{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T12:32:27Z","timestamp":1791981147131,"version":"4.4.0"},"reference-count":62,"publisher":"American Chemical Society (ACS)","issue":"7","license":[{"start":{"date-parts":[[2025,2,16]],"date-time":"2025-02-16T00:00:00Z","timestamp":1739664000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001026","name":"National Breast Cancer Foundation","doi-asserted-by":"publisher","award":["IIRS-18-164"],"award-info":[{"award-number":["IIRS-18-164"]}],"id":[{"id":"10.13039\/501100001026","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001774","name":"University of Sydney","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001774","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1137064"],"award-info":[{"award-number":["GNT1137064"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1170739"],"award-info":[{"award-number":["GNT1170739"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000947","name":"Australian Cancer Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000947","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009287","name":"NSW Health","doi-asserted-by":"publisher","award":["CMP-01"],"award-info":[{"award-number":["CMP-01"]}],"id":[{"id":"10.13039\/501100009287","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001171","name":"Cancer Institute NSW","doi-asserted-by":"publisher","award":["2017\/TPG001"],"award-info":[{"award-number":["2017\/TPG001"]}],"id":[{"id":"10.13039\/501100001171","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001171","name":"Cancer Institute NSW","doi-asserted-by":"publisher","award":["REG171150"],"award-info":[{"award-number":["REG171150"]}],"id":[{"id":"10.13039\/501100001171","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021954","name":"Tour de Cure","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100021954","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009119","name":"Children's Medical Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009119","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["H2020- SC1-DTH-2018-1"],"award-info":[{"award-number":["H2020- SC1-DTH-2018-1"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001047","name":"Ian Potter Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001047","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001102","name":"Cancer Council NSW","doi-asserted-by":"publisher","award":["IG 18-01"],"award-info":[{"award-number":["IG 18-01"]}],"id":[{"id":"10.13039\/501100001102","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Medical Research Futures Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,2,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Many liquid chromatography\u2013mass spectrometry (LC\u2013MS) studies have compared formalin-fixed paraffin-embedded (FFPE) tissues with matched fresh-frozen (FF) tissues to examine the effect of preservation techniques on the proteome; however, few studies have included the phosphoproteome. A high degree of overlap and correlation between the two preservation techniques would demonstrate the importance of FFPE tissues as a valuable biomedical resource. Our aim was to quantitatively compare the proteome and phosphoproteome of matched FFPE and FF tissues using data-independent acquisition LC\u2013MS. Four organs from three rats were cut in half to produce matched FFPE and FF tissue pairs. Excellent overlaps of 85\u201397% for the proteome and 82\u201398% for the phosphoproteome were observed, depending on the organ type, between the two preservation techniques. Most of the unique identifications were found in FF with less than 0.3% being unique to FFPE tissues. Strong agreement between FFPE and FF matched tissue pairs was observed with Pearson correlation coefficients of 0.93\u20130.97 and 0.79\u20130.87 for the proteome and phosphoproteome, respectively. Digestion efficiency was slightly higher in FFPE (92\u201394%) than in FF tissues (86\u201389%), and