{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T11:37:34Z","timestamp":1781005054231,"version":"3.54.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Proteomics has particularly evolved to become of high interest for the field of biomarker discovery and drug development. Especially the combination of liquid chromatography and mass spectrometry (LC\/MS) has proven to be a powerful technique for analyzing protein mixtures. Clinically orientated proteomic studies will have to compare hundreds of LC\/MS runs at a time. In order to compare different runs, sophisticated preprocessing steps have to be performed. An important step is the retention time (rt) alignment of LC\/MS runs. Especially non-linear shifts in the rt between pairs of LC\/MS runs make this a crucial and non-trivial problem.<\/jats:p>\n               <jats:p>Results: For the purpose of demonstrating the particular importance of correcting non-linear rt shifts, we evaluate and compare different alignment algorithms. We present and analyze two versions of a new algorithm that is based on regression techniques, once assuming and estimating only linear shifts and once also allowing for the estimation of non-linear shifts. As an example for another type of alignment method we use an established alignment algorithm based on shifting vectors that we adapted to allow for correcting non-linear shifts also. In a simulation study, we show that rt alignment procedures that can estimate non-linear shifts yield clearly better alignments. This is even true under mild non-linear deviations.<\/jats:p>\n               <jats:p>Availability: R code for the regression-based alignment methods and simulated datasets are available at http:\/\/www.statistik.tu-dortmund.de\/genetik-publikationen-alignment.html<\/jats:p>\n               <jats:p>Contact: \u00a0katharina.podwojski@tu-dortmund.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp052","type":"journal-article","created":{"date-parts":[[2009,1,29]],"date-time":"2009-01-29T01:31:13Z","timestamp":1233192673000},"page":"758-764","source":"Crossref","is-referenced-by-count":83,"title":["Retention time alignment algorithms for LC\/MS data must consider non-linear shifts"],"prefix":"10.1093","volume":"25","author":[{"given":"Katharina","family":"Podwojski","sequence":"first","affiliation":[{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"},{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arno","family":"Fritsch","sequence":"additional","affiliation":[{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel C.","family":"Chamrad","sequence":"additional","affiliation":[{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wolfgang","family":"Paul","sequence":"additional","affiliation":[{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"},{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara","family":"Sitek","sequence":"additional","affiliation":[{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"},{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"St\u00fchler","sequence":"additional","affiliation":[{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"},{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petra","family":"Mutzel","sequence":"additional","affiliation":[{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Stephan","sequence":"additional","affiliation":[{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helmut E.","family":"Meyer","sequence":"additional","affiliation":[{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wolfgang","family":"Urfer","sequence":"additional","affiliation":[{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katja","family":"Ickstadt","sequence":"additional","affiliation":[{"name":"1 Fakult\u00e4t Statistik, Technische Universit\u00e4t Dortmund, 44221 Dortmund, 2Zentrum f\u00fcr Angewandte Proteomik, Dortmund, 3Protagen AG, Otto-Hahn-Str. 15, 44227 Dortmund, 4Fakult\u00e4t f\u00fcr Informatik, Technische Universit\u00e4t Dortmund, 44221 Dortmund and 5Medizinisches Proteom-Center (MPC), Ruhr-Universit\u00e4t Bochum, 44801 Bochum, 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