<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of hal-01607343</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-05-03T04:43:11+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">SpecOMS: A Full Open Modification Search Method Performing All-to-All Spectra Comparisons within Minutes</title>
            <author role="aut">
              <persName>
                <forename type="first">Matthieu</forename>
                <surname>David</surname>
              </persName>
              <email type="md5">cbd2234588dfa895ef9a3414c2b2a648</email>
              <email type="domain">inra.fr</email>
              <idno type="idhal" notation="string">matthieu-david</idno>
              <idno type="idhal" notation="numeric">17624</idno>
              <idno type="halauthorid" notation="string">36491-17624</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-9405-8892</idno>
              <affiliation ref="#struct-37769"/>
            </author>
            <author role="crp">
              <persName>
                <forename type="first">Guillaume</forename>
                <surname>Fertin</surname>
              </persName>
              <email type="md5">e617d377105f08911523aec7e7a39202</email>
              <email type="domain">univ-nantes.fr</email>
              <idno type="idhal" notation="string">guillaume-fertin</idno>
              <idno type="idhal" notation="numeric">11485</idno>
              <idno type="halauthorid" notation="string">1943-11485</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-8251-2012</idno>
              <idno type="IDREF">https://www.idref.fr/095050612</idno>
              <affiliation ref="#struct-441569"/>
              <affiliation ref="#struct-473973"/>
              <affiliation ref="#struct-481374"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Hélène</forename>
                <surname>Rogniaux</surname>
              </persName>
              <email type="md5">f3b3d556000d3c502b74ff92957f49dc</email>
              <email type="domain">inrae.fr</email>
              <idno type="idhal" notation="string">helene-rogniaux</idno>
              <idno type="idhal" notation="numeric">1147005</idno>
              <idno type="halauthorid" notation="string">628503-1147005</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-6083-2034</idno>
              <idno type="IDREF">https://www.idref.fr/197194818</idno>
              <affiliation ref="#struct-37769"/>
            </author>
            <author role="crp">
              <persName>
                <forename type="first">Dominique</forename>
                <surname>Tessier</surname>
              </persName>
              <email type="md5">0e5e6190100fef244dc5b0f101761bd3</email>
              <email type="domain">inrae.fr</email>
              <idno type="idhal" notation="numeric">1220554</idno>
              <idno type="halauthorid" notation="string">415231-1220554</idno>
              <idno type="ORCID">https://orcid.org/0000-0003-1503-7693</idno>
              <affiliation ref="#struct-37769"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Archive Ouverte</forename>
                <surname>ProdInra</surname>
              </persName>
              <email type="md5">9e5ed7d56b52b3d4383123b1ffb42236</email>
              <email type="domain">inrae.fr</email>
            </editor>
            <funder>Region Pays de la Loire (France) GRIOTE program</funder>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2017-10-02 23:47:41</date>
              <date type="whenModified">2026-02-26 12:16:07</date>
              <date type="whenReleased">2017-10-02 23:47:41</date>
              <date type="whenProduced">2017</date>
              <fs>
                <f name="inra_publicVise_local" notation="string" n="SC">
                  <string>inra_publicVise_local_SC</string>
                </f>
              </fs>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="132775">
                <persName>
                  <forename>Archive Ouverte</forename>
                  <surname>ProdInra</surname>
                </persName>
                <email type="md5">9e5ed7d56b52b3d4383123b1ffb42236</email>
                <email type="domain">inrae.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-01607343</idno>
            <idno type="halUri">https://hal.science/hal-01607343</idno>
            <idno type="halBibtex">david:hal-01607343</idno>
            <idno type="halRefHtml">&lt;i&gt;Journal of Proteome Research&lt;/i&gt;, 2017, 16 (8), pp.3030-3038. &lt;a target="_blank" href="https://dx.doi.org/10.1021/acs.jproteome.7b00308"&gt;&amp;#x27E8;10.1021/acs.jproteome.7b00308&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">Journal of Proteome Research, 2017, 16 (8), pp.3030-3038. &amp;#x27E8;10.1021/acs.jproteome.7b00308&amp;#x27E9;</idno>
