{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,15]],"date-time":"2025-10-15T17:36:53Z","timestamp":1760549813742},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Accurate cross-sample peak alignment and reliable intensity normalization is a critical step for robust quantitative analysis in untargetted metabolomics since tandem mass spectrometry (MS\/MS) is rarely used for compound identification. Therefore shortcomings in the data processing steps can easily introduce false positives due to misalignments and erroneous normalization adjustments in large sample studies.<\/jats:p>\n               <jats:p>Results: In this work, we developed a software package MetTailor featuring two novel data preprocessing steps to remedy drawbacks in the existing processing tools. First, we propose a novel dynamic block summarization (DBS) method for correcting misalignments from peak alignment algorithms, which alleviates missing data problem due to misalignments. For the purpose of verifying correct re-alignments, we propose to use the cross-sample consistency in isotopic intensity ratios as a quality metric. Second, we developed a flexible intensity normalization procedure that adjusts normalizing factors against the temporal variations in total ion chromatogram (TIC) along the chromatographic retention time (RT). We first evaluated the DBS algorithm using a curated metabolomics dataset, illustrating that the algorithm identifies misaligned peaks and correctly realigns them with good sensitivity. We next demonstrated the DBS algorithm and the RT-based normalization procedure in a large-scale dataset featuring &amp;gt;100 sera samples in primary Dengue infection study. Although the initial alignment was successful for the majority of peaks, the DBS algorithm still corrected \u223c7000 misaligned peaks in this data and many recovered peaks showed consistent isotopic patterns with the peaks they were realigned to. In addition, the RT-based normalization algorithm efficiently removed visible local variations in TIC along the RT, without sacrificing the sensitivity of detecting differentially expressed metabolites.<\/jats:p>\n               <jats:p>Availability and implementation: The R package MetTailor is freely available at the SourceForge website http:\/\/mettailor.sourceforge.net\/.<\/jats:p>\n               <jats:p>Contact: \u00a0hyung_won_choi@nuhs.edu.sg<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv434","type":"journal-article","created":{"date-parts":[[2015,7,29]],"date-time":"2015-07-29T00:29:38Z","timestamp":1438129778000},"page":"3645-3652","source":"Crossref","is-referenced-by-count":4,"title":["MetTailor: dynamic block summary and intensity normalization for robust analysis of mass spectrometry data in metabolomics"],"prefix":"10.1093","volume":"31","author":[{"given":"Gengbo","family":"Chen","sequence":"first","affiliation":[{"name":"1 Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore,"}]},{"given":"Liang","family":"Cui","sequence":"additional","affiliation":[{"name":"2 Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology, Singapore, Singapore and"}]},{"given":"Guo Shou","family":"Teo","sequence":"additional","affiliation":[{"name":"1 Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore,"}]},{"given":"Choon Nam","family":"Ong","sequence":"additional","affiliation":[{"name":"1 Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore,"},{"name":"3 National University of Singapore Environment Research Institute, Singapore, Singapore"}]},{"given":"Chuen Seng","family":"Tan","sequence":"additional","affiliation":[{"name":"1 Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore,"}]},{"given":"Hyungwon","family":"Choi","sequence":"additional","affiliation":[{"name":"1 Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore,"}]}],"member":"286","published-online":{"date-parts":[[2015,7,27]]},"reference":[{"key":"2023020202402013500_btv434-B1","doi-asserted-by":"crossref","first-page":"e2373","DOI":"10.1371\/journal.pntd.0002373","article-title":"Serum metabolome and lipidome changes in adult patients with primary dengue infection","volume":"7","author":"Cui","year":"2013","journal-title":"PLoS Neglected Trop. 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