{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T23:19:00Z","timestamp":1790378340135,"version":"4.1.0"},"reference-count":44,"publisher":"Elsevier BV","issue":"9","license":[{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,7,29]],"date-time":"2025-07-29T00:00:00Z","timestamp":1753747200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["mcponline.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Molecular &amp; Cellular Proteomics"],"published-print":{"date-parts":[[2025,9]]},"DOI":"10.1016\/j.mcpro.2025.101044","type":"journal-article","created":{"date-parts":[[2025,7,29]],"date-time":"2025-07-29T16:21:36Z","timestamp":1753806096000},"page":"101044","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":13,"title":["High-Throughput Proteomic and Phosphoproteomic Analysis of Formalin-Fixed Paraffin-Embedded Tissues"],"prefix":"10.1016","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-6996-5251","authenticated-orcid":false,"given":"Moe","family":"Haines","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-6540-7629","authenticated-orcid":false,"given":"John R.","family":"Thorup","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7583-8292","authenticated-orcid":false,"given":"Simone","family":"Gohsman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6886-8936","authenticated-orcid":false,"given":"Claudia","family":"Ctortecka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chelsea","family":"Newton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1784-9196","authenticated-orcid":false,"given":"Dan C.","family":"Rohrer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Galen","family":"Hostetter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3914-133X","authenticated-orcid":false,"given":"D.R.","family":"Mani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9300-1448","authenticated-orcid":false,"given":"Michael A.","family":"Gillette","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6040-4854","authenticated-orcid":false,"given":"Shankha","family":"Satpathy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7203-4299","authenticated-orcid":false,"given":"Steven A.","family":"Carr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.mcpro.2025.101044_bib1","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1038\/s42003-024-06354-8","article-title":"Novel FFPE proteomics method suggests prolactin induced protein as hormone induced cytoskeleton remodeling spatial biomarker","volume":"7","author":"Faktor","year":"2024","journal-title":"Commun. Biol."},{"key":"10.1016\/j.mcpro.2025.101044_bib2","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1074\/mcp.RA117.000189","article-title":"Spatial tissue proteomics quantifies Inter- and intratumor heterogeneity in hepatocellular carcinoma (HCC)","volume":"17","author":"Buczak","year":"2018","journal-title":"Mol. Cell. Proteomics."},{"key":"10.1016\/j.mcpro.2025.101044_bib3","doi-asserted-by":"crossref","first-page":"2305","DOI":"10.1002\/1878-0261.12570","article-title":"High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification","volume":"13","author":"Zhu","year":"2019","journal-title":"Mol. Oncol."},{"key":"10.1016\/j.mcpro.2025.101044_bib4","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1002\/path.5420","article-title":"A streamlined mass spectrometry-based proteomics workflow for large-scale FFPE tissue analysis","volume":"251","author":"Coscia","year":"2020","journal-title":"J. Pathol."},{"key":"10.1016\/j.mcpro.2025.101044_bib5","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1038\/s44318-024-00289-w","article-title":"Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study","volume":"44","author":"T\u00fcshaus","year":"2024","journal-title":"EMBO J."},{"key":"10.1016\/j.mcpro.2025.101044_bib6","doi-asserted-by":"crossref","first-page":"e466","DOI":"10.1002\/ctm2.466","article-title":"A biobanking turning-point in the use of formalin-fixed, paraffin tumor blocks to unveil kinase signaling in melanoma","volume":"11","author":"Velasquez","year":"2021","journal-title":"Clin. Transl. Med."},{"key":"10.1016\/j.mcpro.2025.101044_bib7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-021-23855-w","article-title":"Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories","volume":"12","author":"Friedrich","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2025.101044_bib8","doi-asserted-by":"crossref","first-page":"5402","DOI":"10.1021\/acs.jproteome.1c00695","article-title":"Evaluation of disposable trap column nanoLC\u2013FAIMS\u2013MS\/MS for the proteomic analysis of FFPE tissue","volume":"20","author":"Eckert","year":"2021","journal-title":"J. Proteome. Res."},{"key":"10.1016\/j.mcpro.2025.101044_bib9","doi-asserted-by":"crossref","DOI":"10.1016\/j.xpro.2023.102381","article-title":"Protocol for deep proteomic profiling of formalin-fixed paraffin-embedded specimens using a spectral library-free approach","volume":"4","author":"Soni","year":"2023","journal-title":"STAR Protoc."},{"key":"10.1016\/j.mcpro.2025.101044_bib10","doi-asserted-by":"crossref","DOI":"10.1016\/j.labinv.2023.100282","article-title":"A high-throughput PIXUL-Matrix-Based toolbox to profile frozen and formalin-fixed paraffin-embedded tissues multiomes","volume":"104","author":"Mar","year":"2024","journal-title":"Lab. Invest."},{"key":"10.1016\/j.mcpro.2025.101044_bib11","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1021\/jasms.3c00099","article-title":"A high-throughput workflow for FFPE tissue proteomics","volume":"34","author":"Pujari","year":"2023","journal-title":"J. Am. Soc. Mass. Spectrom."