<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<jPostDataset id="JPST000449" formatVersion="1.0">
  <Project id="JPST000449" pxid="PXD010327" doi="10.6019/PXD010327" createdDate="2018-07-05" modifiedDate="2018-11-11" mode="complete" jpostRevision="0" type="Mass spectrometry" announced="true">
    <Title>Retention Order Reversal of Phosphorylated and Unphosphorylated Peptides in Reversed-Phase LC/MS</Title>
    <Description>Protein phosphorylation is one of the most ubiquitous post-translational modifications in human, and trypsin-digested phosphorylated peptides have been analyzed by reversed phase LC/MS using C18-silica columns under the acidic conditions to profile human phosphoproteomes. Here, we reported that phosphopeptides generally retain stronger than their unphosphorylated counterparts when C18-silica columns are used with acetic acid or formic acid as an ion-pairing reagent, whereas the retention order is reversed when less hydrophobic stationary phases such as C4-silica columns are used or more acidic and hydrophobic ion-pairing reagents such as trifluoroacetic acid are used with C18-silica columns. These phenomena could be explained by smaller S-values of phosphopeptides in linear solvation strength theory, based on the reduced net charge caused by intramolecular interaction between phosphate and basic groups.</Description>
    <AnnouncementDate>2018-11-11</AnnouncementDate>
    <Note/>
  </Project>
  <presetSummary>
    <Species>
      <PresetElement id="9606" value="Homo sapiens (Human)"/>
    </Species>
    <Instrument>
      <PresetElement id="MS:1000932" value="TripleTOF 5600"/>
      <PresetElement id="MS:1001911" value="Q Exactive"/>
    </Instrument>
    <Modification>
      <PresetElement id="MOD:01060" ontologyName="S-carboxamidomethyl-L-cysteine" value="Carbamidomethyl (C)"/>
      <PresetElement id="MOD:00048" ontologyName="O4'-phospho-L-tyrosine" value="Phospho (Y)"/>
      <PresetElement id="MOD:00047" ontologyName="O-phospho-L-threonine" value="Phospho (T)"/>
      <PresetElement id="MOD:00046" ontologyName="O-phospho-L-serine" value="Phospho (S)"/>
      <PresetElement id="MOD:00719" ontologyName="L-methionine sulfoxide" value="Oxidation (M)"/>
    </Modification>
  </presetSummary>
  <Contact>
    <Name>Kosuke Ogata</Name>
    <Affiliation>Kyoto university</Affiliation>
    <PrincipalInvestigator>Yasushi Ishihama</PrincipalInvestigator>
  </Contact>
  <Relation>
    <Keywords>phosphopeptides, retention order reversal, linear solvation strength theory, reversed-phase LC, ion-pairing</Keywords>
    <PubMed>
      <PubMedId>30058604</PubMedId>
      <PubMedInfo>Ogata K, Krokhin OV, Ishihama Y Retention Order Reversal of Phosphorylated and Unphosphorylated Peptides in Reversed-Phase LC/MS. Anal Sci. 2018 Sep 10;34(9):1037-1041</PubMedInfo>
    </PubMed>
  </Relation>
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          <tissue id="BTO:0000567">HeLa cell</tissue>
          <celltype id="CL:0000066">epithelial cell</celltype>
          <disease/>
          <note/>
          <title>HeLa phospho (HAMMOC enriched)</title>
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          <variableModification id="MOD:00719" name="L-methionine sulfoxide">Oxidation (M)</variableModification>
          <title>Trypsin/P phospho</title>
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          <instrumentMode>DDA-high res.</instrumentMode>
          <purpose>Qualification</purpose>
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          <celltype id="CL:0000066">epithelial cell</celltype>
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          <note/>
          <title>HeLa phospho (HAMMOC enriched)</title>
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          <title>RP fractionation - TiO2</title>
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          <variableModification id="MOD:00719" name="L-methionine sulfoxide">Oxidation (M)</variableModification>
          <title>Trypsin/P phospho</title>
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          <instrument id="MS:1000932">TripleTOF 5600</instrument>
          <instrumentMode>DDA-high res.</instrumentMode>
          <purpose>Qualification</purpose>
          <quantificationPlatform>Precursor ion label free</quantificationPlatform>
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          <note/>
          <title>TT5600</title>
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          <title>Trypsin/P phospho</title>
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          <instrumentMode>DDA-high res.</instrumentMode>
          <purpose>Qualification</purpose>
          <quantificationPlatform>Precursor ion label free</quantificationPlatform>
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          <species id="9606">Homo sapiens (Human)</species>
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          <celltype id="CL:0000066">epithelial cell</celltype>
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          <note/>
          <title>HeLa phospho (HAMMOC enriched)</title>
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          <title>RP fractionation - TiO2</title>
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          <enzyme id="MS:1001313">Trypsin/P</enzyme>
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          <variableModification id="MOD:00719" name="L-methionine sulfoxide">Oxidation (M)</variableModification>
          <title>Trypsin/P phospho</title>
        </Enzyme_Mod>
        <MS_mode id="M0000000242">
          <instrument id="MS:1000932">TripleTOF 5600</instrument>
          <instrumentMode>DDA-high res.</instrumentMode>
          <purpose>Qualification</purpose>
          <quantificationPlatform>Precursor ion label free</quantificationPlatform>
          <plex>-</plex>
          <note/>
          <title>TT5600</title>
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          <celltype id="CL:0000066">epithelial cell</celltype>
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          <title>HeLa phospho (HAMMOC enriched)</title>
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          <instrumentMode>DDA-high res.</instrumentMode>
          <purpose>Qualification</purpose>
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          <disease/>
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          <title>HeLa phospho (HAMMOC enriched)</title>
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          <instrument id="MS:1000932">TripleTOF 5600</instrument>
          <instrumentMode>DDA-high res.</instrumentMode>
          <purpose>Qualification</purpose>
          <quantificationPlatform>Precursor ion label free</quantificationPlatform>
          <plex>-</plex>
          <note/>
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          <disease/>
          <note/>
          <title>HeLa phospho (HAMMOC enriched)</title>
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          <note/>
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          <title>RP fractionation - TiO2</title>
        </Fractionation>
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          <enzyme id="MS:1001313">Trypsin/P</enzyme>
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          <taxonomy id="9606">Homo sapiens (Human)</taxonomy>
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          <quantificationPlatform>Precursor ion label free</quantificationPlatform>
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          <note/>
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          <quantificationPlatform>Precursor ion label free</quantificationPlatform>
          <plex>-</plex>
          <note/>
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          <plex>-</plex>
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          <quantificationPlatform>Precursor ion label free</quantificationPlatform>
          <plex>-</plex>
          <note/>
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