a search of a data subset for formaldehyde induced chemical modifications revealed that only 0.05% of precursors were unique to FFPE tissues. This suggests that with quality sample preparation methods it is not necessary to include formaldehyde induced chemical modifications when analyzing FFPE tissues. We attribute the lower number of identifications in FFPE tissues to inaccurate peptide quantitation, which resulted in a lower MS peptide load and tryptic peptide enrichment load. Our results demonstrate that both proteomic and phosphoproteomic analyses of FFPE and FF tissues are highly comparable and highlight the suitability of FFPE tissues for both proteomic and phosphoproteomic analysis.<\/jats:p>","DOI":"10.1021\/acsomega.4c09289","type":"journal-article","created":{"date-parts":[[2025,2,16]],"date-time":"2025-02-16T09:54:11Z","timestamp":1739699651000},"page":"6891-6900","source":"Crossref","is-referenced-by-count":15,"title":["Overlap of Formalin-Fixed Paraffin-Embedded and Fresh-Frozen\nMatched Tissues for Proteomics and Phosphoproteomics"],"prefix":"10.1021","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7186-0620","authenticated-orcid":true,"given":"Erin M.","family":"Humphries","sequence":"first","affiliation":[{"name":"The University of Sydney , , , ,","place":["Westmead, NSW, Australia, 2145"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7276-1760","authenticated-orcid":true,"given":"Peter G.","family":"Hains","sequence":"additional","affiliation":[{"name":"The University of Sydney , , , ,","place":["Westmead, NSW, Australia, 2145"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7878-0313","authenticated-orcid":true,"given":"Phillip J.","family":"Robinson","sequence":"additional","affiliation":[{"name":"The University of Sydney , , , ,","place":["Westmead, NSW, Australia, 2145"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2025,2,16]]},"reference":[{"issue":"7","key":"2026081811150171800_cit1","doi-asserted-by":"publisher","first-page":"3688","DOI":"10.1021\/pr100234w","article-title":"Proteome,\nPhosphoproteome, and N-Glycoproteome Are Quantitatively Preserved\nin Formalin-Fixed Paraffin-Embedded Tissue and Analyzable by High-Resolution\nMass Spectrometry","volume":"9","author":"Ostasiewicz","year":"2010","journal-title":"J. Proteome. Res."},{"issue":"8","key":"2026081811150171800_cit2","doi-asserted-by":"publisher","first-page":"2368","DOI":"10.1039\/c1mb05113j","article-title":"Protein phosphorylation\nanalysis in archival clinical cancer samples by shotgun and targeted\nproteomics approaches","volume":"7","author":"Gamez-Pozo","year":"2011","journal-title":"Mol. Biosyst"},{"issue":"12","key":"2026081811150171800_cit3","doi-asserted-by":"publisher","first-page":"5748","DOI":"10.1021\/pr300560y","article-title":"Variability\nof protein and phosphoprotein levels in\nclinical tissue specimens during the preanalytical phase","volume":"11","author":"Gundisch","year":"2012","journal-title":"J. Proteome. Res."},{"issue":"7","key":"2026081811150171800_cit4","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1111\/jop.13327","article-title":"Integrated proteomics,\nphosphoproteomics and metabolomics analyses reveal similarities among\ngiant cell granulomas of the jaws with different genetic mutations","volume":"51","author":"Vitorio","year":"2022","journal-title":"J. Oral. Pathol. Med."},{"issue":"4","key":"2026081811150171800_cit5","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1111\/jop.13282","article-title":"Quantitative proteomic study reveals differential\nexpression of matricellular proteins between fibrous dysplasia and\ncemento-ossifying fibroma pathogenesis","volume":"51","author":"Duarte-Andrade","year":"2022","journal-title":"J. Oral.\nPathol. Med."},{"issue":"1","key":"2026081811150171800_cit6","doi-asserted-by":"publisher","first-page":"3576","DOI":"10.1038\/s41467-021-23855-w","article-title":"Comprehensive micro-scaled proteome\nand phosphoproteome characterization of archived retrospective cancer\nrepositories","volume":"12","author":"Friedrich","year":"2021","journal-title":"Nat. Commun."