﻿<?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="cb56d967-b4f4-4ffc-99e4-3c5635be8b90" />
    <measured_results time_normal_area="true">
      <replicate name="purified_r-protein_Trypsin1_N=3_0.0001">
        <sample_file id="purified_r-protein_Trypsin1_N-3_0.0001_f0" file_path="C:\Users\81809\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190222\01_ribosome 0.0002.lcd" sample_name="01_ribosome 0.0002" modified_time="2019-02-22T22:12:43">
          <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_Trypsin1_N=3_0.001">
        <sample_file id="purified_r-protein_Trypsin1_N-3_0.001_f0" file_path="C:\Users\81809\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190222\03_ribosome 0.002.lcd" sample_name="03_ribosome 0.002" modified_time="2019-02-23T00:05:50">
          <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>
      <replicate name="purified_r-protein_Trypsin1_N=3_0.01">
        <sample_file id="purified_r-protein_Trypsin1_N-3_0.01_f0" file_path="C:\Users\81809\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190222\05_ribosome 0.01.lcd" sample_name="05_ribosome 0.01" modified_time="2019-02-23T01:58:57">
          <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_Trypsin1_N=3_0.025">
        <sample_file id="purified_r-protein_Trypsin1_N-3_0.025_f0" file_path="C:\Users\81809\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190222\07_ribosome 0.025.lcd" sample_name="07_ribosome 0.025" modified_time="2019-02-23T03:52:08">
          <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_Trypsin1_N=3_0.5">
        <sample_file id="purified_r-protein_Trypsin1_N-3_0.5_f0" file_path="C:\Users\81809\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190222\09_ribosome 0.5.lcd" sample_name="09_ribosome 0.5" modified_time="2019-02-23T05:45:15">
          <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_Trypsin1_N=3_0.1">
        <sample_file id="purified_r-protein_Trypsin1_N-3_0.1_f0" file_path="C:\Users\81809\Dropbox\共有：プロトコル MS 8060（law data &amp; methods)\Mori\190222\11_ribosome 0.1.lcd" sample_name="11_ribosome 0.1" modified_time="2019-02-23T07:38:21">
          <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|P0A7L0|RL1_ECOLI" description="50S ribosomal protein L1 OS=Escherichia coli (strain K12) GN=rplA PE=1 SV=2" accession="P0A7L0" gene="rplA" species="Escherichia coli (strain K12)" preferred_name="RL1_ECOLI" websearch_status="X" auto_manage_children="false">
    <sequence>
        AKLTKRMRVI REKVDATKQY DINEAIALLK ELATAKFVES VDVAVNLGID
        ARKSDQNVRG ATVLPHGTGR SVRVAVFTQG ANAEAAKAAG AELVGMEDLA
        DQIKKGEMNF DVVIASPDAM RVVGQLGQVL GPRGLMPNPK VGTVTPNVAE
        AVKNAKAGQV RYRNDKNGII HTTIGKVDFD ADKLKENLEA LLVALKKAKP
        TQAKGVYIKK VSISTTMGAG VAVDQAGLSA SVN</sequence>
    <peptide auto_manage_children="false" sequence="GATVLPHGTGR" modified_sequence="GATVLPHGTGR" start="59" end="70" prev_aa="R" next_aa="S" calc_neutral_pep_mass="1064.572691" num_missed_cleavages="0" avg_measured_retention_time="21.66905">
      <peptide_results>
        <peptide_result replicate="purified_r-protein_Trypsin1_N=3_0.0001" peak_count_ratio="1" retention_time="21.5196323" />
        <peptide_result replicate="purified_r-protein_Trypsin1_N=3_0.001" peak_count_ratio="1" retention_time="21.7152328" />
        <peptide_result replicate="purified_r-protein_Trypsin1_N=3_0.01" peak_count_ratio="1" retention_time="21.7804337" />
