MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation
Identifieur interne : 000143 ( Main/Exploration ); précédent : 000142; suivant : 000144MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation
Auteurs : Sven Degroeve [Belgique] ; Davy Maddelein [Belgique] ; Lennart Martens [Belgique]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2015.
Abstract
We present an MS2 peak intensity prediction server that computes MS2 charge 2+ and 3+ spectra from peptide sequences for the most common fragment ions. The server integrates the Unimod public domain post-translational modification database for modified peptides. The prediction model is an improvement of the previously published MS2PIP model for Orbitrap-LTQ CID spectra. Predicted MS2 spectra can be downloaded as a spectrum file and can be visualized in the browser for comparisons with observations. In addition, we added prediction models for HCD fragmentation (Q-Exactive Orbitrap) and show that these models compute accurate intensity predictions on par with CID performance. We also show that training prediction models for CID and HCD separately improves the accuracy for each fragmentation method. The MS2PIP prediction server is accessible from
Url:
DOI: 10.1093/nar/gkv542
PubMed: 25990723
PubMed Central: 4489309
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000050
- to stream Pmc, to step Curation: 000050
- to stream Pmc, to step Checkpoint: 000116
- to stream Ncbi, to step Merge: 000314
- to stream Ncbi, to step Curation: 000314
- to stream Ncbi, to step Checkpoint: 000314
- to stream Main, to step Merge: 000143
- to stream Main, to step Curation: 000143
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">MS<sup>2</sup>PIP prediction server: compute and visualize MS<sup>2</sup> peak intensity predictions for CID and HCD fragmentation</title><author><name sortKey="Degroeve, Sven" sort="Degroeve, Sven" uniqKey="Degroeve S" first="Sven" last="Degroeve">Sven Degroeve</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Maddelein, Davy" sort="Maddelein, Davy" uniqKey="Maddelein D" first="Davy" last="Maddelein">Davy Maddelein</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Martens, Lennart" sort="Martens, Lennart" uniqKey="Martens L" first="Lennart" last="Martens">Lennart Martens</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25990723</idno><idno type="pmc">4489309</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489309</idno><idno type="RBID">PMC:4489309</idno><idno type="doi">10.1093/nar/gkv542</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000050</idno><idno type="wicri:Area/Pmc/Curation">000050</idno><idno type="wicri:Area/Pmc/Checkpoint">000116</idno><idno type="wicri:Area/Ncbi/Merge">000314</idno><idno type="wicri:Area/Ncbi/Curation">000314</idno><idno type="wicri:Area/Ncbi/Checkpoint">000314</idno><idno type="wicri:Area/Main/Merge">000143</idno><idno type="wicri:Area/Main/Curation">000143</idno><idno type="wicri:Area/Main/Exploration">000143</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">MS<sup>2</sup>PIP prediction server: compute and visualize MS<sup>2</sup> peak intensity predictions for CID and HCD fragmentation</title><author><name sortKey="Degroeve, Sven" sort="Degroeve, Sven" uniqKey="Degroeve S" first="Sven" last="Degroeve">Sven Degroeve</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Maddelein, Davy" sort="Maddelein, Davy" uniqKey="Maddelein D" first="Davy" last="Maddelein">Davy Maddelein</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Martens, Lennart" sort="Martens, Lennart" uniqKey="Martens L" first="Lennart" last="Martens">Lennart Martens</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent</wicri:regionArea><wicri:noRegion>B-9000 Ghent</wicri:noRegion></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>We present an MS<sup>2</sup> peak intensity prediction server that computes MS<sup>2</sup> charge 2+ and 3+ spectra from peptide sequences for the most common fragment ions. The server integrates the Unimod public domain post-translational modification database for modified peptides. The prediction model is an improvement of the previously published MS<sup>2</sup>PIP model for Orbitrap-LTQ CID spectra. Predicted MS<sup>2</sup> spectra can be downloaded as a spectrum file and can be visualized in the browser for comparisons with observations. In addition, we added prediction models for HCD fragmentation (Q-Exactive Orbitrap) and show that these models compute accurate intensity predictions on par with CID performance. We also show that training prediction models for CID and HCD separately improves the accuracy for each fragmentation method. The MS<sup>2</sup>PIP prediction server is accessible from <ext-link ext-link-type="uri" xlink:href="http://iomics.ugent.be/ms2pip">http://iomics.ugent.be/ms2pip</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Wells, J M" uniqKey="Wells J">J.M. Wells</name></author><author><name sortKey="Mcluckey, S A" uniqKey="Mcluckey S">S.A. McLuckey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Olsen, J V" uniqKey="Olsen J">J.V. Olsen</name></author><author><name sortKey="Macek, B" uniqKey="Macek B">B. Macek</name></author><author><name sortKey="Lange, O" uniqKey="Lange O">O. Lange</name></author><author><name sortKey="Makarov, A" uniqKey="Makarov