},{"issue":"14","key":"2026081811150171800_cit7","doi-asserted-by":"publisher","first-page":"3930","DOI":"10.1158\/0008-5472.CAN-21-0214","article-title":"Quantitative analysis of tyrosine phosphorylation\nfrom FFPE tissues reveals patient specific signaling networks","volume":"81","author":"Kohale","year":"2021","journal-title":"Cancer. Res."},{"issue":"1","key":"2026081811150171800_cit8","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2022.100877","article-title":"Proteomics\nseparates adult-type diffuse high-grade\ngliomas in metabolic subgroups independent of 1p\/19q codeletion and\nacross IDH mutational status","volume":"4","author":"Bader","year":"2023","journal-title":"Cell Rep. Med."},{"key":"2026081811150171800_cit9","doi-asserted-by":"publisher","first-page":"9300","DOI":"10.1182\/blood-2022-168618","article-title":"Differential Phosphoproteomics Deciphers Physiopathology\nof High-Risk Mantle Cell Lymphoma","volume":"140","author":"Fuseau","year":"2022","journal-title":"Blood"},{"key":"2026081811150171800_cit10","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1016\/j.ccell.2020.08.002","article-title":"Integrated\nOmics of Metastatic Colorectal Cancer","volume":"38","author":"Li","year":"2020","journal-title":"Cancer\nCell"},{"issue":"10","key":"2026081811150171800_cit11","doi-asserted-by":"publisher","first-page":"5188","DOI":"10.1021\/pr100664e","article-title":"Proteomic Analysis of\nPAXgene-Fixed Tissues","volume":"9","author":"Ergin","year":"2010","journal-title":"J. Proteome. Res."},{"issue":"8","key":"2026081811150171800_cit12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0023780","article-title":"One-step preservation\nof phosphoproteins and tissue morphology at room temperature for diagnostic\nand research specimens","volume":"6","author":"Mueller","year":"2011","journal-title":"PLoS One"},{"issue":"3","key":"2026081811150171800_cit13","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1007\/s00428-012-1248-5","article-title":"Systematic\ncomparison of tissue fixation\nwith alternative fixatives to conventional tissue fixation with buffered\nformalin in a xenograft-based model","volume":"461","author":"Nietner","year":"2012","journal-title":"Virchows\nArch"},{"issue":"11","key":"2026081811150171800_cit14","doi-asserted-by":"publisher","first-page":"e113608","DOI":"10.1371\/journal.pone.0113608","article-title":"Immunohistochemistry\nof colorectal cancer biomarker phosphorylation requires controlled\ntissue fixation","volume":"9","author":"Theiss","year":"2014","journal-title":"PLoS One"},{"issue":"3","key":"2026081811150171800_cit15","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1111\/his.12268","article-title":"Determination\nof phosphorylated proteins in tissue specimens requires high-quality\nsamples collected under stringent conditions","volume":"64","author":"Wolf","year":"2014","journal-title":"Histopathology"},{"issue":"1","key":"2026081811150171800_cit16","doi-asserted-by":"publisher","first-page":"e54138","DOI":"10.1371\/journal.pone.0054138","article-title":"Rapid Two-Temperature Formalin Fixation","volume":"8","author":"Chafin","year":"2013","journal-title":"PLoS One"},{"issue":"1","key":"2026081811150171800_cit17","doi-asserted-by":"publisher","first-page":"2147","DOI":"10.1038\/s41598-020-58257-3","article-title":"Effect\nof immediate cold formalin fixation on phosphoprotein IHC tumor biomarker\nsignal in liver tumors using a cold transport device","volume":"10","author":"Lerch","year":"2020","journal-title":"Sci. Rep"},{"issue":"10","key":"2026081811150171800_cit18","doi-asserted-by":"publisher","first-page":"1998","DOI":"10.1074\/mcp.M700596-MCP200","article-title":"A Portrait\nof Tissue Phosphoprotein Stability in the\nClinical Tissue Procurement Process","volume":"7","author":"Espina","year":"2008","journal-title":"Mol. Cell.