{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T18:16:43Z","timestamp":1776795403680,"version":"3.51.2"},"reference-count":77,"publisher":"Elsevier BV","issue":"11","license":[{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,9,14]],"date-time":"2023-09-14T00:00:00Z","timestamp":1694649600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 CA216051"],"award-info":[{"award-number":["R01 CA216051"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 CA244236"],"award-info":[{"award-number":["R01 CA244236"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["30 CA091842"],"award-info":[{"award-number":["30 CA091842"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["1 TR002345"],"award-info":[{"award-number":["1 TR002345"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007930","name":"Institute of Clinical and Translational Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007930","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["mcponline.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Molecular & Cellular Proteomics"],"published-print":{"date-parts":[[2023,11]]},"DOI":"10.1016\/j.mcpro.2023.100647","type":"journal-article","created":{"date-parts":[[2023,9,15]],"date-time":"2023-09-15T04:36:03Z","timestamp":1694752563000},"page":"100647","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":18,"title":["Targeted Proteomic Quantitation of NRF2 Signaling and Predictive Biomarkers in HNSCC"],"prefix":"10.1016","volume":"22","author":[{"given":"Nathan T.","family":"Wamsley","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9360-7340","authenticated-orcid":false,"given":"Emily M.","family":"Wilkerson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Guan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7571-4222","authenticated-orcid":false,"given":"Kyle M.","family":"LaPak","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Travis P.","family":"Schrank","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3374-050X","authenticated-orcid":false,"given":"Brittany J.","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2368-8859","authenticated-orcid":false,"given":"Robert W.","family":"Sprung","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Petra Erdmann","family":"Gilmore","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9918-453X","authenticated-orcid":false,"given":"Sophie P.","family":"Gerndt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4626-2324","authenticated-orcid":false,"given":"Ryan S.","family":"Jackson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Randal C.","family":"Paniello","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrik","family":"Pipkorn","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sidharth V.","family":"Puram","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jason T.","family":"Rich","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reid R.","family":"Townsend","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e9 P.","family":"Zevallos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9475-1686","authenticated-orcid":false,"given":"Paul","family":"Zolkind","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Quynh-Thu","family":"Le","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1584-5423","authenticated-orcid":false,"given":"Dennis","family":"Goldfarb","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael B.","family":"Major","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.mcpro.2023.100647_bib1","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/s41572-020-00224-3","article-title":"Head and neck squamous cell carcinoma","volume":"6","author":"Johnson","year":"2020","journal-title":"Nat. Rev. Dis. Primers"},{"key":"10.1016\/j.mcpro.2023.100647_bib2","first-page":"7","article-title":"Cancer statistics, 2022","volume":"72","author":"Siegel","year":"2022","journal-title":"CA Cancer J. Clin."