{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T06:50:04Z","timestamp":1774335004855,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,12,2]],"date-time":"2019-12-02T00:00:00Z","timestamp":1575244800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"name":"MRC Flexible Training Supplement","award":["MR\/K501311\/1"],"award-info":[{"award-number":["MR\/K501311\/1"]}]},{"name":"University of Manchester President\u2019s Doctoral Scholarship"},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["MR\/N00583X\/1"],"award-info":[{"award-number":["MR\/N00583X\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Manchester Molecular Pathology Innovation Centre"},{"name":"National Institute for Health Research Manchester Biomedical Research Centre"},{"DOI":"10.13039\/501100012041","name":"Versus Arthritis","doi-asserted-by":"publisher","award":["21754"],"award-info":[{"award-number":["21754"]}],"id":[{"id":"10.13039\/501100012041","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/M008959\/1"],"award-info":[{"award-number":["MR\/M008959\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017008","name":"Cancer Research UK Manchester Centre","doi-asserted-by":"crossref","award":["C5759\/A25254"],"award-info":[{"award-number":["C5759\/A25254"]}],"id":[{"id":"10.13039\/501100017008","id-type":"DOI","asserted-by":"crossref"}]},{"name":"British Heart Foundation Personal Chair"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Data-independent acquisition mass spectrometry allows for comprehensive peptide detection and relative quantification than standard data-dependent approaches. While less prone to missing values, these still exist. Current approaches for handling the so-called missingness have challenges. We hypothesized that non-random missingness is a useful biological measure and demonstrate the importance of analysing missingness for proteomic discovery within a longitudinal study of disease activity.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The magnitude of missingness did not correlate with mean peptide concentration. The magnitude of missingness for each protein strongly correlated between collection time points (baseline, 3\u2009months, 6\u2009months; R\u2009=\u20090.95\u20130.97, confidence interval = 0.94\u20130.97) indicating little time-dependent effect. This allowed for the identification of proteins with outlier levels of missingness that differentiate between the patient groups characterized by different patterns of disease activity. The association of these proteins with disease activity was confirmed by machine learning techniques. Our novel approach complements analyses on complete observations and other missing value strategies in biomarker prediction of disease activity.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz898","type":"journal-article","created":{"date-parts":[[2019,11,27]],"date-time":"2019-11-27T12:13:15Z","timestamp":1574856795000},"page":"2217-2223","source":"Crossref","is-referenced-by-count":33,"title":["The use of missing values in proteomic data-independent acquisition mass spectrometry to enable disease activity discrimination"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5445-6906","authenticated-orcid":false,"given":"Kathryn A","family":"McGurk","sequence":"first","affiliation":[{"name":"Division of 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Manchester, UK"},{"name":"Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre , Manchester, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1314-413X","authenticated-orcid":false,"given":"Anna","family":"Nicolaou","sequence":"additional","affiliation":[{"name":"Laboratory for Lipidomics and Lipid Biology, Division of Pharmacy and Optometry , UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernard D","family":"Keavney","sequence":"additional","affiliation":[{"name":"Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology Medicine and Health, University of Manchester , Manchester, 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