25.94" start_time="25.7866669" end_time="26.26" fwhm="0.04864605" area="842813" background="27920.2285" height="175580.609" truncated="0" identified="false" user_set="TRUE" />
        </precursor_results>
        <transition fragment_type="b" fragment_ordinal="2" calc_neutral_mass="188.079707" product_charge="1" cleavage_aa="T" loss_neutral_mass="0">
          <precursor_mz>518.255361</precursor_mz>
          <product_mz>189.086983</product_mz>
          <collision_energy>18.239807</collision_energy>
          <transition_results>
            <transition_peak replicate="rpmE_13C" retention_time="25.94" start_time="25.7866669" end_time="26.26" area="842813" background="27920.2285" height="175580.609" fwhm="0.04864605" truncated="false" identified="false" rank="1" points_across="197" user_set="TRUE" />
          </transition_results>
        </transition>
      </precursor>
    </peptide>
    <peptide auto_manage_children="false" sequence="CHPFFTGK" modified_sequence="C[+57.021464]HPFFTGK" start="39" end="47" prev_aa="K" next_aa="Q" calc_neutral_pep_mass="992.453822" num_missed_cleavages="0" avg_measured_retention_time="25.285">
      <implicit_modifications>
        <implicit_static_modifications>
          <implicit_modification index_aa="0" modification_name="Carbamidomethyl (C)" mass_diff="+57" />
        </implicit_static_modifications>
        <implicit_heavy_modifications>
          <implicit_modification index_aa="7" modification_name="Label:13C(6)15N(2) (C-term K)" mass_diff="+8" />
        </implicit_heavy_modifications>
      </implicit_modifications>
      <peptide_results>
        <peptide_result replicate="rpmE_13C" peak_count_ratio="1" retention_time="25.285" />
      </peptide_results>
      <precursor charge="2" calc_neutral_mass="992.453822" precursor_mz="497.234187" auto_manage_children="false" collision_energy="19.381167" modified_sequence="C[+57.0]HPFFTGK">
        <precursor_results>
          <precursor_peak replicate="rpmE_13C" peak_count_ratio="1" retention_time="25.3333321" start_time="25.17" end_time="25.3499985" fwhm="0.09269583" area="5864.71875" background="8205.612" height="1589.09375" truncated="0" identified="false" user_set="TRUE" />
        </precursor_results>
        <transition fragment_type="y" fragment_ordinal="3" calc_neutral_mass="304.17467" product_charge="1" cleavage_aa="T" loss_neutral_mass="0">
          <precursor_mz>497.234187</precursor_mz>
          <product_mz>305.181946</product_mz>
          <collision_energy>19.381167</collision_energy>
          <transition_results>
            <transition_peak replicate="rpmE_13C" retention_time="25.3333321" start_time="25.17" end_time="25.3499985" area="5864.71875" background="8205.612" height="1589.09375" fwhm="0.09269583" truncated="false" identified="false" rank="1" points_across="75" user_set="TRUE" />
          </transition_results>
        </transition>
      </precursor>
      <precursor charge="2" isotope_label="heavy" calc_neutral_mass="1000.468021" precursor_mz="501.241287" auto_manage_children="false" collision_energy="19.381167" modified_sequence="C[+57.0]HPFFTGK[+8.0]">
        <precursor_results>
          <precursor_peak replicate="rpmE_13C" peak_count_ratio="1" retention_time="25.2366657" start_time="25.17" end_time="25.3499985" fwhm="0.0345721543" area="37660.93" background="14475.5352" height="6569.367" truncated="0" identified="false" user_set="TRUE" />
        </precursor_results>
        <transition fragment_type="y" fragment_ordinal="3" calc_neutral_mass="312.188869" product_charge="1" cleavage_aa="T" loss_neutral_mass="0">
          <precursor_mz>501.241287</precursor_mz>
          <product_mz>313.196145</product_mz>
          <collision_energy>19.381167</collision_energy>
          <transition_results>
            <transition_peak replicate="rpmE_13C" retention_time="25.2366657" start_time="25.17" end_time="25.3499985" area="37660.93" background="14475.5352" height="6569.367" fwhm="0.0345721543" truncated="false" identified="false" rank="1" points_across="75" user_set="TRUE" />
          </transition_results>
        </transition>
      </precursor>
    </peptide>
  </protein>
</srm_settings>