{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:48:04Z","timestamp":1787028484435,"version":"build-2736575974"},"reference-count":28,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2022,9,18]],"date-time":"2022-09-18T00:00:00Z","timestamp":1663459200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Egyptian Cancer Network (ECN), USA","award":["identification"],"award-info":[{"award-number":["identification"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Metabolomics is a potential approach to paving new avenues for clinical diagnosis, molecular medicine, and therapeutic drug monitoring and development. The conventional metabolomics analysis pipeline depends on the data-independent acquisition (DIA) technique. Although powerful, it still suffers from stochastic, non-reproducible ion selection across samples. Despite the presence of different metabolomics workbenches, metabolite identification remains a tedious and time-consuming task. Consequently, sequential windowed acquisition of all theoretical MS (SWATH) acquisition has attracted much attention to overcome this limitation. This article aims to develop a novel SWATH platform for data analysis with a generation of an accurate mass spectral library for metabolite identification using SWATH acquisition. The workflow was validated using inclusion\/exclusion compound lists. The false-positive identification was 3.4% from the non-endogenous drugs with 96.6% specificity. The workflow has proven to overcome background noise despite the complexity of the SWATH sample. From the Human Metabolome Database (HMDB), 1282 compounds were tested in various biological samples to demonstrate the feasibility of the workflow. The current study identified 377 compounds in positive and 303 in negative modes with 392 unique non-redundant metabolites. Finally, a free software tool, SASA, was developed to analyze SWATH-acquired samples using the proposed pipeline.<\/jats:p>","DOI":"10.3390\/ijms231810908","type":"journal-article","created":{"date-parts":[[2022,9,18]],"date-time":"2022-09-18T23:39:22Z","timestamp":1663544362000},"page":"10908","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["A Novel Approach of SWATH-Based Metabolomics Analysis Using the Human Metabolome Database Spectral Library"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2948-9845","authenticated-orcid":false,"given":"Hassan","family":"Shikshaky","sequence":"first","affiliation":[{"name":"Proteomics and Metabolomics Research Program, Basic Research Department, Children\u2019s Cancer Hospital Egypt 57357, Cairo 11441, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0973-2630","authenticated-orcid":false,"given":"Eman Abdelnaby","family":"Ahmed","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Research Program, Basic Research Department, Children\u2019s Cancer Hospital Egypt 57357, Cairo 11441, Egypt"},{"name":"Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali Mostafa","family":"Anwar","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Research Program, Basic Research Department, Children\u2019s Cancer Hospital Egypt 57357, Cairo 11441, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aya","family":"Osama","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Research Program, Basic Research Department, Children\u2019s Cancer Hospital Egypt 57357, Cairo 11441, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shahd","family":"Ezzeldin","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Research Program, Basic Research Department, Children\u2019s Cancer Hospital Egypt 57357, Cairo 11441, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antony","family":"Nasr","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Research Program, Basic Research Department, Children\u2019s Cancer Hospital Egypt 57357, Cairo 11441, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9711-6242","authenticated-orcid":false,"given":"Sebaey","family":"Mahgoub","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Research Program, Basic Research Department, Children\u2019s Cancer Hospital Egypt 57357, Cairo 11441, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7507-9935","authenticated-orcid":false,"given":"Sameh","family":"Magdeldin","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Research Program, Basic Research Department, Children\u2019s Cancer Hospital Egypt 57357, Cairo 11441, Egypt"},{"name":"Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,9,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"38885","DOI":"10.1038\/srep38885","article-title":"Systematic assessment of seven solvent and solid-phase extraction methods for metabolomics analysis of human plasma by LC-MS","volume":"6","author":"Sitnikov","year":"2016","journal-title":"Sci. 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