﻿<?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="Carbamidomethyl (C)" aminoacid="C" formula="H3C2NO" unimod_id="4" short_name="CAM" />
        </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="y,b" 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="5d433edd-4c96-4a4e-8ca8-8b60df82f9e5" />
    <measured_results time_normal_area="true">
      <replicate name="purified_r-protein_Trypsin2_N=1_0.01">
        <sample_file id="purified_r-protein_Trypsin2_N-1_0.01_f0" file_path="D:\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190302\4_ribosome 0.01 1.lcd" sample_name="4_ribosome 0.01 1" modified_time="2019-03-03T04:49:10">
          <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_Trypsin2_N=1_0.1">
        <sample_file id="purified_r-protein_Trypsin2_N-1_0.1_f0" file_path="D:\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190302\5_ribosome 0.1 1.lcd" sample_name="5_ribosome 0.1 1" modified_time="2019-03-03T06:42:15">
          <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_Trypsin2_N=1_0.25">
        <sample_file id="purified_r-protein_Trypsin2_N-1_0.25_f0" file_path="D:\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190302\6_ribosome 0.25 1.lcd" sample_name="6_ribosome 0.25 1" modified_time="2019-03-03T08:35:20">
          <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_Trypsin2_N=1_0.5">
        <sample_file id="purified_r-protein_Trypsin2_N-1_0.5_f0" file_path="D:\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190302\9_ribosome 0.5 1.lcd" sample_name="9_ribosome 0.5 1" modified_time="2019-03-03T10:28:29">
          <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_Trypsin2_N=1_1">
        <sample_file id="purified_r-protein_Trypsin2_N-1_1_f0" file_path="D:\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190302\1_ribosome 1.lcd" sample_name="1_ribosome 1" modified_time="2019-03-02T23:09:50">
          <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|P60422|RL2_ECOLI" description="50S ribosomal protein L2 OS=Escherichia coli (strain K12) GN=rplB PE=1 SV=2" accession="P60422" gene="rplB" species="Escherichia coli (strain K12)" preferred_name="RL2_ECOLI" websearch_status="X" auto_manage_children="false">
    <sequence>
        AVVKCKPTSP GRRHVVKVVN PELHKGKPFA PLLEKNSKSG GRNNNGRITT
        RHIGGGHKQA YRIVDFKRNK DGIPAVVERL EYDPNRSANI ALVLYKDGER
        RYILAPKGLK AGDQIQSGVD AAIKPGNTLP MRNIPVGSTV HNVEMKPGKG
        GQLARSAGTY VQIVARDGAY VTLRLRSGEM RKVEADCRAT LGEVGNAEHM
        LRVLGKAGAA RWRGVRPTVR GTAMNPVDHP HGGGEGRNFG KHPVTPWGVQ
        TKGKKTRSNK RTDKFIVRRR SK</sequence>
    <peptide auto_manage_children="false" sequence="GKPFAPLLEK" modified_sequence="GKPFAPLLEK" start="25" end="35" prev_aa="K" next_aa="N" calc_neutral_pep_mass="1098.643731" num_missed_cleavages="0" avg_measured_retention_time="28.4135742">
      <peptide_results>
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        <peptide_result replicate="purified_r-protein_Trypsin2_N=1_0.1" peak_count_ratio="1" retention_time="28.5192" />
        <peptide_result replicate="purified_r-protein_Trypsin2_N=1_0.25" peak_count_ratio="1" retention_time="28.4570675" />
        <peptide_result replicate="purified_r-protein_Trypsin2_N=1_0.5" peak_count_ratio="1" retention_time="28.3949337" />
        <peptide_result replicate="purified_r-protein_Trypsin2_N=1_1" peak_count_ratio="1" retention_time="28.1464" />
      </peptide_results>
      <precursor charge="2" calc_neutral_mass="1098.643731" precursor_mz="550.329142" auto_manage_children="false" collision_energy="21.504966" modified_sequence="GKPFAPLLEK">
        <precursor_results>
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        </precursor_results>
        <transition fragment_type="b" fragment_ordinal="2" calc_neutral_mass="185.116427" product_charge="1" cleavage_aa="K" loss_neutral_mass="0">
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          <product_mz>186.123703</product_mz>
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        </transition>
        <transition fragment_type="y" fragment_ordinal="8" calc_neutral_mass="913.527304" product_charge="1" cleavage_aa="P" loss_neutral_mass="0">
          <precursor_mz>550.329142</precursor_mz>
          <product_mz>914.53458</product_mz>
          <collision_energy>21.504966</collision_energy>
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        </transition>
        <transition fragment_type="y" fragment_ordinal="6" calc_neutral_mass="669.406127" product_charge="1" cleavage_aa="A" loss_neutral_mass="0">
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          <product_mz>670.413403</product_mz>
          <collision_energy>21.504966</collision_energy>
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          </transition_results>
        </transition>
      </precursor>
    </peptide>
    <peptide auto_manage_children="false" sequence="YILAPK" modified_sequence="YILAPK" start="101" end="107" prev_aa="R" next_aa="G" calc_neutral_pep_mass="703.426862" num_missed_cleavages="0" avg_measured_retention_time="25.36944">
      <peptide_results>
        <peptide_result replicate="purified_r-protein_Trypsin2_N=1_0.01" peak_count_ratio="1" retention_time="25.506134" />
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      <precursor charge="2" calc_neutral_mass="703.426862" precursor_mz="352.720707" auto_manage_children="false" collision_energy="13.600628" modified_sequence="YILAPK">
        <precursor_results>
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        </precursor_results>
        <transition fragment_type="y" fragment_ordinal="5" calc_neutral_mass="540.363533" product_charge="1" cleavage_aa="I" loss_neutral_mass="0">
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          <product_mz>541.370809</product_mz>
          <collision_energy>13.600628</collision_energy>
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        <transition fragment_type="y" fragment_ordinal="2" calc_neutral_mass="243.158292" product_charge="1" cleavage_aa="P" loss_neutral_mass="0">
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        MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV
        TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEEF TVGQSISVEL
        FADVKKVDVT GTSKGKGFAG TVKRWNFRTQ DATHGNSLSH RVPGSIGQNQ
        TPGKVFKGKK MAGQMGNERV TVQSLDVVRV DAERNLLLVK GAVPGATGSD
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