\nProteomics"},{"issue":"5","key":"2026081811150171800_cit19","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1038\/labinvest.2015.37","article-title":"Critical roles\nof specimen type and temperature before and during fixation in the\ndetection of phosphoproteins in breast cancer tissues","volume":"95","author":"Gundisch","year":"2015","journal-title":"Lab. Invest"},{"issue":"10","key":"2026081811150171800_cit20","doi-asserted-by":"publisher","first-page":"4424","DOI":"10.1021\/pr400451z","article-title":"Delayed times to tissue fixation\nresult in unpredictable\nglobal phosphoproteome changes","volume":"12","author":"Gundisch","year":"2013","journal-title":"J. Proteome.\nRes."},{"issue":"5","key":"2026081811150171800_cit21","doi-asserted-by":"publisher","first-page":"R76","DOI":"10.1186\/bcr2719","article-title":"Extreme loss of immunoreactive p-Akt and p-Erk1\/2 during\nroutine fixation of primary breast cancer","volume":"12","author":"Pinhel","year":"2010","journal-title":"Breast\nCancer Res."},{"issue":"3","key":"2026081811150171800_cit22","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1038\/labinvest.2014.139","article-title":"Preanalytical\nvariables and phosphoepitope expression\nin FFPE tissue: quantitative epitope assessment after variable cold\nischemic time","volume":"95","author":"Vassilakopoulou","year":"2015","journal-title":"Lab. Invest"},{"issue":"12","key":"2026081811150171800_cit23","doi-asserted-by":"publisher","first-page":"4338","DOI":"10.1158\/1078-0432.CCR-05-0422","article-title":"Stability of Phosphoprotein as a Biological Marker of Tumor Signaling","volume":"11","author":"Baker","year":"2005","journal-title":"Clinical. Cancer. Research"},{"key":"2026081811150171800_cit24","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1007\/s12014-010-9055-y","article-title":"A Technical Assessment\nof the Utility of Reverse Phase Protein Arrays for the Study of the\nFunctional Proteome in Non-microdissected Human Breast Cancers","volume":"6","author":"Hennessy","year":"2010","journal-title":"Clin. Proteomics"},{"issue":"6","key":"2026081811150171800_cit25","first-page":"2073","article-title":"Ischemic Time Impacts Biological\nIntegrity of Phospho-proteins in PI3K\/Akt, Erk\/MAPK, and p38 MAPK\nSignaling Networks","volume":"31","author":"Holzer","year":"2011","journal-title":"Anticancer Res."},{"issue":"6","key":"2026081811150171800_cit26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0021043","article-title":"Formalin Fixation at\nLow Temperature Better Preserves\nNucleic Acid Integrity","volume":"6","author":"Bussolati","year":"2011","journal-title":"PLoS One"},{"issue":"5","key":"2026081811150171800_cit27","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1369\/00221554231174069","article-title":"Epitope Lability of Phosphorylated\nBiomarkers of the\nDNA Damage Response Pathway Results in Increased Vulnerability to\nEffects of Delayed or Incomplete Formalin Fixation","volume":"71","author":"Wiseman","year":"2023","journal-title":"J. Histochem Cytochem"},{"key":"2026081811150171800_cit28","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/s12014-018-9202-4","article-title":"Residual tissue repositories\nas a resource for population-based cancer proteomic studies","volume":"15","author":"Piehowski","year":"2018","journal-title":"Clin Proteomics"},{"issue":"2","key":"2026081811150171800_cit29","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1021\/pr400960r","article-title":"Phosphoproteome Analysis of Formalin-Fixed\nand Paraffin-Embedded Tissue Sections Mounted on Microscope Slides","volume":"13","author":"Wakabayashi","year":"2014","journal-title":"J. Proteome. Res."