},{"key":"10.1016\/j.mcpro.2023.100647_bib3","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/s41416-019-0602-7","article-title":"Human papillomavirus as a driver of head and neck cancers","volume":"122","author":"Sabatini","year":"2020","journal-title":"Br. J. Cancer"},{"key":"10.1016\/j.mcpro.2023.100647_bib4","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1056\/NEJMoa0912217","article-title":"Human papillomavirus and survival of patients with oropharyngeal cancer","volume":"363","author":"Ang","year":"2010","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.mcpro.2023.100647_bib5","doi-asserted-by":"crossref","first-page":"2289","DOI":"10.1016\/S0140-6736(21)01550-6","article-title":"Head and neck cancer","volume":"398","author":"Mody","year":"2021","journal-title":"Lancet"},{"key":"10.1016\/j.mcpro.2023.100647_bib6","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1038\/s41416-018-0131-9","article-title":"Efficacy and safety of pembrolizumab in recurrent\/metastatic head and neck squamous cell carcinoma: pooled analyses after long-term follow-up in KEYNOTE-012","volume":"119","author":"Mehra","year":"2018","journal-title":"Br. J. Cancer"},{"key":"10.1016\/j.mcpro.2023.100647_bib7","article-title":"Immunotherapy in head and neck squamous cell carcinoma: an updated review","volume":"33","author":"Parmar","year":"2022","journal-title":"Cancer Treat Res. Commun."},{"key":"10.1016\/j.mcpro.2023.100647_bib8","doi-asserted-by":"crossref","first-page":"13568","DOI":"10.1073\/pnas.0806268105","article-title":"Cancer related mutations in NRF2 impair its recognition by Keap1-Cul3 E3 ligase and promote malignancy","volume":"105","author":"Shibata","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2023.100647_bib9","doi-asserted-by":"crossref","first-page":"1627","DOI":"10.1089\/ars.2010.3219","article-title":"Gain of Nrf2 function in non-small-cell lung cancer cells confers radioresistance","volume":"13","author":"Singh","year":"2010","journal-title":"Antioxid. Redox Signal."},{"key":"10.1016\/j.mcpro.2023.100647_bib10","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s12885-017-3907-z","article-title":"Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer","volume":"18","author":"Namani","year":"2018","journal-title":"BMC Cancer"},{"key":"10.1016\/j.mcpro.2023.100647_bib11","doi-asserted-by":"crossref","first-page":"675","DOI":"10.21873\/cgp.20289","article-title":"SOD2- and NRF2-associated gene signature to predict radioresistance in head and neck cancer","volume":"18","author":"Noh","year":"2021","journal-title":"Cancer Genomics Proteomics"},{"key":"10.1016\/j.mcpro.2023.100647_bib12","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1038\/s41374-022-00776-w","article-title":"The antioxidative stress regulator Nrf2 potentiates radioresistance of oral squamous cell carcinoma accompanied with metabolic modulation","volume":"102","author":"Matsuoka","year":"2022","journal-title":"Lab. Invest."},{"key":"10.1016\/j.mcpro.2023.100647_bib13","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1002\/lio2.588","article-title":"Correlation of alterations in the KEAP1\/CUL3\/NFE2L2 pathway with radiation failure in larynx squamous cell carcinoma","volume":"6","author":"Sheth","year":"2021","journal-title":"Laryngoscope Investig. Otolaryngol."},{"key":"10.1016\/j.mcpro.2023.100647_bib14","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1158\/0008-5472.CAN-22-1903","article-title":"NFE2L2 mutations enhance radioresistance in head and neck cancer by modulating intratumoral myeloid cells","volume":"83","author":"Guan","year":"2023","journal-title":"Cancer Res."},{"key":"10.1016\/j.mcpro.2023.100647_bib15","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1158\/0008-5472.CAN-18-2723","article-title":"NRF2 activation in cancer: from DNA to protein","volume":"79","author":"Cloer","year":"2019","journal-title":"Cancer Res."},{"key":"10.1016\/j.mcpro.2023.100647_bib16","article-title":"Influence of tumor mutational burden, inflammatory gene expression profile, and PD-L1 expression on response to pembrolizumab in head and neck squamous cell carcinoma","volume":"10","author":"Haddad","year":"2022","journal-title":"J.\u00a0Immunother. Cancer"},{"key":"10.1016\/j.mcpro.2023.100647_bib17","doi-asserted-by":"crossref","DOI":"10.1016\/j.ctrv.2020.101977","article-title":"Biomarkers for immunotherapy response in head and neck cancer","volume":"84","author":"Gavrielatou","year":"2020","journal-title":"Cancer Treat Rev."},{"key":"10.1016\/j.mcpro.2023.100647_bib18","doi-asserted-by":"crossref","DOI":"10.1126\/science.aar3593","article-title":"Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy","volume":"362","author":"Cristescu","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.mcpro.2023.100647_bib19","doi-asserted-by":"crossref","first-page":"2930","DOI":"10.1172\/JCI91190","article-title":"IFN-gamma-related mRNA profile predicts clinical response to PD-1 blockade","volume":"127","author":"Ayers","year":"2017","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.mcpro.2023.100647_bib20","doi-asserted-by":"crossref","first-page":"8477","DOI":"10.1128\/MCB.24.19.8477-8486.2004","article-title":"The Keap1-BTB protein is an adaptor that bridges Nrf2 to a Cul3-based E3 ligase: oxidative stress sensing by a Cul3-Keap1 ligase","volume":"24","author":"Cullinan","year":"2004","journal-title":"Mol. Cell Biol."