{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,8,31]],"date-time":"2023-08-31T09:10:27Z","timestamp":1693473027454},"reference-count":19,"publisher":"Wiley","issue":"7-8","license":[{"start":{"date-parts":[[2011,7,13]],"date-time":"2011-07-13T00:00:00Z","timestamp":1310515200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"name":"NIH","award":["CA126118"],"award-info":[{"award-number":["CA126118"]}]},{"name":"ARRA","award":["3R01CA126118-04S1"],"award-info":[{"award-number":["3R01CA126118-04S1"]}]},{"name":"Advanced Proteomics Platforms and Computational Sciences Program within the Clinical Proteomics Initiative of the National Cancer Institute"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteomics Clinical Apps"],"published-print":{"date-parts":[[2011,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p><jats:bold>Purpose:<\/jats:bold> To demonstrate robust detection of biomarkers in broad\u2010mass\u2010range TOF\u2010MS data.<\/jats:p><jats:p><jats:bold>Experimental Design:<\/jats:bold> Spectra were obtained for two serum protein profiling studies: (i) 2\u2013200\u2009kDa for 132 patients, 67 healthy and 65 diagnosed as having adult T\u2010cell leukemia and (ii) 2\u2013100\u2009kDa for 140 patients, 70 pairs, each with matched prostate\u2010specific antigen (PSA) levels and biopsy\u2010confirmed diagnoses of one benign and one prostate cancer. Signal processing was performed on raw spectra and peak data were normalized using four methods. Feature selection was performed using Bayesian Network Analysis and a classifier was tested on withheld data. Identification of candidate biomarkers was pursued.<\/jats:p><jats:p><jats:bold>Results:<\/jats:bold> Integrated peak intensities were resolved over full spectra. Normalization using local noise values was superior to global methods in reducing peak correlations, reducing replicate variability and improving feature selection stability. For the leukemia data set, potential disease biomarkers were detected and were found to be predictive for withheld data. Preliminary assignments of protein IDs were consistent with published results and LC\u2010MS\/MS identification. No prostate\u2010specific\u2010antigen\u2010independent biomarkers were detected in the prostate cancer data set.<\/jats:p><jats:p><jats:bold>Conclusions and clinical relevance:<\/jats:bold> Signal processing, local signal\u2010to\u2010noise (SNR) normalization and Bayesian Network Analysis feature selection facilitate robust detection and identification of biomarker proteins in broad\u2010mass\u2010range clinical TOF\u2010MS data.<\/jats:p>","DOI":"10.1002\/prca.201000095","type":"journal-article","created":{"date-parts":[[2011,6,17]],"date-time":"2011-06-17T18:27:33Z","timestamp":1308335253000},"page":"440-447","update-policy":"http:\/\/dx.doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Improved signal processing and normalization for biomarker protein detection in broad\u2010mass\u2010range TOF mass spectra from clinical samples"],"prefix":"10.1002","volume":"5","author":[{"given":"Maureen B.","family":"Tracy","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William E.","family":"Cooke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christine L.","family":"Gatlin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lisa H.","family":"Cazares","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dennis M.","family":"Weaver","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"O. John","family":"Semmes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eugene R.","family":"Tracy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dennis M.","family":"Manos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dariya I.","family":"Malyarenko","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2011,7,13]]},"reference":[{"key":"e_1_2_7_2_2","doi-asserted-by":"publisher","DOI":"10.1373\/clinchem.2006.069252"},{"key":"e_1_2_7_3_2","first-page":"347","article-title":"Proteomics and Mass Spectrometry for Cancer Biomarker Discovery","volume":"2","author":"Lu M.","year":"2007","journal-title":"Biomark. 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