        <peptide_result replicate="purified_r-protein_Trypsin1_N=3_0.025" peak_count_ratio="1" retention_time="21.7152328" />
        <peptide_result replicate="purified_r-protein_Trypsin1_N=3_0.5" peak_count_ratio="1" retention_time="21.6826324" />
        <peptide_result replicate="purified_r-protein_Trypsin1_N=3_0.1" peak_count_ratio="1" retention_time="21.6011333" />
      </peptide_results>
      <precursor charge="2" calc_neutral_mass="1064.572691" precursor_mz="533.293622" auto_manage_children="false" collision_energy="20.823545" modified_sequence="GATVLPHGTGR">
        <precursor_results>
          <precursor_peak replicate="purified_r-protein_Trypsin1_N=3_0.0001" peak_count_ratio="1" retention_time="21.5196323" start_time="21.340332" end_time="21.8619328" fwhm="0.202935711" area="25545.1934" background="0" height="1200" truncated="0" identified="false" user_set="TRUE" />
          <precursor_peak replicate="purified_r-protein_Trypsin1_N=3_0.001" peak_count_ratio="1" retention_time="21.7152328" start_time="21.5522327" end_time="22.0575333" fwhm="0.174358636" area="80345.61" background="0" height="4921.687" truncated="0" identified="false" user_set="TRUE" />
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          <precursor_peak replicate="purified_r-protein_Trypsin1_N=3_0.5" peak_count_ratio="1" retention_time="21.6826324" start_time="21.4381332" end_time="22.2368336" fwhm="0.138797939" area="2945997" background="35297.3555" height="193663" truncated="0" identified="false" user_set="TRUE" />
          <precursor_peak replicate="purified_r-protein_Trypsin1_N=3_0.1" peak_count_ratio="1" retention_time="21.6011333" start_time="21.4707336" end_time="22.0738335" fwhm="0.146658286" area="6745336" background="56430.76" height="455556" truncated="0" identified="false" user_set="TRUE" />
        </precursor_results>
        <transition fragment_type="y" fragment_ordinal="6" calc_neutral_mass="623.313957" product_charge="1" cleavage_aa="P" loss_neutral_mass="0">
          <precursor_mz>533.293622</precursor_mz>
          <product_mz>624.321233</product_mz>
          <collision_energy>20.823545</collision_energy>
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        </transition>
        <transition fragment_type="b" fragment_ordinal="3" calc_neutral_mass="229.106256" product_charge="1" cleavage_aa="T" loss_neutral_mass="0">
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          <product_mz>230.113532</product_mz>
          <collision_energy>20.823545</collision_energy>
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        </transition>
        <transition fragment_type="b" fragment_ordinal="4" calc_neutral_mass="328.17467" product_charge="1" cleavage_aa="V" loss_neutral_mass="0">
          <precursor_mz>533.293622</precursor_mz>
          <product_mz>329.181946</product_mz>
          <collision_energy>20.823545</collision_energy>
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            <transition_peak replicate="purified_r-protein_Trypsin1_N=3_0.0001" retention_time="21.7315331" start_time="21.340332" end_time="21.8619328" area="5674.25146" background="0" height="600" fwhm="0.202935711" truncated="false" identified="false" rank="3" points_across="13" user_set="TRUE" />
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          </transition_results>
        </transition>
      </precursor>
    </peptide>