},{"issue":"2","key":"2026081811150171800_cit30","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1002\/cncr.20774","article-title":"Akt phosphorylation\nis a risk factor for early disease recurrence and poor prognosis in\nhepatocellular carcinoma","volume":"103","author":"Nakanishi","year":"2005","journal-title":"Cancer"},{"issue":"3","key":"2026081811150171800_cit31","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1038\/modpathol.3800995","article-title":"Phospho-S6 ribosomal protein: a potential\nnew predictive\nsarcoma marker for targeted mTOR therapy","volume":"21","author":"Iwenofu","year":"2008","journal-title":"Modern\nPathology"},{"issue":"3","key":"2026081811150171800_cit32","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1007\/s10549-008-0267-z","article-title":"Immunohistochemical\nvalidation of multiple phospho-specific epitopes for estrogen receptor\n\u03b1 (ER\u03b1) in tissue microarrays of ER\u03b1 positive human\nbreast carcinomas","volume":"118","author":"Skliris","year":"2009","journal-title":"Breast Cancer Res. Treat"},{"issue":"1","key":"2026081811150171800_cit33","doi-asserted-by":"publisher","first-page":"22373","DOI":"10.1038\/s41598-022-26715-9","article-title":"A reverse\nphase protein array based phospho-antibody characterization approach\nand its applicability for clinical derived tissue specimens","volume":"12","author":"Wang","year":"2022","journal-title":"Sci. Rep"},{"issue":"10","key":"2026081811150171800_cit34","doi-asserted-by":"publisher","first-page":"1288","DOI":"10.1038\/s41374-020-0455-y","article-title":"Multiclass\ncancer classification\nin fresh frozen and formalin-fixed paraffin-embedded tissue by DigiWest\nmultiplex protein analysis","volume":"100","author":"Bockmayr","year":"2020","journal-title":"Lab. Invest"},{"key":"2026081811150171800_cit35","doi-asserted-by":"publisher","first-page":"391","DOI":"10.14670\/HH-23.391","article-title":"Isolation of high quality protein samples from punches\nof formalin fixed and paraffin embedded tissue blocks","volume":"23","author":"Kroll","year":"2008","journal-title":"Histol, Histopathol."},{"key":"2026081811150171800_cit36","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.202200085","article-title":"Comparison\nof matched formalin-fixed paraffin embedded and fresh frozen meningioma\ntissue reveals bias in proteomic profiles","volume":"22","author":"Schoffman","year":"2022","journal-title":"Proteomics"},{"issue":"10","key":"2026081811150171800_cit37","doi-asserted-by":"publisher","first-page":"4179","DOI":"10.1021\/acs.jproteome.0c00354","article-title":"Phosphorylation\nRatio Determination in Fresh-Frozen\nand Formalin-Fixed Paraffin-Embedded Tissue with Targeted Mass Spectrometry","volume":"19","author":"Zeneyedpour","year":"2020","journal-title":"J. Proteome. Res."},{"issue":"9","key":"2026081811150171800_cit38","doi-asserted-by":"publisher","first-page":"2237","DOI":"10.1021\/acs.jproteome.2c00409","article-title":"In-Depth\nMass Spectrometry-Based Proteomics\nof Formalin-Fixed, Paraffin-Embedded Tissues with a Spatial Resolution\nof 50-200 mum","volume":"21","author":"Nwosu","year":"2022","journal-title":"J. Proteome. Res."},{"key":"2026081811150171800_cit39","unstructured":"Xue, C.\n          , Sensitive, Accurate\nInvestigation of Biotherapeutics and Biomarker\/Target Levels in Both\nFresh and FFPE Tissues. Master of Science Thesis,\nState University of New York at Buffalo, 2020."},{"issue":"2","key":"2026081811150171800_cit40","doi-asserted-by":"publisher","first-page":"973","DOI":"10.1021\/acs.jproteome.9b00686","article-title":"HYPERsol:\nHigh-Quality\nData from Archival FFPE Tissue for Clinical Proteomics","volume":"19","author":"Marchione","year":"2020","journal-title":"J. Proteome. Res."},{"issue":"7","key":"2026081811150171800_cit41","doi-asserted-by":"publisher","first-page":"2907","DOI":"10.1021\/acs.jproteome.0c00334","article-title":"Accelerated\nLysis and Proteolytic Digestion of Biopsy-Level\nFresh-Frozen and FFPE Tissue Samples Using Pressure Cycling Technology","volume":"19","author":"Gao","year":"2020","journal-title":"J. Proteome. Res."