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Diagnosis is based on renal biopsy and the condition is treated using immunosuppressive drugs; however nephrotic syndrome treatment efficacy varies among patients. Multi-omic urine analyses can discover new markers of nephrotic syndrome that can be used to develop personalized treatments. For proteomics, a protease inhibitor (PI) is sometimes added at sample collection to conserve proteins but its impact on urine metabolic phenotyping needs to be evaluated. Urine from controls (n = 4) and idiopathic membranous nephropathy (iMN) patients (n = 6) were collected with and without PI addition and analysed using 1H NMR spectroscopy and UPLC-MS. PI-related data features were observed in the 1H NMR spectra but their removal followed by a median fold change normalisation, eliminated the PI contribution. PI-related metabolites in UPLC-MS data had limited effect on metabolic patterns specific to iMN. When using an appropriate data processing pipeline, PI-containing urine samples are appropriate for 1H NMR and MS metabolic profiling of patients with nephrotic syndrome.<\/jats:p>\n                  <jats:p\/>","DOI":"10.1039\/c8mo00190a","type":"journal-article","created":{"date-parts":[[2019,1,9]],"date-time":"2019-01-09T05:34:31Z","timestamp":1547012071000},"page":"39-49","update-policy":"https:\/\/doi.org\/10.1039\/rsc_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["NMR and MS urinary metabolic phenotyping in kidney diseases is fit-for-purpose in the presence of a protease inhibitor"],"prefix":"10.1093","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9022-0159","authenticated-orcid":false,"given":"Claire L","family":"Boulang\u00e9","sequence":"first","affiliation":[{"name":"Metabometrix Ltd a , Sir Alexander Fleming Building South Kensington, London SW7 2AZ UK \u00a0 manuja.kaluarachchi@imperial.ac.uk"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2768-2358","authenticated-orcid":false,"given":"Ilse M","family":"Rood","sequence":"additional","affiliation":[{"name":"Department of Nephrology, Radboud University Medical Center b , Nijmegen, Geert Grooteplein Zuid 8 PO Box 9101 6500 HB Nijmegen The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joram M","family":"Posma","sequence":"additional","affiliation":[{"name":"Imperial College London, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine c , Sir Alexander Fleming Building South Kensington, London SW7 2AZ UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0916-6360","authenticated-orcid":false,"given":"John C","family":"Lindon","sequence":"additional","affiliation":[{"name":"Imperial College London, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine c , Sir Alexander Fleming Building South Kensington, London SW7 2AZ UK"},{"name":"Metabometrix Ltd a , Sir Alexander Fleming Building South Kensington, London SW7 2AZ UK \u00a0 manuja.kaluarachchi@imperial.ac.uk"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elaine","family":"Holmes","sequence":"additional","affiliation":[{"name":"Imperial College London, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine c , Sir Alexander Fleming Building South Kensington, London SW7 2AZ UK"},{"name":"Metabometrix Ltd a , Sir Alexander Fleming Building South Kensington, London SW7 2AZ UK \u00a0 manuja.kaluarachchi@imperial.ac.uk"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jack F M","family":"Wetzels","sequence":"additional","affiliation":[{"name":"Department of Nephrology, Radboud University Medical Center b , Nijmegen, Geert Grooteplein Zuid 8 PO Box 9101 6500 HB Nijmegen The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeroen K J","family":"Deegens","sequence":"additional","affiliation":[{"name":"Department of Nephrology, Radboud University Medical Center b , Nijmegen, Geert Grooteplein Zuid 8 PO Box 9101 6500 HB Nijmegen The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3769-8310","authenticated-orcid":false,"given":"Manuja R","family":"Kaluarachchi","sequence":"additional","affiliation":[{"name":"Metabometrix Ltd a , Sir Alexander Fleming Building South Kensington, London SW7 2AZ UK \u00a0 manuja.kaluarachchi@imperial.ac.uk"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,1,9]]},"reference":[{"key":"2026010815050214100_cit1","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1016\/S0272-6386(97)90485-6","volume":"30","author":"Haas","year":"1997","journal-title":"Am. 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Boulang\u00e9 (ORCID)","URL":"http:\/\/orcid.org\/0000-0002-9022-0159","name":"identifier","group":{"name":"author_identifiers","label":"IDENTIFIERS"}},{"value":"Ilse M. Rood (ORCID)","URL":"http:\/\/orcid.org\/0000-0003-2768-2358","name":"identifier","group":{"name":"author_identifiers","label":"IDENTIFIERS"}},{"value":"John C. Lindon (ORCID)","URL":"http:\/\/orcid.org\/0000-0002-0916-6360","name":"identifier","group":{"name":"author_identifiers","label":"IDENTIFIERS"}},{"value":"Manuja R. 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