{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T00:56:54Z","timestamp":1792803414387,"version":"4.5.0"},"reference-count":246,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2021,5,21]],"date-time":"2021-05-21T00:00:00Z","timestamp":1621555200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Chinese NSFC","award":["81821002"],"award-info":[{"award-number":["81821002"]}]},{"name":"Chinese NSFC","award":["81790251"],"award-info":[{"award-number":["81790251"]}]},{"name":"National Key Research and Development Project of China","award":["2020YFA0509400"],"award-info":[{"award-number":["2020YFA0509400"]}]},{"name":"National Key Research and Development Project of China","award":["2020YFC2002705"],"award-info":[{"award-number":["2020YFC2002705"]}]},{"name":"Guangdong Basic and Applied Basic Research Foundation","award":["2019B030302012"],"award-info":[{"award-number":["2019B030302012"]}]},{"name":"Sichuan Applied Basic Research Project","award":["2020YJ0107"],"award-info":[{"award-number":["2020YJ0107"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>As of 2020 the human genome and proteome are both at &gt;90% completion based on high stringency analyses. This has been largely achieved by major technological advances over the last 20 years and has enlarged our understanding of human health and disease, including cancer, and is supporting the current trend towards personalized\/precision medicine. This is due to improved screening, novel therapeutic approaches and an increased understanding of underlying cancer biology. However, cancer is a complex, heterogeneous disease modulated by genetic, molecular, cellular, tissue, population, environmental and socioeconomic factors, which evolve with time. In spite of recent advances in treatment that have resulted in improved patient outcomes, prognosis is still poor for many patients with certain cancers (e.g., mesothelioma, pancreatic and brain cancer) with a high death rate associated with late diagnosis. In this review we overview key hallmarks of cancer (e.g., autophagy, the role of redox signaling), current unmet clinical needs, the requirement for sensitive and specific biomarkers for early detection, surveillance, prognosis and drug monitoring, the role of the microbiome and the goals of personalized\/precision medicine, discussing how emerging omics technologies can further inform on these areas. Exemplars from recent onco-proteogenomic-related publications will be given. Finally, we will address future perspectives, not only from the standpoint of perceived advances in treatment, but also from the hurdles that have to be overcome.<\/jats:p>","DOI":"10.3390\/cancers13112512","type":"journal-article","created":{"date-parts":[[2021,5,21]],"date-time":"2021-05-21T13:15:15Z","timestamp":1621602915000},"page":"2512","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":82,"title":["Proteomics, Personalized Medicine and Cancer"],"prefix":"10.3390","volume":"13","author":[{"given":"Miao","family":"Su","sequence":"first","affiliation":[{"name":"State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences &amp; Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhe","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences &amp; Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Zhou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences &amp; Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao","family":"Han","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences &amp; Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Canhua","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences &amp; Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5480-4715","authenticated-orcid":false,"given":"Edouard C.","family":"Nice","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,5,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"209","DOI":"10.3322\/caac.21660","article-title":"Global cancer statistics 2020: Globocan estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"71","author":"Sung","year":"2021","journal-title":"CA Cancer J. Clin."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3322\/caac.21654","article-title":"Cancer statistics, 2021","volume":"71","author":"Siegel","year":"2021","journal-title":"CA Cancer J. Clin."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2513","DOI":"10.1200\/JCO.2005.00.992","article-title":"Mutations of the epidermal growth factor receptor gene predict prolonged survival after gefitinib treatment in patients with non-small-cell lung cancer with postoperative recurrence","volume":"23","author":"Mitsudomi","year":"2005","journal-title":"J. Clin. Oncol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Middleton, J., Stover, D., and Hai, T. (2018). Chemotherapy-exacerbated breast cancer metastasis: A paradox explainable by dysregulated adaptive-response. Int. J. Mol. Sci., 19.","DOI":"10.20944\/preprints201808.0489.v1"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"eaan0026","DOI":"10.1126\/scitranslmed.aan0026","article-title":"Neoadjuvant chemotherapy induces breast cancer metastasis through a tmem-mediated mechanism","volume":"9","author":"Karagiannis","year":"2017","journal-title":"Sci. Transl. Med."