A">A. Makarov</name></author><author><name sortKey="Horning, S" uniqKey="Horning S">S. Horning</name></author><author><name sortKey="Mann, M" uniqKey="Mann M">M. Mann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Degroeve, S" uniqKey="Degroeve S">S. Degroeve</name></author><author><name sortKey="Martens, L" uniqKey="Martens L">L. Martens</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yates, J R Rd" uniqKey="Yates J">J.R. 3rd Yates</name></author><author><name sortKey="Morgan, S F" uniqKey="Morgan S">S.F. Morgan</name></author><author><name sortKey="Gatlin, C L" uniqKey="Gatlin C">C.L. Gatlin</name></author><author><name sortKey="Griffin, P R" uniqKey="Griffin P">P.R. Griffin</name></author><author><name sortKey="Eng, J K" uniqKey="Eng J">J.K. Eng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Hoffmann, E" uniqKey="De Hoffmann E">E. De Hoffmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Helsens, K" uniqKey="Helsens K">K. Helsens</name></author><author><name sortKey="Colaert, N" uniqKey="Colaert N">N. Colaert</name></author><author><name sortKey="Barsnes, H" uniqKey="Barsnes H">H. Barsnes</name></author><author><name sortKey="Muth, T" uniqKey="Muth T">T. Muth</name></author><author><name sortKey="Flikka, K" uniqKey="Flikka K">K. Flikka</name></author><author><name sortKey="Staes, A" uniqKey="Staes A">A. Staes</name></author><author><name sortKey="Timmerman, E" uniqKey="Timmerman E">E. Timmerman</name></author><author><name sortKey="Wortelkamp, S" uniqKey="Wortelkamp S">S. Wortelkamp</name></author><author><name sortKey="Sickmann, A" uniqKey="Sickmann A">A. Sickmann</name></author><author><name sortKey="Vandekerckhove, J" uniqKey="Vandekerckhove J">J. Vandekerckhove</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marx, H" uniqKey="Marx H">H. Marx</name></author><author><name sortKey="Lemeer, S" uniqKey="Lemeer S">S. Lemeer</name></author><author><name sortKey="Schliep, J E" uniqKey="Schliep J">J.E. Schliep</name></author><author><name sortKey="Matheron, L" uniqKey="Matheron L">L. Matheron</name></author><author><name sortKey="Mohammed, S" uniqKey="Mohammed S">S. Mohammed</name></author><author><name sortKey="Cox, J" uniqKey="Cox J">J. Cox</name></author><author><name sortKey="Mann, M" uniqKey="Mann M">M. Mann</name></author><author><name sortKey="Heck, A J R" uniqKey="Heck A">A.J.R. Heck</name></author><author><name sortKey="Kuster, B" uniqKey="Kuster B">B. Kuster</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mallick, P" uniqKey="Mallick P">P. Mallick</name></author><author><name sortKey="Schirle, M" uniqKey="Schirle M">M. Schirle</name></author><author><name sortKey="Chen, S S" uniqKey="Chen S">S.S. Chen</name></author><author><name sortKey="Flory, M R" uniqKey="Flory M">M.R. Flory</name></author><author><name sortKey="Lee, H" uniqKey="Lee H">H. Lee</name></author><author><name sortKey="Martin, D" uniqKey="Martin D">D. Martin</name></author><author><name sortKey="Ranish, J" uniqKey="Ranish J">J. Ranish</name></author><author><name sortKey="Raught, B" uniqKey="Raught B">B. Raught</name></author><author><name sortKey="Schmitt, R" uniqKey="Schmitt R">R. Schmitt</name></author><author><name sortKey="Werner, T" uniqKey="Werner T">T. Werner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Perkins, D N" uniqKey="Perkins D">D.N. Perkins</name></author><author><name sortKey="Pappin, D J" uniqKey="Pappin D">D.J. Pappin</name></author><author><name sortKey="Creasy, D M" uniqKey="Creasy D">D.M. Creasy</name></author><author><name sortKey="Cottrell, J S" uniqKey="Cottrell J">J.S. Cottrell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Michalski, A" uniqKey="Michalski A">A. Michalski</name></author><author><name sortKey="Neuhauser, N" uniqKey="Neuhauser N">N. Neuhauser</name></author><author><name sortKey="Cox, J" uniqKey="Cox J">J. Cox</name></author><author><name sortKey="Mann, M" uniqKey="Mann M">M. Mann</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Belgique</li></country></list><tree><country name="Belgique"><noRegion><name sortKey="Degroeve, Sven" sort="Degroeve, Sven" uniqKey="Degroeve S" first="Sven" last="Degroeve">Sven Degroeve</name></noRegion><name sortKey="Degroeve, Sven" sort="Degroeve, Sven" uniqKey="Degroeve S" first="Sven" last="Degroeve">Sven Degroeve</name><name sortKey="Maddelein, Davy" sort="Maddelein, Davy" uniqKey="Maddelein D" first="Davy" last="Maddelein">Davy Maddelein</name><name sortKey="Maddelein, Davy" sort="Maddelein, Davy" uniqKey="Maddelein D" first="Davy" last="Maddelein">Davy Maddelein</name><name sortKey="Martens, Lennart" sort="Martens, Lennart" uniqKey="Martens L" first="Lennart" last="Martens">Lennart Martens</name><name sortKey="Martens, Lennart" sort="Martens, Lennart" uniqKey="Martens L" first="Lennart" last="Martens">Lennart Martens</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Belgique/explor/OpenAccessBelV2/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000143 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000143 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Belgique
|area= OpenAccessBelV2
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:4489309
|texte= MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:25990723" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a OpenAccessBelV2
| This area was generated with Dilib version V0.6.25. |  |