{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:11:27Z","timestamp":1761487887690},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Mass spectrometry (MS), such as the surface-enhanced laser desorption and ionization time-of-flight (SELDI-TOF) MS, provides a potentially promising proteomic technology for biomarker discovery. An important matter for such a technology to be used routinely is its reproducibility. It is of significant interest to develop quantitative measures to evaluate the quality and reliability of different experimental methods.<\/jats:p><jats:p>Results: We compare the quality of SELDI-TOF MS data using unfractionated, fractionated plasma samples and abundant protein depletion methods in terms of the numbers of detected peaks and reliability. Several statistical quality-control and quality-assessment techniques are proposed, including the Graeco\u2013Latin square design for the sample allocation on a Protein chip, the use of the pairwise Pearson correlation coefficient as the similarity measure between the spectra in conjunction with multi-dimensional scaling (MDS) for graphically evaluating similarity of replicates and assessing outlier samples; and the use of the reliability ratio for evaluating reproducibility. Our results show that the number of peaks detected is similar among the three sample preparation technologies, and the use of the Sigma multi-removal kit does not improve peak detection. Fractionation of plasma samples introduces more experimental variability. The peaks detected using the unfractionated plasma samples have the highest reproducibility as determined by the reliability ratio.<\/jats:p><jats:p>Availability: Our algorithm for assessment of SELDI-TOF experiment quality is available at http:\/\/www.biostat.harvard.edu\/~xlin<\/jats:p><jats:p>Contact: \u00a0harezlak@post.harvard.edu<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm346","type":"journal-article","created":{"date-parts":[[2007,7,12]],"date-time":"2007-07-12T00:39:20Z","timestamp":1184200760000},"page":"2441-2448","source":"Crossref","is-referenced-by-count":11,"title":["Quantitative quality-assessment techniques to compare fractionation and depletion methods in SELDI-TOF mass spectrometry experiments"],"prefix":"10.1093","volume":"23","author":[{"given":"Jaroslaw","family":"Harezlak","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Environmental Health, Harvard School of Public Health 655 Huntington Avenue Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mike","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Environmental Health, Harvard School of Public Health 655 Huntington Avenue Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Christiani","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Environmental Health, Harvard School of Public Health 655 Huntington Avenue Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xihong","family":"Lin","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Environmental Health, Harvard School of Public Health 655 Huntington Avenue Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,7,11]]},"reference":[{"key":"2023041106215470100_","first-page":"3609","article-title":"Serum protein Fingerprinting coupled with a pattern matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men","volume":"62","author":"Adam","year":"2002","journal-title":"Cancer Res"},{"key":"2023041106215470100_","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1515\/CCLM.2005.022","article-title":"Optimization and evaluation of surface\u2013enhanced laser desorption\/ionization time\u2013offlight mass spectrometry (SELDI\u2013TOF MS) with reversed\u2013phase protein arrays for protein profiling","volume":"43","author":"Aivado","year":"2005","journal-title":"Clin. 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