},{"key":"10.1016\/j.mcpro.2023.100647_bib21","doi-asserted-by":"crossref","first-page":"7130","DOI":"10.1128\/MCB.24.16.7130-7139.2004","article-title":"Oxidative stress sensor Keap1 functions as an adaptor for Cul3-based E3 ligase to regulate proteasomal degradation of Nrf2","volume":"24","author":"Kobayashi","year":"2004","journal-title":"Mol. Cell Biol."},{"key":"10.1016\/j.mcpro.2023.100647_bib22","doi-asserted-by":"crossref","first-page":"10941","DOI":"10.1128\/MCB.24.24.10941-10953.2004","article-title":"Keap1 is a redox-regulated substrate adaptor protein for a Cul3-dependent ubiquitin ligase complex","volume":"24","author":"Zhang","year":"2004","journal-title":"Mol. Cell Biol."},{"key":"10.1016\/j.mcpro.2023.100647_bib23","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1152\/physrev.00023.2017","article-title":"The KEAP1-NRF2 system: a thiol-based sensor-effector apparatus for maintaining redox homeostasis","volume":"98","author":"Yamamoto","year":"2018","journal-title":"Physiol. Rev."},{"key":"10.1016\/j.mcpro.2023.100647_bib24","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/s41573-018-0008-x","article-title":"Therapeutic targeting of the NRF2 and KEAP1 partnership in chronic diseases","volume":"18","author":"Cuadrado","year":"2019","journal-title":"Nat. Rev. Drug Discov."},{"key":"10.1016\/j.mcpro.2023.100647_bib25","doi-asserted-by":"crossref","first-page":"716","DOI":"10.3390\/antiox9080716","article-title":"Current landscape of NRF2 biomarkers in clinical trials","volume":"9","author":"Yagishita","year":"2020","journal-title":"Antioxidants (Basel)"},{"key":"10.1016\/j.mcpro.2023.100647_bib26","doi-asserted-by":"crossref","first-page":"310","DOI":"10.3389\/fonc.2018.00310","article-title":"Immune checkpoint inhibition in head and neck cancer","volume":"8","author":"Forster","year":"2018","journal-title":"Front. Oncol."},{"key":"10.1016\/j.mcpro.2023.100647_bib27","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1038\/s41388-020-01611-6","article-title":"Is PD-L1 a consistent biomarker for anti-PD-1 therapy? The model of balstilimab in a virally-driven tumor","volume":"40","author":"Grossman","year":"2021","journal-title":"Oncogene"},{"key":"10.1016\/j.mcpro.2023.100647_bib28","doi-asserted-by":"crossref","first-page":"1705","DOI":"10.1074\/mcp.RA117.000037","article-title":"Quantitative mass spectrometry analysis of PD-L1 protein expression, N-glycosylation and expression stoichiometry with PD-1 and PD-L2 in human melanoma","volume":"16","author":"Morales-Betanzos","year":"2017","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2023.100647_bib29","doi-asserted-by":"crossref","first-page":"9805","DOI":"10.1038\/s41598-020-66902-0","article-title":"Analysis of immune checkpoint drug targets and tumor proteotypes in non-small cell lung cancer","volume":"10","author":"Liebler","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.mcpro.2023.100647_bib30","doi-asserted-by":"crossref","first-page":"e8503","DOI":"10.15252\/msb.20188503","article-title":"A\u00a0deep proteome and transcriptome abundance atlas of 29 healthy human tissues","volume":"15","author":"Wang","year":"2019","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.mcpro.2023.100647_bib31","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.cell.2019.12.023","article-title":"Quantitative proteomics of the cancer cell line encyclopedia","volume":"180","author":"Nusinow","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.mcpro.2023.100647_bib32","doi-asserted-by":"crossref","first-page":"4941","DOI":"10.1038\/s41388-018-0314-0","article-title":"Targeting the upstream transcriptional activator of PD-L1 as an alternative strategy in melanoma therapy","volume":"37","author":"Zhu","year":"2018","journal-title":"Oncogene"},{"key":"10.1016\/j.mcpro.2023.100647_bib33","doi-asserted-by":"crossref","DOI":"10.1016\/j.redox.2023.102644","article-title":"A\u00a0pan-cancer analysis shows immunoevasive characteristics in NRF2 hyperactive squamous malignancies","volume":"61","author":"Harkonen","year":"2023","journal-title":"Redox Biol."},{"key":"10.1016\/j.mcpro.2023.100647_bib34","article-title":"Glutathione peroxidase 2 is a metabolic driver of the tumor immune microenvironment and immune checkpoint inhibitor response","volume":"10","author":"Ahmed","year":"2022","journal-title":"J.