},{"key":"10.1016\/j.mcpro.2025.101044_bib12","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1021\/acs.jproteome.9b00686","article-title":"HYPERsol: high-quality data from archival FFPE tissue for clinical proteomics","volume":"19","author":"Marchione","year":"2020","journal-title":"J. Proteome. Res."},{"key":"10.1016\/j.mcpro.2025.101044_bib13","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s12014-020-09287-6","article-title":"Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues","volume":"17","author":"Herrera","year":"2020","journal-title":"Clin. Proteomics."},{"key":"10.1016\/j.mcpro.2025.101044_bib14","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1021\/pr400960r","article-title":"Phosphoproteome analysis of formalin-fixed and paraffin-embedded tissue sections mounted on microscope slides","volume":"13","author":"Wakabayashi","year":"2014","journal-title":"J. Proteome. Res."},{"key":"10.1016\/j.mcpro.2025.101044_bib15","doi-asserted-by":"crossref","first-page":"4179","DOI":"10.1021\/acs.jproteome.0c00354","article-title":"Phosphorylation ratio determination in fresh-frozen and formalin-fixed paraffin-embedded tissue with targeted mass spectrometry","volume":"19","author":"Zeneyedpour","year":"2020","journal-title":"J. Proteome. Res."},{"key":"10.1016\/j.mcpro.2025.101044_bib16","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1074\/mcp.M114.044305","article-title":"Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues","volume":"14","author":"Bruderer","year":"2015","journal-title":"Mol. Cell. Proteomics."},{"key":"10.1016\/j.mcpro.2025.101044_bib17","doi-asserted-by":"crossref","first-page":"4154","DOI":"10.1038\/s41467-023-39869-5","article-title":"Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform","volume":"14","author":"Yu","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2025.101044_bib18","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","article-title":"DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput","volume":"17","author":"Demichev","year":"2020","journal-title":"Nat. Methods."},{"key":"10.1016\/j.mcpro.2025.101044_bib19","doi-asserted-by":"crossref","first-page":"2180","DOI":"10.1158\/2159-8290.CD-22-0043","article-title":"NCOA4-Mediated ferritinophagy is a pancreatic cancer dependency via maintenance of iron bioavailability for iron-sulfur cluster proteins","volume":"12","author":"Santana-Codina","year":"2022","journal-title":"Cancer Discov."},{"key":"10.1016\/j.mcpro.2025.101044_bib20","doi-asserted-by":"crossref","DOI":"10.1016\/j.mcpro.2022.100279","article-title":"Rapid and In-Depth coverage of the (Phospho-)Proteome with deep libraries and optimal window design for diaPASEF","volume":"21","author":"Skowronek","year":"2022","journal-title":"Mol. Cell. Proteomics."},{"key":"10.1016\/j.mcpro.2025.101044_bib21","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1038\/s41467-020-14381-2","article-title":"Microscaled proteogenomic methods for precision oncology","volume":"11","author":"Satpathy","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2025.101044_bib22","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1038\/s41467-020-14609-1","article-title":"Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries","volume":"11","author":"Bekker-Jensen","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2025.101044_bib23","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/nbt.2377","article-title":"A cross-platform toolkit for mass spectrometry and proteomics","volume":"30","author":"Chambers","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.mcpro.2025.101044_bib24","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/s41592-021-01176-6","article-title":"PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis","volume":"18","author":"Mani","year":"2021","journal-title":"Nat. Methods."},{"key":"10.1016\/j.mcpro.2025.101044_bib25","doi-asserted-by":"crossref","first-page":"4348","DOI":"10.1016\/j.cell.2021.07.016","article-title":"A proteogenomic portrait of lung squamous cell carcinoma","volume":"184","author":"Satpathy","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.mcpro.2025.101044_bib26","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.cell.2020.06.013","article-title":"Proteogenomic characterization reveals therapeutic vulnerabilities in lung adenocarcinoma","volume":"182","author":"Gillette","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.mcpro.2025.101044_bib27","doi-asserted-by":"crossref","first-page":"1436","DOI":"10.1016\/j.cell.2020.10.036","article-title":"Proteogenomic landscape of breast cancer tumorigenesis and targeted therapy","volume":"183","author":"Krug","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.mcpro.2025.101044_bib28","doi-asserted-by":"crossref","DOI":"10.15252\/msb.20199111","article-title":"Automated sample preparation with SP3 for low-input clinical proteomics","volume":"16","author":"M\u00fcller","year":"2020","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.mcpro.2025.101044_bib29","doi-asserted-by":"crossref","first-page":"13358","DOI":"10.1021\/acs.analchem.3c04479","article-title":"Quantitative comparison of deparaffinization, rehydration, and extraction methods for FFPE tissue proteomics and phosphoproteomics","volume":"96","author":"Humphries","year":"2024","journal-title":"Anal. Chem."},{"key":"10.1016\/j.mcpro.2025.101044_bib30","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1074\/mcp.RA118.001259","article-title":"Streamlined protocol for deep proteomic profiling of FAC-sorted cells and its application to freshly isolated murine immune cells","volume":"18","author":"Myers","year":"2019","journal-title":"Mol. Cell. Proteomics."