            <availability status="restricted"/>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="UNIV-NANTES">Université de Nantes</idno>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="EC-NANTES">Ecole Centrale de Nantes</idno>
            <idno type="stamp" n="INRA">INRA - Institut national de la recherche agronomique</idno>
            <idno type="stamp" n="UNAM">l'unam - université nantes angers le mans</idno>
            <idno type="stamp" n="LS2N">Laboratoire des Sciences du Numérique de Nantes</idno>
            <idno type="stamp" n="LS2N-COMBI" corresp="LS2N">LS2N - équipe COMBI ( Combinatoire et Bio-informatique )</idno>
            <idno type="stamp" n="AGREENIUM">Archive ouverte en agrobiosciences</idno>
            <idno type="stamp" n="INSTITUTS-TELECOM">composantes instituts telecom </idno>
            <idno type="stamp" n="INRAE">Institut National de Recherche en Agriculture, Alimentation et Environnement</idno>
            <idno type="stamp" n="NANTES-UNIVERSITE">Nantes Université</idno>
            <idno type="stamp" n="UNIV-NANTES-AV2022">Université de Nantes</idno>
            <idno type="stamp" n="NU-CENTRALE">École Centrale de Nantes</idno>
            <idno type="stamp" n="BIBS">Plateforme Bioressources : Imagerie, Biochimie &amp; Structure</idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="2">International</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">SpecOMS: A Full Open Modification Search Method Performing All-to-All Spectra Comparisons within Minutes</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Matthieu</forename>
                    <surname>David</surname>
                  </persName>
                  <email type="md5">cbd2234588dfa895ef9a3414c2b2a648</email>
                  <email type="domain">inra.fr</email>
                  <idno type="idhal" notation="string">matthieu-david</idno>
                  <idno type="idhal" notation="numeric">17624</idno>
                  <idno type="halauthorid" notation="string">36491-17624</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-9405-8892</idno>
                  <affiliation ref="#struct-37769"/>
                </author>
                <author role="crp">
                  <persName>
                    <forename type="first">Guillaume</forename>
                    <surname>Fertin</surname>
                  </persName>
                  <email type="md5">e617d377105f08911523aec7e7a39202</email>
                  <email type="domain">univ-nantes.fr</email>
                  <idno type="idhal" notation="string">guillaume-fertin</idno>
                  <idno type="idhal" notation="numeric">11485</idno>
                  <idno type="halauthorid" notation="string">1943-11485</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-8251-2012</idno>
                  <idno type="IDREF">https://www.idref.fr/095050612</idno>
                  <affiliation ref="#struct-441569"/>
                  <affiliation ref="#struct-473973"/>
                  <affiliation ref="#struct-481374"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Hélène</forename>
                    <surname>Rogniaux</surname>
                  </persName>
                  <email type="md5">f3b3d556000d3c502b74ff92957f49dc</email>
                  <email type="domain">inrae.fr</email>
                  <idno type="idhal" notation="string">helene-rogniaux</idno>
                  <idno type="idhal" notation="numeric">1147005</idno>
                  <idno type="halauthorid" notation="string">628503-1147005</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-6083-2034</idno>
                  <idno type="IDREF">https://www.idref.fr/197194818</idno>
                  <affiliation ref="#struct-37769"/>
                </author>
                <author role="crp">
                  <persName>
                    <forename type="first">Dominique</forename>
                    <surname>Tessier</surname>
                  </persName>
                  <email type="md5">0e5e6190100fef244dc5b0f101761bd3</email>
                  <email type="domain">inrae.fr</email>
                  <idno type="idhal" notation="numeric">1220554</idno>
                  <idno type="halauthorid" notation="string">415231-1220554</idno>
                  <idno type="ORCID">https://orcid.org/0000-0003-1503-7693</idno>
                  <affiliation ref="#struct-37769"/>
                </author>
              </analytic>
              <monogr>
                <idno type="localRef">ACL+</idno>