\u00a0Immunother. Cancer"},{"key":"10.1016\/j.mcpro.2023.100647_bib35","doi-asserted-by":"crossref","DOI":"10.1136\/esmoopen-2020-000706","article-title":"STK11 and KEAP1 mutations as prognostic biomarkers in an observational real-world lung adenocarcinoma cohort","volume":"5","author":"Papillon-Cavanagh","year":"2020","journal-title":"ESMO Open"},{"key":"10.1016\/j.mcpro.2023.100647_bib36","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1038\/s41588-021-00778-2","article-title":"Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens","volume":"53","author":"Papalexi","year":"2021","journal-title":"Nat. Genet."},{"key":"10.1016\/j.mcpro.2023.100647_bib37","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1074\/mcp.O114.043968","article-title":"Large-Scale targeted proteomics using internal standard triggered-parallel reaction monitoring (IS-PRM)","volume":"14","author":"Gallien","year":"2015","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2023.100647_bib38","doi-asserted-by":"crossref","first-page":"2495","DOI":"10.1158\/0008-5472.CAN-20-3804","article-title":"High-density, targeted monitoring of tyrosine phosphorylation reveals activated signaling networks in human tumors","volume":"81","author":"Stopfer","year":"2021","journal-title":"Cancer Res."},{"key":"10.1016\/j.mcpro.2023.100647_bib39","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2111173118","article-title":"Absolute quantification of tumor antigens using embedded MHC-I isotopologue calibrants","volume":"118","author":"Stopfer","year":"2021","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2023.100647_bib40","doi-asserted-by":"crossref","first-page":"8836","DOI":"10.1038\/s41598-019-45237-5","article-title":"A\u00a0sensitive and simple targeted proteomics approach to quantify transcription factor and membrane proteins of the unfolded protein response pathway in glioblastoma cells","volume":"9","author":"Nguyen","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.mcpro.2023.100647_bib41","series-title":"SureQuant Intelligence-Driven MS: A New Paradigm for Targeted Quantitation","author":"Gajadhar","year":"2020"},{"key":"10.1016\/j.mcpro.2023.100647_bib42","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1002\/path.5420","article-title":"A\u00a0streamlined mass spectrometry\u2013based proteomics workflow for large-scale FFPE tissue analysis","volume":"251","author":"Coscia","year":"2020","journal-title":"J.\u00a0Pathol."},{"key":"10.1016\/j.mcpro.2023.100647_bib43","doi-asserted-by":"crossref","first-page":"3930","DOI":"10.1158\/0008-5472.CAN-21-0214","article-title":"Quantitative analysis of tyrosine phosphorylation from FFPE tissues reveals patient-specific signaling networks","volume":"81","author":"Kohale","year":"2021","journal-title":"Cancer Res."},{"key":"10.1016\/j.mcpro.2023.100647_bib44","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1074\/mcp.M113.036095","article-title":"Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach","volume":"13","author":"Carr","year":"2014","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2023.100647_bib45","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/nmeth.4153","article-title":"Building ProteomeTools based on a complete synthetic human proteome","volume":"14","author":"Zolg","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.mcpro.2023.100647_bib46","doi-asserted-by":"crossref","first-page":"D512","DOI":"10.1093\/nar\/gku1267","article-title":"PhosphoSitePlus, 2014: mutations, PTMs and recalibrations","volume":"43","author":"Hornbeck","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mcpro.2023.100647_bib47","doi-asserted-by":"crossref","first-page":"D1271","DOI":"10.1093\/nar\/gkx1029","article-title":"Proteomicsdb","volume":"46","author":"Schmidt","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mcpro.2023.100647_bib48","doi-asserted-by":"crossref","first-page":"13434","DOI":"10.1021\/acs.analchem.1c01375","article-title":"Global extraction from parallel reaction monitoring to quantify background peptides for improved normalization and quality control in targeted proteomics","volume":"93","author":"Chambers","year":"2021","journal-title":"Anal. Chem."