{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:06:48Z","timestamp":1761743208189,"version":"3.37.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2826,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Automatic classification of high-resolution mass spectrometry proteomic data has increasing potential in the early diagnosis of cancer. We propose a new procedure of biomarker discovery in serum protein profiles based on: (i) discrete wavelet transformation of the spectra; (ii) selection of discriminative wavelet coefficients by a statistical test and (iii) building and evaluating a support vector machine classifier by double cross-validation with attention to the generalizability of the results. In addition to the evaluation results (total recognition rate, sensitivity and specificity), the procedure provides the biomarker patterns, i.e. the parts of spectra which discriminate cancer and control individuals. The evaluation was performed on matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) serum protein profiles of 66 colorectal cancer patients and 50 controls.<\/jats:p><jats:p>Results: Our procedure provided a high recognition rate (97.3%), sensitivity (98.4%) and specificity (95.8%). The extracted biomarker patterns mostly represent the peaks expressing mean differences between the cancer and control spectra. However, we showed that the discriminative power of a peak is not simply expressed by its mean height and cannot be derived by comparison of the mean spectra. The obtained classifiers have high generalization power as measured by the number of support vectors. This prevents overfitting and contributes to the reproducibility of the results, which is required to find biomarkers differentiating cancer patients from healthy individuals.<\/jats:p><jats:p>Availability: The data and scripts used in this study are available at http:\/\/www.math.uni-bremen.de\/~theodore\/MALDIDWT.<\/jats:p><jats:p>Contact: \u00a0theodore@math.uni-bremen.de<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn662","type":"journal-article","created":{"date-parts":[[2009,2,25]],"date-time":"2009-02-25T16:13:41Z","timestamp":1235578421000},"page":"643-649","source":"Crossref","is-referenced-by-count":58,"title":["Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation"],"prefix":"10.1093","volume":"25","author":[{"given":"Theodore","family":"Alexandrov","sequence":"first","affiliation":[{"name":"1 Center for Industrial Mathematics, University of Bremen, D-28334 Bremen, 2Bruker Daltonik GmbH, D-28359 Bremen, Germany, 3Department of Medical Statistics and Bioinformatics, Leiden University Medical Center (LUMC), 2300 RC Leiden, The Netherlands, 4Department of Parasitology and 5Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jens","family":"Decker","sequence":"additional","affiliation":[{"name":"1 Center for Industrial Mathematics, University of Bremen, D-28334 Bremen, 2Bruker Daltonik GmbH, D-28359 Bremen, Germany, 3Department of Medical Statistics and Bioinformatics, Leiden University Medical Center (LUMC), 2300 RC Leiden, The Netherlands, 4Department of Parasitology and 5Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bart","family":"Mertens","sequence":"additional","affiliation":[{"name":"1 Center for Industrial Mathematics, University of Bremen, D-28334 Bremen, 2Bruker Daltonik GmbH, D-28359 Bremen, Germany, 3Department of Medical Statistics and Bioinformatics, Leiden University Medical Center (LUMC), 2300 RC Leiden, The Netherlands, 4Department of Parasitology and 5Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andre M.","family":"Deelder","sequence":"additional","affiliation":[{"name":"1 Center for Industrial Mathematics, University of Bremen, D-28334 Bremen, 2Bruker Daltonik GmbH, D-28359 Bremen, Germany, 3Department of Medical Statistics and Bioinformatics, Leiden University Medical Center (LUMC), 2300 RC Leiden, The Netherlands, 4Department of Parasitology and 5Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rob A. 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M.","family":"Tollenaar","sequence":"additional","affiliation":[{"name":"1 Center for Industrial Mathematics, University of Bremen, D-28334 Bremen, 2Bruker Daltonik GmbH, D-28359 Bremen, Germany, 3Department of Medical Statistics and Bioinformatics, Leiden University Medical Center (LUMC), 2300 RC Leiden, The Netherlands, 4Department of Parasitology and 5Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Maass","sequence":"additional","affiliation":[{"name":"1 Center for Industrial Mathematics, University of Bremen, D-28334 Bremen, 2Bruker Daltonik GmbH, D-28359 Bremen, Germany, 3Department of Medical Statistics and Bioinformatics, Leiden University Medical Center (LUMC), 2300 RC Leiden, The Netherlands, 4Department of Parasitology and 5Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Herbert","family":"Thiele","sequence":"additional","affiliation":[{"name":"1 Center for Industrial Mathematics, University of Bremen, D-28334 Bremen, 2Bruker Daltonik GmbH, D-28359 Bremen, Germany, 3Department of Medical Statistics and Bioinformatics, Leiden University Medical Center (LUMC), 2300 RC Leiden, The Netherlands, 4Department of Parasitology and 5Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,1,6]]},"reference":[{"key":"2023013110112037900_B1","first-page":"43","article-title":"Generalization performance of support vector machines and other pattern classifiers","volume-title":"Advances in kernel methods: SV learning.","author":"Bartlett","year":"1999"},{"key":"2023013110112037900_B2","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/429496a","article-title":"Proteomics and cancer: Running before we can walk?","volume":"429","author":"Check","year":"2004","journal-title":"Nature"},{"key":"2023013110112037900_B3","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/nbt0305-291","article-title":"Serum proteomics profiling \u2013 a young technology begins to mature","volume":"23","author":"Coombes","year":"2005","journal-title":"Nat. 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