{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T04:56:10Z","timestamp":1761540970900,"version":"3.37.3"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Time-resolved hydrogen exchange (HX) followed by mass spectrometry (MS) is a key technology for studying protein structure, dynamics and interactions. HX experiments deliver a time-dependent distribution of deuteration levels of peptide sequences of the protein of interest. The robust and complete estimation of this distribution for as many peptide fragments as possible is instrumental to understanding dynamic protein-level HX behavior. Currently, this data interpretation step still is a bottleneck in the overall HX\/MS workflow.<\/jats:p><jats:p>Results: We propose HeXicon, a novel algorithmic workflow for automatic deuteration distribution estimation at increased sequence coverage. Based on an L1-regularized feature extraction routine, HeXicon extracts the full deuteration distribution, which allows insight into possible bimodal exchange behavior of proteins, rather than just an average deuteration for each time point. Further, it is capable of addressing ill-posed estimation problems, yielding sparse and physically reasonable results. HeXicon makes use of existing peptide sequence information, which is augmented by an inferred list of peptide candidates derived from a known protein sequence. In conjunction with a supervised classification procedure that balances sensitivity and specificity, HeXicon can deliver results with increased sequence coverage.<\/jats:p><jats:p>Availability: The entire HeXicon workflow has been implemented in C++ and includes a graphical user interface. It is available at http:\/\/hci.iwr.uni-heidelberg.de\/software.php.<\/jats:p><jats:p>Contact: \u00a0fred.hamprecht@iwr.uni-heidelberg.de<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq165","type":"journal-article","created":{"date-parts":[[2010,5,4]],"date-time":"2010-05-04T00:13:31Z","timestamp":1272932011000},"page":"1535-1541","source":"Crossref","is-referenced-by-count":39,"title":["Deuteration distribution estimation with improved sequence coverage for HX\/MS experiments"],"prefix":"10.1093","volume":"26","author":[{"given":"Xinghua","family":"Lou","sequence":"first","affiliation":[{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"}]},{"given":"Marc","family":"Kirchner","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"},{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"},{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"}]},{"given":"Bernhard Y.","family":"Renard","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"},{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"}]},{"given":"Ullrich","family":"K\u00f6the","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"}]},{"given":"Sebastian","family":"Boppel","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"}]},{"given":"Christian","family":"Graf","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"}]},{"given":"Chung-Tien","family":"Lee","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"}]},{"given":"Judith A. J.","family":"Steen","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"},{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"}]},{"given":"Hanno","family":"Steen","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"},{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"}]},{"given":"Matthias P.","family":"Mayer","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"}]},{"given":"Fred A.","family":"Hamprecht","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"},{"name":"1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany, 2 Proteomics Center at Children's Hospital Boston, 3 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA, 4 Zentrum f\u00fcr Molekulare Biologie der Universit\u00e4t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany and 5 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,5,3]]},"reference":[{"key":"2023012508041492400_B1","doi-asserted-by":"crossref","first-page":"1543","DOI":"10.1016\/j.jasms.2006.07.017","article-title":"Extraction of local hydrogen exchange data from HDX CAD MS measurements by deconvolution of isotopic distributions of fragment ions","volume":"17","author":"Abzalimov","year":"2006","journal-title":"J. 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