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"188519","DOI":"10.1016\/j.bbcan.2021.188519","article-title":"Long non-coding rnas and cancer metastasis: Molecular basis and therapeutic implications","volume":"1875","author":"Ming","year":"2021","journal-title":"Biochim. Biophys. Acta Rev. Cancer"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/j.canlet.2015.03.038","article-title":"Ac1mmyr2 impairs high dose paclitaxel-induced tumor metastasis by targeting mir-21\/cdk5 axis","volume":"362","author":"Ren","year":"2015","journal-title":"Cancer Lett."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Nice, E. (2020). The status of proteomics as we enter the 2020s: Towards personalised\/precision medicine. Anal. Biochem., 113840.","DOI":"10.1016\/j.ab.2020.113840"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1126\/science.1058040","article-title":"The sequence of the human genome","volume":"291","author":"Venter","year":"2001","journal-title":"Science"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"5301","DOI":"10.1038\/s41467-020-19045-9","article-title":"A high-stringency blueprint of the human proteome","volume":"11","author":"Adhikari","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/S0092-8674(00)81683-9","article-title":"The hallmarks of cancer","volume":"100","author":"Hanahan","year":"2000","journal-title":"Cell"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e4995","DOI":"10.1002\/bmc.4995","article-title":"The separation sciences, the front end to proteomics: An historical perspective","volume":"35","author":"Nice","year":"2021","journal-title":"Biomed. Chromatogr."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"4735","DOI":"10.1021\/acs.jproteome.0c00485","article-title":"Research on the human proteome reaches a major milestone: >90% of predicted human proteins now credibly detected, according to the hupo human proteome project","volume":"19","author":"Omenn","year":"2020","journal-title":"J. Proteome Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1042\/CS20050006","article-title":"The molecular make-up of a tumour: Proteomics in cancer research","volume":"108","author":"Kolch","year":"2005","journal-title":"Clin. Sci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"7436849","DOI":"10.1155\/2016\/7436849","article-title":"The size of the human proteome: The width and depth","volume":"2016","author":"Ponomarenko","year":"2016","journal-title":"Int. J. Anal. Chem."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"15434","DOI":"10.1021\/jacs.6b08787","article-title":"Simultaneous time-dependent surface-enhanced raman spectroscopy, metabolomics, and proteomics reveal cancer cell death mechanisms associated with gold nanorod photothermal therapy","volume":"138","author":"Ali","year":"2016","journal-title":"J. Am. Chem. Soc."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1090","DOI":"10.1002\/elps.11501601185","article-title":"Progress with gene-product mapping of the mollicutes: Mycoplasma genitalium","volume":"16","author":"Wasinger","year":"1995","journal-title":"Electrophoresis"},{"key":"ref_19","unstructured":"The Financial Times (The Financial Times, 2021). Proteomics: Searching for the Real Stuff of Life, The Financial Times."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Al-Wajeeh, A., Salhimi, S., Al-Mansoub, M., Khalid, I., Harvey, T., Latiff, A., and Ismail, M. (2020). Comparative proteomic analysis of different stages of breast cancer tissues using ultra high performance liquid chromatography tandem mass spectrometer. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0227404"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.chroma.2007.06.015","article-title":"Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomics analysis","volume":"1168","author":"Nice","year":"2007","journal-title":"J. Chromatogr. A"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Duong, V., Park, J., and Lee, H. (2020). Review of three-dimensional liquid chromatography platforms for bottom-up proteomics. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21041524"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1021\/acs.analchem.8b04894","article-title":"Recent advances in multidimensional separation for proteome analysis","volume":"91","author":"Yuan","year":"2019","journal-title":"Anal. Chem."