                <idno type="halJournalId" status="VALID">16093</idno>
                <idno type="issn">1535-3893</idno>
                <idno type="eissn">1535-3907</idno>
                <title level="j">Journal of Proteome Research</title>
                <imprint>
                  <publisher>American Chemical Society</publisher>
                  <biblScope unit="volume">16</biblScope>
                  <biblScope unit="issue">8</biblScope>
                  <biblScope unit="pp">3030-3038</biblScope>
                  <date type="datePub">2017</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1021/acs.jproteome.7b00308</idno>
              <idno type="prodinra">408323</idno>
              <idno type="pubmed">28660767</idno>
              <idno type="wos">000407307800032</idno>
              <ref target="https://archives-publications.inrae.fr/408323.pdf" type="seeAlso"/>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <keywords scheme="author">
                <term xml:lang="en">algorithms</term>
                <term xml:lang="en">spectra comparison</term>
                <term xml:lang="en">open modification search</term>
                <term xml:lang="en">peptide identification</term>
                <term xml:lang="en">bioinformatics</term>
                <term xml:lang="en">proteomics</term>
                <term xml:lang="en">MS/MS</term>
                <term xml:lang="en">PTM</term>
                <term xml:lang="en">pattern-matching</term>
              </keywords>
              <classCode scheme="halDomain" n="sdv">Life Sciences [q-bio]</classCode>
              <classCode scheme="halTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halOldTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halTreeTypology" n="ART">Journal articles</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>The analysis of discovery proteomics experiments relies on algorithms that identify peptides from their tandem mass spectra. The almost exhaustive interpretation of these spectra remains an unresolved issue. At present, an important number of missing interpretations is probably due to peptides displaying post-translational modifications and variants that yield spectra that are particularly difficult to interpret. However, the emergence of a new generation of mass spectrometers that provide high fragment ion accuracy has paved the way for more efficient algorithms. We present a new software, SpecOMS, that can handle the computational complexity of pairwise comparisons of spectra in the context of large volumes. SpecOMS can compare a whole set of experimental spectra generated by a discovery proteomics experiment to a whole set of theoretical spectra deduced from a protein database in a few minutes on a standard workstation. SpecOMS can ingeniously exploit those capabilities to improve the peptide identification process, allowing strong competition between all possible peptides for spectrum interpretation. Remarkably, this software resolves the drawbacks (i.e., efficiency problems and decreased sensitivity) that usually accompany open modification searches. We highlight this promising approach using results obtained from the analysis of a public human data set downloaded from the PRIDE (PRoteomics IDEntification) database.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-37769" status="OLD">
          <orgName>Unité de recherche sur les Biopolymères, Interactions Assemblages</orgName>
          <orgName type="acronym">BIA</orgName>
          <date type="end">2019-12-31</date>
          <desc>
            <address>
              <addrLine>Site de la Géraudière - BP 71627 - 44316 Nantes Cedex 3</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation name="UR1268" active="#struct-92114" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-441569" status="VALID">
          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <idno type="ROR">https://ror.org/02feahw73</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cnrs.fr/</ref>
          </desc>
        </org>
        <org type="laboratory" xml:id="struct-473973" status="OLD">
          <idno type="IdRef">203637585</idno>
          <idno type="RNSR">201722241F</idno>
          <idno type="ROR">https://ror.org/02snf8m58</idno>
          <orgName>Laboratoire des Sciences du Numérique de Nantes</orgName>
          <orgName type="acronym">LS2N</orgName>
          <date type="start">2017-01-01</date>
          <date type="end">2021-12-31</date>
          <desc>
            <address>
              <addrLine>Université de Nantes – faculté des Sciences et Techniques (FST)2 Chemin de la HoussinièreBP 92208, 44322 Nantes Cedex 3</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.ls2n.fr</ref>