},{"key":"10.1016\/j.mcpro.2025.101044_bib31","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/nmeth.2834","article-title":"Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells","volume":"11","author":"Kulak","year":"2014","journal-title":"Nat. Methods."},{"key":"10.1016\/j.mcpro.2025.101044_bib32","doi-asserted-by":"crossref","first-page":"2568","DOI":"10.1002\/pmic.201400454","article-title":"Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding","volume":"15","author":"Zhang","year":"2015","journal-title":"Proteomics"},{"key":"10.1016\/j.mcpro.2025.101044_bib33","doi-asserted-by":"crossref","first-page":"2203","DOI":"10.1074\/mcp.O115.056515","article-title":"Formalin-fixed, paraffin-embedded tissues (FFPE) as a robust source for the profiling of native and protease-generated protein amino termini","volume":"15","author":"Lai","year":"2016","journal-title":"Mol. Cell. Proteomics."},{"key":"10.1016\/j.mcpro.2025.101044_bib34","doi-asserted-by":"crossref","first-page":"4065","DOI":"10.1038\/s41467-020-17921-y","article-title":"Identification of modified peptides using localization-aware open search","volume":"11","author":"Yu","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2025.101044_bib35","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.TIR120.002216","article-title":"PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results","volume":"20","author":"Geiszler","year":"2021","journal-title":"Mol. Cell. Proteomics."},{"key":"10.1016\/j.mcpro.2025.101044_bib36","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/nature13148","article-title":"Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy","volume":"509","author":"Mancias","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.mcpro.2025.101044_bib37","doi-asserted-by":"crossref","first-page":"R123","DOI":"10.1530\/JOE-16-0594","article-title":"STEAP4: its emerging role in metabolism and homeostasis of cellular iron and copper","volume":"234","author":"Scarl","year":"2017","journal-title":"J. Endocrinol."},{"key":"10.1016\/j.mcpro.2025.101044_bib38","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1002\/pro.3711","article-title":"KEGG mapper for inferring cellular functions from protein sequences","volume":"29","author":"Kanehisa","year":"2020","journal-title":"Protein Sci."},{"key":"10.1016\/j.mcpro.2025.101044_bib39","doi-asserted-by":"crossref","first-page":"213","DOI":"10.3727\/096504019X15668125347026","article-title":"(1AD) PRKAA1 promotes proliferation and inhibits apoptosis of gastric cancer cells through activating JNK1 and Akt pathways","volume":"28","author":"Zhang","year":"2020","journal-title":"Oncol. Res."},{"key":"10.1016\/j.mcpro.2025.101044_bib40","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1111\/cyt.12921","article-title":"The phosphatase PTPN1\/PTP1B is a candidate marker of better chemotherapy response in metastatic high-grade serous carcinoma","volume":"32","author":"Davidson","year":"2021","journal-title":"Cytopathology"},{"key":"10.1016\/j.mcpro.2025.101044_bib41","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1083\/jcb.201501090","article-title":"TRAMM\/TrappC12 plays a role in chromosome congression, kinetochore stability, and CENP-E recruitment","volume":"209","author":"Milev","year":"2015","journal-title":"J. Cell. Biol."},{"key":"10.1016\/j.mcpro.2025.101044_bib42","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.molcel.2013.08.044","article-title":"Phosphorylation of BRAF by AMPK impairs BRAF-KSR1 association and cell proliferation","volume":"52","author":"Shen","year":"2013","journal-title":"Mol. Cell."},{"key":"10.1016\/j.mcpro.2025.101044_bib43","article-title":"Pan-cancer study of SHC-adaptor protein 1 (SHC1) as a diagnostic, prognostic and immunological biomarker in human cancer","volume":"13","author":"Chen","year":"2022","journal-title":"Front. Genet."},{"key":"10.1016\/j.mcpro.2025.101044_bib44","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2020.100871","article-title":"PTPRA phosphatase regulates GDNF-dependent RET signaling and inhibits the RET mutant MEN2A oncogenic potential","volume":"23","author":"Yadav","year":"2020","journal-title":"iScience"}],"container-title":["Molecular &amp; Cellular Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535947625001434?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535947625001434?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T06:48:13Z","timestamp":1759301293000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1535947625001434"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9]]},"references-count":44,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2025,9]]}},"alternative-id":["S1535947625001434"],"URL":"https:\/\/doi.org\/10.1016\/j.mcpro.2025.101044","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.11.17.624038","asserted-by":"object"}]},"ISSN":["1535-9476"],"issn-type":[{"value":"1535-9476","type":"print"}],"subject":[],"published":{"date-parts":[[2025,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"High-Throughput Proteomic and Phosphoproteomic Analysis of Formalin-Fixed Paraffin-Embedded Tissues","name":"articletitle","label":"Article Title"},{"value":"Molecular & Cellular Proteomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.mcpro.2025.101044","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology\u00e9","name":"copyright","label":"Copyright"}],"article-number":"101044"}}