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/978-3-319-41448-5_5","article-title":"Improving Proteome Coverage by Reducing Sample Complexity via Chromatography","volume":"919","author":"Kota","year":"2016","journal-title":"Adv Exp Med Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1021\/acs.jproteome.0c00670","article-title":"Extending the depth of human plasma proteome coverage using simple fractionation techniques","volume":"20","author":"Kaur","year":"2021","journal-title":"J. Proteome Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s12014-019-9255-z","article-title":"Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel","volume":"16","author":"Ahn","year":"2019","journal-title":"Clin. Proteom."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.cels.2016.03.002","article-title":"Proteomics moves into the fast lane","volume":"2","author":"Riley","year":"2016","journal-title":"Cell Syst."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1700180","DOI":"10.1002\/pmic.201700180","article-title":"What is targeted proteomics? A concise revision of targeted acquisition and targeted data analysis in mass spectrometry","volume":"17","year":"2017","journal-title":"Proteomics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1016\/j.cell.2016.06.041","article-title":"Human srmatlas: A resource of targeted assays to quantify the complete human proteome","volume":"166","author":"Kusebauch","year":"2016","journal-title":"Cell"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/nmeth.3234","article-title":"Dia mass spectrometry","volume":"12","author":"Doerr","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e8126","DOI":"10.15252\/msb.20178126","article-title":"Data-independent acquisition-based swath-ms for quantitative proteomics: A tutorial","volume":"14","author":"Ludwig","year":"2018","journal-title":"Mol. Syst. Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/s41467-017-00249-5","article-title":"Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of swath-mass spectrometry","volume":"8","author":"Collins","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1007\/978-1-4939-6990-6_20","article-title":"Quantitative mass spectrometry by isotope dilution and multiple reaction monitoring (mrm)","volume":"1606","author":"Russo","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/j.jprot.2014.10.017","article-title":"Parallel reaction monitoring (prm) and selected reaction monitoring (srm) exhibit comparable linearity, dynamic range and precision for targeted quantitative hdl proteomics","volume":"113","author":"Ronsein","year":"2015","journal-title":"J. Proteom."},{"key":"ref_35","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":"ref_36","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. Proteom."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1007\/978-1-4939-6730-8_23","article-title":"Itraq-based shotgun proteomics approach for relative protein quantification","volume":"1546","author":"Domont","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/978-1-4939-6740-7_4","article-title":"Label-based and label-free strategies for protein quantitation","volume":"1549","author":"Anand","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"O111-016717","DOI":"10.1074\/mcp.O111.016717","article-title":"Targeted data extraction of the ms\/ms spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis","volume":"11","author":"Gillet","year":"2012","journal-title":"Mol. Cell. Proteom."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1373\/clinchem.2018.300756","article-title":"Optimization and comparison of information-dependent acquisition (ida) to sequential window acquisition of all theoretical fragment ion spectra (swath) for high-resolution mass spectrometry in clinical toxicology","volume":"65","author":"Whitman","year":"2019","journal-title":"Clin. Chem."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1111\/1755-0998.13229","article-title":"Probing swath-ms as a tool for proteome level quantification in a nonmodel fish","volume":"20","author":"Monroe","year":"2020","journal-title":"Mol. Ecol. Resour."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.1016\/j.celrep.2016.06.086","article-title":"Tails n-terminomics and proteomics show protein degradation dominates over proteolytic processing by cathepsins in pancreatic tumors","volume":"16","author":"Prudova","year":"2016","journal-title":"Cell Rep."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1093\/oxfordjournals.aje.a115146","article-title":"A study of repeatability of dietary data over a seven-year period","volume":"129","author":"Jain","year":"1989","journal-title":"Am. J. Epidemiol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1136\/ard.2009.118919","article-title":"Itraq-based proteomic identification of leucine-rich alpha-2 glycoprotein as a novel inflammatory biomarker in autoimmune diseases","volume":"69","author":"Serada","year":"2010","journal-title":"Ann. Rheum. Dis."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"2745","DOI":"10.2147\/OTT.S153375","article-title":"Leucine-rich alpha-2-glycoprotein-1 is up-regulated in colorectal cancer and is a tumor promoter","volume":"11","author":"Zhang","year":"2018","journal-title":"OncoTargets Ther."