},{"issue":"11","key":"2026081811150171800_cit42","doi-asserted-by":"publisher","first-page":"2305","DOI":"10.1002\/1878-0261.12570","article-title":"High-throughput proteomic analysis of FFPE\ntissue samples facilitates\ntumor stratification","volume":"13","author":"Zhu","year":"2019","journal-title":"Mol. Oncol"},{"issue":"9","key":"2026081811150171800_cit43","doi-asserted-by":"publisher","first-page":"5841","DOI":"10.1021\/acs.analchem.8b00379","article-title":"Parallel Proteomic Workflow for Mass Spectrometric\nAnalysis of Tissue Samples Preserved by Different Methods","volume":"90","author":"Holfeld","year":"2018","journal-title":"Anal. Chem."},{"issue":"8","key":"2026081811150171800_cit44","doi-asserted-by":"publisher","first-page":"1988","DOI":"10.1074\/mcp.M800518-MCP200","article-title":"Equivalence\nof Protein Inventories\nObtained from Formalin-fixed Paraffin-embedded and Frozen Tissue in\nMultidimensional Liquid Chromatography-Tandem Mass Spectrometry Shotgun\nProteomic Analysis","volume":"8","author":"Sprung","year":"2009","journal-title":"Mol. Cell. Proteomics"},{"issue":"8","key":"2026081811150171800_cit45","doi-asserted-by":"publisher","DOI":"10.1002\/ctm2.466","article-title":"A biobanking turning-point in the use of formalin-fixed,\nparaffin tumor blocks to unveil kinase signaling in melanoma","volume":"11","author":"Velasquez","year":"2021","journal-title":"Clin. Transl. Med."},{"key":"2026081811150171800_cit46","doi-asserted-by":"publisher","first-page":"13358","DOI":"10.1021\/acs.analchem.3c04479","article-title":"Quantitative\ncomparison of deparaffinisation, rehydration and extraction methods\nfor FFPE tissue proteomics and phosphoproteomics","volume":"96","author":"Humphries","year":"2024","journal-title":"Anal. Chem."},{"issue":"27","key":"2026081811150171800_cit47","doi-asserted-by":"publisher","first-page":"4093","DOI":"10.1021\/acs.analchem.3c04708","article-title":"Heat \u2018n\nBeat: A universal high-throughput end-to-end proteomics sample processing\nplatform in under an hour","volume":"96","author":"Xavier","year":"2024","journal-title":"Anal. Chem."},{"key":"2026081811150171800_cit48","doi-asserted-by":"publisher","first-page":"2355","DOI":"10.1021\/acs.jproteome.4c00010","article-title":"High-Throughput\nProteomics and Phosphoproteomics of Rat Tissues Using Microflow Zeno\nSWATH","volume":"23","author":"Humphries","year":"2024","journal-title":"J. Proteome. Res."},{"key":"2026081811150171800_cit49","doi-asserted-by":"publisher","DOI":"10.1101\/2023.10.11.561927","article-title":"Optimising\nSpectronaut search parameters to improve data quality with minimal\nproteome coverage reductions in DIA analyses of heterogeneous samples","author":"Baker","year":"2023","journal-title":"bioRxiv"},{"issue":"1","key":"2026081811150171800_cit50","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1186\/1471-2164-9-488","article-title":"BioVenn\u2013a web application\nfor the comparison and visualization of biological lists using area-proportional\nVenn diagrams","volume":"9","author":"Hulsen","year":"2008","journal-title":"BMC Genomics"},{"issue":"2","key":"2026081811150171800_cit51","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1021\/acs.jproteome.8b00523","article-title":"NormalyzerDE:\nOnline Tool for Improved\nNormalization of Omics Expression Data and High-Sensitivity Differential\nExpression Analysis","volume":"18","author":"Willforss","year":"2019","journal-title":"J. Proteome. Res."},{"issue":"1","key":"2026081811150171800_cit52","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1038\/s41467-020-14609-1","article-title":"Rapid and site-specific deep phosphoproteome profiling\nby data-independent acquisition without the need for spectral libraries","volume":"11","author":"Bekker-Jensen","year":"2020","journal-title":"Nat. Commun."