    <peptide auto_manage_children="false" sequence="VAVFTQGANAEAAK" modified_sequence="VAVFTQGANAEAAK" start="73" end="87" prev_aa="R" next_aa="A" calc_neutral_pep_mass="1375.709579" num_missed_cleavages="0" avg_measured_retention_time="25.178133">
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        <peptide_result replicate="purified_r-protein_Trypsin1_N=3_0.001" peak_count_ratio="1" retention_time="25.1457329" />
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        <peptide_result replicate="purified_r-protein_Trypsin1_N=3_0.1" peak_count_ratio="1" retention_time="25.0809326" />
      </peptide_results>
      <precursor charge="2" calc_neutral_mass="1375.709579" precursor_mz="688.862065" auto_manage_children="false" collision_energy="27.046283" modified_sequence="VAVFTQGANAEAAK">
        <precursor_results>
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          <product_mz>731.368243</product_mz>
          <collision_energy>27.046283</collision_energy>
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        RYILAPKGLK AGDQIQSGVD AAIKPGNTLP MRNIPVGSTV HNVEMKPGKG
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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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        MRLNTLSPAE GSKKAGKRLG RGIGSGLGKT GGRGHKGQKS RSGGGVRRGF
        EGGQMPLYRR LPKFGFTSRK AAITAEIRLS DLAKVEGGVV DLNTLKAANI
        IGIQIEFAKV ILAGEVTTPV TVRGLRVTKG ARAAIEAAGG KIEE</sequence>
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        METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV
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        MTESFAQLFE ESLKEIETRP GSIVRGVVVA IDKDVVLVDA GLKSESAIPA
        EQFKNAQGEL EIQVGDEVDV ALDAVEDGFG ETLLSREKAK RHEAWITLEK
        AYEDAETVTG VINGKVKGGF TVELNGIRAF LPGSLVDVRP VRDTLHLEGK
        ELEFKVIKLD QKRNNVVVSR RAVIESENSA ERDQLLENLQ EGMEVKGIVK
        NLTDYGAFVD LGGVDGLLHI TDMAWKRVKH PSEIVNVGDE ITVKVLKFDR
        ERTRVSLGLK QLGEDPWVAI AKRYPEGTKL TGRVTNLTDY GCFVEIEEGV
        EGLVHVSEMD WTNKNIHPSK VVNVGDVVEV MVLDIDEERR RISLGLKQCK
        ANPWQQFAET HNKGDRVEGK IKSITDFGIF IGLDGGIDGL VHLSDISWNV
        AGEEAVREYK KGDEIAAVVL QVDAERERIS LGVKQLAEDP FNNWVALNKK
        GAIVTGKVTA VDAKGATVEL ADGVEGYLRA SEASRDRVED ATLVLSVGDE
        VEAKFTGVDR KNRAISLSVR AKDEADEKDA IATVNKQEDA NFSNNAMAEA
        FKAAKGE</sequence>
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        ATVSMRDMLK AGVHFGHQTR YWNPKMKPFI FGARNKVHII NLEKTVPMFN
        EALAELNKIA SRKGKILFVG TKRAASEAVK DAALSCDQFF VNHRWLGGML
        TNWKTVRQSI KRLKDLETQS QDGTFDKLTK KEALMRTREL EKLENSLGGI
        KDMGGLPDAL FVIDADHEHI AIKEANNLGI PVFAIVDTNS DPDGVDFVIP
        GNDDAIRAVT LYLGAVAATV REGRSQDLAS QAEESFVEAE</sequence>
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        ATVSMRDMLK AGVHFGHQTR YWNPKMKPFI FGARNKVHII NLEKTVPMFN
        EALAELNKIA SRKGKILFVG TKRAASEAVK DAALSCDQFF VNHRWLGGML
        TNWKTVRQSI KRLKDLETQS QDGTFDKLTK KEALMRTREL EKLENSLGGI
        KDMGGLPDAL FVIDADHEHI AIKEANNLGI PVFAIVDTNS DPDGVDFVIP
        GNDDAIRAVT LYLGAVAATV REGRSQDLAS QAEESFVEAE</sequence>
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        VCRVRLTNGF EVTSYIGGEG HNLQEHSVIL IRGGRVKDLP GVRYHTVRGA
        LDCSGVKDRK QARSKYGVKR PKA</sequence>
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        QIDTLRDEVA KFVVEGDLRR EISMSIKRLM DLGCYRGLRH RRGLPVRGQR
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