},{"key":"10.1016\/j.mcpro.2023.100647_bib49","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/nbt.2377","article-title":"A\u00a0cross-platform toolkit for mass spectrometry and proteomics","volume":"30","author":"Chambers","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.mcpro.2023.100647_bib50","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1021\/pr301024c","article-title":"A\u00a0proteomics search algorithm specifically designed for high-resolution tandem mass spectra","volume":"12","author":"Wenger","year":"2013","journal-title":"J.\u00a0Proteome Res."},{"key":"10.1016\/j.mcpro.2023.100647_bib51","first-page":"2825","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Fabian Pedregosa","year":"2011","journal-title":"J.\u00a0Machine Learn. Res."},{"key":"10.1016\/j.mcpro.2023.100647_bib52","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"Cox","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.mcpro.2023.100647_bib53","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1074\/mcp.M115.054510","article-title":"Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translational modification patterns in patient samples","volume":"15","author":"Noberini","year":"2016","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2023.100647_bib54","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.2023.100647_bib55","doi-asserted-by":"crossref","first-page":"2513","DOI":"10.1074\/mcp.M113.031591","article-title":"Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ","volume":"13","author":"Cox","year":"2014","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2023.100647_bib56","doi-asserted-by":"crossref","first-page":"4348","DOI":"10.1016\/j.cell.2021.07.016","article-title":"A\u00a0proteogenomic portrait of lung squamous cell carcinoma","volume":"184","author":"Satpathy","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.mcpro.2023.100647_bib57","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/j.ccell.2020.12.007","article-title":"Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma","volume":"39","author":"Huang","year":"2021","journal-title":"Cancer Cell"},{"key":"10.1016\/j.mcpro.2023.100647_bib58","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.2023.100647_bib59","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.cell.2016.03.014","article-title":"On the dependency of cellular protein levels on mRNA abundance","volume":"165","author":"Liu","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.mcpro.2023.100647_bib60","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1002\/path.5504","article-title":"A\u00a0conditional mouse expressing an activating mutation in NRF2 displays hyperplasia of the upper gastrointestinal tract and decreased white adipose tissue","volume":"252","author":"Bowman","year":"2020","journal-title":"J.\u00a0Pathol."},{"key":"10.1016\/j.mcpro.2023.100647_bib61","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.\u00a0Proteome Res."},{"key":"10.1016\/j.mcpro.2023.100647_bib62","doi-asserted-by":"crossref","first-page":"3291","DOI":"10.1021\/acs.analchem.2c04264","article-title":"ASAP horizontal line automated sonication-free acid-assisted proteomes horizontal line from cells and FFPE tissues","volume":"95","author":"Barnabas","year":"2023","journal-title":"Anal. Chem."},{"key":"10.1016\/j.mcpro.2023.100647_bib63","doi-asserted-by":"crossref","first-page":"1538","DOI":"10.1038\/s41467-018-04004-2","article-title":"Nuclear receptor NR2F6 inhibition potentiates responses to PD-L1\/PD-1 cancer immune checkpoint blockade","volume":"9","author":"Klepsch","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2023.100647_bib64","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/j.immuni.2008.06.008","article-title":"The nuclear orphan receptor NR2F6 suppresses lymphocyte activation and T helper 17-dependent autoimmunity","volume":"29","author":"Hermann-Kleiter","year":"2008","journal-title":"Immunity"},{"key":"10.1016\/j.mcpro.2023.100647_bib65","doi-asserted-by":"crossref","first-page":"3274","DOI":"10.1038\/s41388-018-0633-1","article-title":"Topoisomerase IIbeta-binding protein 1 activates expression of E2F1 and p73 in HPV-positive cells for genome amplification upon epithelial differentiation","volume":"38","author":"Hong","year":"2019","journal-title":"Oncogene"},{"key":"10.1016\/j.mcpro.2023.100647_bib66","doi-asserted-by":"crossref","first-page":"6250","DOI":"10.1158\/1078-0432.CCR-20-4789","article-title":"Recurrent human papillomavirus-related head and neck cancer undergoes metabolic reprogramming and is driven by oxidative phosphorylation","volume":"27","author":"Vyas","year":"2021","journal-title":"Clin. Cancer Res."