},{"issue":"5","key":"2026081811150171800_cit53","doi-asserted-by":"publisher","first-page":"1400","DOI":"10.1074\/mcp.M114.044305","article-title":"Extending\nthe limits of quantitative proteome profiling with data-independent\nacquisition and application to acetaminophen-treated three-dimensional\nliver microtissues","volume":"14","author":"Bruderer","year":"2015","journal-title":"Mol. Cell. Proteomics"},{"key":"2026081811150171800_cit54","doi-asserted-by":"publisher","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt:\nthe Universal Protein Knowledgebase in 2023","volume":"51","author":"The\nUniProt Consortium.","year":"2023","journal-title":"Nucleic Acids Res."},{"issue":"12","key":"2026081811150171800_cit55","doi-asserted-by":"publisher","first-page":"5402","DOI":"10.1021\/acs.jproteome.1c00695","article-title":"Evaluation of Disposable\nTrap Column\nnanoLC-FAIMS-MS\/MS for the Proteomic Analysis of FFPE Tissue","volume":"20","author":"Eckert","year":"2021","journal-title":"J. Proteome. Res."},{"issue":"5","key":"2026081811150171800_cit56","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcpro.2024.100754","article-title":"Systematic Optimization\nof Automated Phosphopeptide\nEnrichment for High-Sensitivity Phosphoproteomics","volume":"23","author":"Bortel","year":"2024","journal-title":"Mol. Cell. Proteomics"},{"issue":"7","key":"2026081811150171800_cit57","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1074\/mcp.T500007-MCP200","article-title":"Highly\nselective enrichment of phosphorylated peptides\nfrom peptide mixtures using titanium dioxide microcolumns","volume":"4","author":"Larsen","year":"2005","journal-title":"Mol. Cell. Proteomics"},{"issue":"4","key":"2026081811150171800_cit58","doi-asserted-by":"publisher","first-page":"1929","DOI":"10.1038\/nprot.2006.185","article-title":"Highly selective\nenrichment of phosphorylated peptides using titanium dioxide","volume":"1","author":"Thingholm","year":"2006","journal-title":"Nat. Protoc"},{"issue":"18","key":"2026081811150171800_cit59","doi-asserted-by":"publisher","first-page":"5749","DOI":"10.1016\/j.jprot.2012.08.007","article-title":"TiSH - a robust\nand sensitive global phosphoproteomics\nstrategy employing a combination of TiO2, SIMAC, and HILIC","volume":"75","author":"Engholm-Keller","year":"2012","journal-title":"J. Proteomics"},{"key":"2026081811150171800_cit60","doi-asserted-by":"publisher","DOI":"10.1101\/2023.04.04.535617","article-title":"\u03bcPhos:\na scalable and sensitive platform for functional phosphoproteomics","author":"Denys","year":"2023","journal-title":"bioRxiv"},{"issue":"9","key":"2026081811150171800_cit61","doi-asserted-by":"publisher","first-page":"1897","DOI":"10.1038\/s41596-018-0014-9","article-title":"High-throughput and\nhigh-sensitivity phosphoproteomics with the EasyPhos platform","volume":"13","author":"Humphrey","year":"2018","journal-title":"Nat. Protoc."},{"issue":"1","key":"2026081811150171800_cit62","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1021\/acs.jproteome.0c00508","article-title":"Zirconium\u00ad(IV)-IMAC Revisited: Improved Performance\nand Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide\nAffinity Enrichment","volume":"20","author":"Arribas\nDiez","year":"2021","journal-title":"J. Proteome. Res."}],"container-title":["ACS Omega"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acsomega.4c09289","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/10\/7\/6891\/40792497\/ao4c09289.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/10\/7\/6891\/40792497\/ao4c09289.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T17:52:22Z","timestamp":1787075542000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/acsodf\/article\/10\/7\/6891\/3652040\/Overlap-of-Formalin-Fixed-Paraffin-Embedded-and"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,16]]},"references-count":62,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2025,2,16]]},"published-print":{"date-parts":[[2025,2,25]]}},"URL":"https:\/\/doi.org\/10.1021\/acsomega.4c09289","relation":{},"ISSN":["2470-1343"],"issn-type":[{"value":"2470-1343","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,16]]}}}