{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T20:56:19Z","timestamp":1777928179216,"version":"3.51.4"},"reference-count":34,"publisher":"SAGE Publications","issue":"9","license":[{"start":{"date-parts":[[2022,9,1]],"date-time":"2022-09-01T00:00:00Z","timestamp":1661990400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["OMICS: A Journal of Integrative Biology"],"published-print":{"date-parts":[[2022,9]]},"abstract":"<jats:p>\n                    Clinical proteomics is a rapidly emerging frontier in laboratory medicine. High-throughput proteomic investigations of biopsy tissues provide mechanistic insights into complex human diseases. For large-scale proteomics, formalin-fixed and paraffin-embedded (FFPE) tissue samples offer a viable alternative to fresh-frozen (FF) tissues that have restricted availability. In this context, meningioma is one of the most common primary brain tumors where innovation in diagnostics and therapeutic targets can benefit from clinical proteomics. We present here an integrated workflow for quantitative proteomics and biomarker validation of meningioma FFPE tissues. Applying label-free quantitative (LFQ) proteomics, we reproducibly (Pearson's correlation: 0.84\u20130.91) obtained an in-depth proteome coverage (nearly 4000 proteins per sample) from 120\u2009min gradient of single unfractionated mass spectrometry run. Furthermore, building upon LFQ data and literature curated set of meningioma-associated proteins, we validated\n                    <jats:italic toggle=\"yes\">VIM<\/jats:italic>\n                    ,\n                    <jats:italic toggle=\"yes\">AHNAK<\/jats:italic>\n                    , and\n                    <jats:italic toggle=\"yes\">CLU<\/jats:italic>\n                    from FFPE tissues using selected reaction monitoring (SRM) assay and compared its performance with FF tissues. This study illustrates how knowledge from label-free proteomics can be integrated for selecting peptides for targeted validation and suggests that FFPE tissues are comparable to FF tissues for SRM assays. This quantitative clinical proteomics workflow is scalable for large-scale clinical diagnostics studies in the future, for example, utilizing the global repository of FFPE tissues in meningioma and possibly in other cancers.\n                  <\/jats:p>","DOI":"10.1089\/omi.2022.0082","type":"journal-article","created":{"date-parts":[[2022,8,29]],"date-time":"2022-08-29T11:48:51Z","timestamp":1661773731000},"page":"512-520","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":4,"title":["Clinical Proteomics for Meningioma: An Integrated Workflow for Quantitative Proteomics and Biomarker Validation in Formalin-Fixed Paraffin-Embedded Tissue Samples"],"prefix":"10.1177","volume":"26","author":[{"given":"Arijit","family":"Mukherjee","sequence":"first","affiliation":[{"name":"Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Susmita","family":"Ghosh","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deeptarup","family":"Biswas","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aishwarya","family":"Rao","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Prakash","family":"Shetty","sequence":"additional","affiliation":[{"name":"Tata Memorial Hospital, Mumbai, India."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sridhar","family":"Epari","sequence":"additional","affiliation":[{"name":"Tata Memorial Hospital, Mumbai, India."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aliasgar","family":"Moiyadi","sequence":"additional","affiliation":[{"name":"Tata Memorial Hospital, Mumbai, India."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sanjeeva","family":"Srivastava","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India."}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2022,9,7]]},"reference":[{"issue":"5","key":"e_1_3_6_2_1","first-page":"369","article-title":"Meningiomas and proteomics: Focus on new potential biomarkers and molecular pathways","volume":"13","author":"Abbritti RV","year":"2016","unstructured":"Abbritti RV, , Polito F, , Cucinotta M, et al. Meningiomas and proteomics: Focus on new potential biomarkers and molecular pathways. Cancer Genomics Proteomics, 2016; 13(5):369\u2013380.","journal-title":"Cancer Genomics Proteomics"},{"key":"e_1_3_6_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19045-9"},{"key":"e_1_3_6_4_1","doi-asserted-by":"publisher","DOI":"10.2144\/000113382"},{"key":"e_1_3_6_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-020-0356-y"},{"key":"e_1_3_6_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/path.5420"},{"key":"e_1_3_6_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2018.12.048"},{"key":"e_1_3_6_8_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.9b00790"},{"key":"e_1_3_6_9_1","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2021.548243"},{"key":"e_1_3_6_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbapap.2014.10.003"},{"key":"e_1_3_6_11_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.8b00505"},{"key":"e_1_3_6_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrc2918"},{"key":"e_1_3_6_13_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201300377"},{"key":"e_1_3_6_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep34949"},{"key":"e_1_3_6_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ab.2016.05.015"},{"key":"e_1_3_6_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg.2018.4"},{"key":"e_1_3_6_17_1","doi-asserted-by":"publisher","DOI":"10.1089\/bio.2012.0052"},{"key":"e_1_3_6_18_1","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2020.543997"},{"key":"e_1_3_6_19_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12014-020-09283-w"},{"key":"e_1_3_6_20_1","doi-asserted-by":"publisher","DOI":"10.3389\/fnins.2020.577755"},{"key":"e_1_3_6_21_1","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2020.01600"},{"key":"e_1_3_6_22_1","doi-asserted-by":"publisher","DOI":"10.1039\/C9MO00082H"},{"key":"e_1_3_6_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/neuonc\/not151"},{"key":"e_1_3_6_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/neuonc\/noz084"},{"key":"e_1_3_6_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2015"},{"key":"e_1_3_6_26_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12014-018-9202-4"},{"key":"e_1_3_6_27_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-17641-3"},{"key":"e_1_3_6_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/0003-2697(74)90034-7"},{"key":"e_1_3_6_29_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep07140"},{"issue":"1","key":"e_1_3_6_30_1","first-page":"1","article-title":"Proteomics pinpoints alterations in grade I meningiomas of male versus female patients","volume":"10","author":"Silva JM","year":"2020","unstructured":"Silva JM, , Wippel HH, , Santos MDM, et al. Proteomics pinpoints alterations in grade I meningiomas of male versus female patients. Sci Rep, 2020; 10(1):1\u201311; doi: 10.1038\/s41598-020-67113-3.","journal-title":"Sci Rep"},{"key":"e_1_3_6_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-00881-z"},{"key":"e_1_3_6_32_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.nbt.2019.05.003"},{"key":"e_1_3_6_33_1","first-page":"5","article-title":"Proteomic sample preparation from formalin fixed and paraffin embedded tissue","author":"Wi\u015bniewski JR.","year":"2013","unstructured":"Wi\u015bniewski JR. Proteomic sample preparation from formalin fixed and paraffin embedded tissue. 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