          </desc>
          <listRelation>
            <relation active="#struct-97058" type="direct"/>
            <relation active="#struct-93263" type="indirect"/>
            <relation active="#struct-111023" type="direct"/>
            <relation name="UMR6004" active="#struct-441569" type="direct"/>
            <relation active="#struct-481355" type="direct"/>
            <relation active="#struct-302102" type="indirect"/>
          </listRelation>
        </org>
        <org type="researchteam" xml:id="struct-481374" status="OLD">
          <orgName>Combinatoire et Bioinformatique</orgName>
          <orgName type="acronym">LS2N - équipe COMBI</orgName>
          <date type="end">2021-12-31</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-473973" type="direct"/>
            <relation active="#struct-97058" type="indirect"/>
            <relation active="#struct-93263" type="indirect"/>
            <relation active="#struct-111023" type="indirect"/>
            <relation name="UMR6004" active="#struct-441569" type="indirect"/>
            <relation active="#struct-481355" type="indirect"/>
            <relation active="#struct-302102" type="indirect"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-92114" status="OLD">
          <idno type="ROR">https://ror.org/01x3gbx83</idno>
          <orgName>Institut National de la Recherche Agronomique</orgName>
          <orgName type="acronym">INRA</orgName>
          <date type="start">1946-05-18</date>
          <date type="end">2019-12-31</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inra.fr</ref>
          </desc>
        </org>
        <org type="regrouplaboratory" xml:id="struct-97058" status="OLD">
          <orgName>Université de Nantes - UFR des Sciences et des Techniques</orgName>
          <orgName type="acronym">UN UFR ST</orgName>
          <date type="end">2021-12-31</date>
          <desc>
            <address>
              <addrLine>2, rue de la Houssinière - BP 92208 - 44322 Nantes cedex 3</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.sciences-techniques.univ-nantes.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-93263" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-93263" status="OLD">
          <idno type="IdRef">026403447</idno>
          <idno type="ROR">https://ror.org/03gnr7b55</idno>
          <orgName>Université de Nantes</orgName>
          <orgName type="acronym">UN</orgName>
          <date type="end">2021-12-31</date>
          <desc>
            <address>
              <addrLine>1, quai de Tourville - BP 13522 - 44035 Nantes cedex 1</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-nantes.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-111023" status="OLD">
          <idno type="IdRef">03063525X</idno>
          <idno type="ISNI">0000000122039289</idno>
          <idno type="ROR">https://ror.org/03nh7d505</idno>
          <orgName>École Centrale de Nantes</orgName>
          <orgName type="acronym">ECN</orgName>
          <date type="end">2021-12-31</date>
          <desc>
            <address>
              <addrLine>1 rue de la Noë - BP 92101 - 44321 Nantes cedex 3</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.ec-nantes.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-481355" status="VALID">
          <idno type="IdRef">202743233</idno>
          <idno type="ROR">https://ror.org/030hj3061</idno>
          <orgName>IMT Atlantique</orgName>
          <orgName type="acronym">IMT Atlantique</orgName>
          <date type="start">2017-01-01</date>
          <desc>
            <address>
              <addrLine>Campus Brest : Technopôle Brest-Iroise CS 8381829238 BREST Cedex 3 -Campus Nantes : 4, rue Alfred Kastler- La chantrerie 44300 NANTES -Campus Rennes :  2 Rue de la Châtaigneraie, 35510 CESSON SEVIGNE</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.imt-atlantique.fr</ref>
          </desc>
          <listRelation>
            <relation active="#struct-302102" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-302102" status="VALID">
          <idno type="IdRef">192427156</idno>
          <idno type="ISNI">000000012202567X</idno>
          <idno type="ROR">https://ror.org/025vp2923</idno>
          <idno type="Wikidata">Q27962533</idno>
          <orgName>Institut Mines-Télécom [Paris]</orgName>
          <orgName type="acronym">IMT</orgName>
          <date type="start">2012-03-01</date>
          <desc>
            <address>
              <addrLine>19 Place Marguerite Perey, 91120 Palaiseau</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.imt.fr/</ref>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>