},{"key":"10.1016\/j.mcpro.2023.100647_bib67","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1002\/hed.27019","article-title":"Treatment de-escalation for HPV+ oropharyngeal cancer: a systematic review and meta-analysis","volume":"44","author":"Petrelli","year":"2022","journal-title":"Head Neck"},{"key":"10.1016\/j.mcpro.2023.100647_bib68","doi-asserted-by":"crossref","DOI":"10.1016\/j.oraloncology.2020.104652","article-title":"Deintensification of treatment for human papillomavirus-related oropharyngeal cancer: current state and future directions","volume":"105","author":"Bigelow","year":"2020","journal-title":"Oral Oncol."},{"key":"10.1016\/j.mcpro.2023.100647_bib69","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/s43856-022-00159-8","article-title":"Proteome and phosphoproteome signatures of recurrence for HPV(+) head and neck squamous cell carcinoma","volume":"2","author":"Kaneko","year":"2022","journal-title":"Commun. Med. (Lond)"},{"key":"10.1016\/j.mcpro.2023.100647_bib70","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/j.redox.2018.07.026","article-title":"A\u00a0distinct class of antioxidant response elements is consistently activated in tumors with NRF2 mutations","volume":"19","author":"Levings","year":"2018","journal-title":"Redox Biol."},{"key":"10.1016\/j.mcpro.2023.100647_bib71","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1016\/j.cels.2017.08.013","article-title":"Widespread post-transcriptional attenuation of genomic copy-number variation in cancer","volume":"5","author":"Goncalves","year":"2017","journal-title":"Cell Syst."},{"key":"10.1016\/j.mcpro.2023.100647_bib72","doi-asserted-by":"crossref","DOI":"10.1111\/aji.13249","article-title":"Cytokine mRNA and protein expression by cell cultures of epithelial ovarian cancer-Methodological considerations on the choice of analytical method for cytokine analyses","volume":"84","author":"Israelsson","year":"2020","journal-title":"Am. J. Reprod. Immunol."},{"key":"10.1016\/j.mcpro.2023.100647_bib73","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.jprot.2013.10.029","article-title":"Technical considerations for large-scale parallel reaction monitoring analysis","volume":"100","author":"Gallien","year":"2014","journal-title":"J.\u00a0Proteomics"},{"key":"10.1016\/j.mcpro.2023.100647_bib74","doi-asserted-by":"crossref","first-page":"2146","DOI":"10.1002\/pmic.201500543","article-title":"Parallel reaction monitoring using quadrupole-Orbitrap mass spectrometer: principle and applications","volume":"16","author":"Bourmaud","year":"2016","journal-title":"Proteomics"},{"key":"10.1016\/j.mcpro.2023.100647_bib75","doi-asserted-by":"crossref","first-page":"e55","DOI":"10.7717\/peerj-cs.55","article-title":"Probabilistic programming in Python using PyMC3","volume":"2","author":"Salvatier","year":"2016","journal-title":"PeerJ Comput. Sci."},{"key":"10.1016\/j.mcpro.2023.100647_bib76","doi-asserted-by":"crossref","first-page":"1902","DOI":"10.1021\/acs.jproteome.0c00919","article-title":"Simplified and unified access to cancer proteogenomic data","volume":"20","author":"Lindgren","year":"2021","journal-title":"J. Prot. Res."},{"key":"10.1016\/j.mcpro.2023.100647_bib77","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1056\/NEJMp1607591","article-title":"Toward a shared vision for cancer genomic data","volume":"375","author":"Grossman","year":"2016","journal-title":"New Engl. J. Med."}],"container-title":["Molecular & Cellular Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535947623001585?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535947623001585?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T01:15:29Z","timestamp":1761527729000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1535947623001585"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11]]},"references-count":77,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2023,11]]}},"alternative-id":["S1535947623001585"],"URL":"https:\/\/doi.org\/10.1016\/j.mcpro.2023.100647","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.03.13.532474","asserted-by":"object"}]},"ISSN":["1535-9476"],"issn-type":[{"value":"1535-9476","type":"print"}],"subject":[],"published":{"date-parts":[[2023,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Targeted Proteomic Quantitation of NRF2 Signaling and Predictive Biomarkers in HNSCC","name":"articletitle","label":"Article Title"},{"value":"Molecular & Cellular Proteomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.mcpro.2023.100647","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology.","name":"copyright","label":"Copyright"}],"article-number":"100647"}}