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1002\/pros.23972","article-title":"Proteomic and transcriptomic profiling of pten gene-knockout mouse model of prostate cancer","volume":"80","author":"Zhang","year":"2020","journal-title":"Prostate"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"103414","DOI":"10.1016\/j.jprot.2019.103414","article-title":"Deciphering novel biomarkers of lymph node metastasis of thyroid papillary microcarcinoma using proteomic analysis of ultrasound-guided fine-needle aspiration biopsy samples","volume":"204","author":"Lin","year":"2019","journal-title":"J. Proteom."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1039\/D0CC06493A","article-title":"Mass defect-based carbonyl activated tags (mdcats) for multiplex data-independent acquisition proteome quantification","volume":"57","author":"Zhang","year":"2021","journal-title":"Chem. Commun."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"543997","DOI":"10.3389\/fonc.2020.543997","article-title":"An integrated quantitative proteomics workflow for cancer biomarker discovery and validation in plasma","volume":"10","author":"Kumar","year":"2020","journal-title":"Front. Oncol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"3175","DOI":"10.1002\/pmic.201500108","article-title":"Quantitative proteomics using silac: Principles, applications, and developments","volume":"15","author":"Chen","year":"2015","journal-title":"Proteomics"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1586\/14789450.2015.982538","article-title":"Super-silac: Current trends and future perspectives","volume":"12","author":"Shenoy","year":"2015","journal-title":"Expert Rev. Proteom."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1007\/s00726-010-0668-2","article-title":"Silac-based proteomic analysis to dissect the \"histone modification signature\" of human breast cancer cells","volume":"41","author":"Cuomo","year":"2011","journal-title":"Amino Acids"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"5973","DOI":"10.1021\/pr500860c","article-title":"Evaluation of data-dependent and -independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites","volume":"13","author":"Bauer","year":"2014","journal-title":"J. Proteome Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2261","DOI":"10.1074\/mcp.O115.050351","article-title":"Peptide immunoaffinity enrichment and targeted mass spectrometry enables multiplex, quantitative pharmacodynamic studies of phospho-signaling","volume":"14","author":"Whiteaker","year":"2015","journal-title":"Mol. Cell. Proteom."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"12407","DOI":"10.1021\/acs.analchem.0c02157","article-title":"Using two peptide isotopologues as internal standards for the streamlined quantification of low-abundance proteins by immuno-mrm and immuno-maldi","volume":"92","author":"Ibrahim","year":"2020","journal-title":"Anal. Chem."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"e1800042","DOI":"10.1002\/bies.201800042","article-title":"Targeted proteomics comes to the benchside and the bedside: Is it ready for us?","volume":"41","author":"Arora","year":"2019","journal-title":"BioEssays"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1038\/s41571-018-0135-7","article-title":"Clinical potential of mass spectrometry-based proteogenomics","volume":"16","author":"Zhang","year":"2019","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1093\/clinchem\/hvaa178","article-title":"Clinical application of multiple reaction monitoring-mass spectrometry to human epidermal growth factor receptor 2 measurements as a potential diagnostic tool for breast cancer therapy","volume":"66","author":"Do","year":"2020","journal-title":"Clin. Chem."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1926","DOI":"10.1002\/elps.201000502","article-title":"Use of multiple reaction monitoring for multiplex analysis of colorectal cancer-associated proteins in human feces","volume":"32","author":"Ang","year":"2011","journal-title":"Electrophoresis"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"103780","DOI":"10.1016\/j.jprot.2020.103780","article-title":"Identification of noninvasive diagnostic biomarkers for hepatocellular carcinoma by urinary proteomics","volume":"225","author":"Zhao","year":"2020","journal-title":"J. Proteom."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"3752","DOI":"10.1021\/pr900080y","article-title":"A comparison of labeling and label-free mass spectrometry-based proteomics approaches","volume":"8","author":"Patel","year":"2009","journal-title":"J. Proteome Res."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Tan, H., Wang, N., Zhang, C., Chan, Y., Yuen, M., and Feng, Y. (2020). Loxl4 fosters an immunosuppressive microenvironment during hepatocarcinogenesis. Hepatology.","DOI":"10.1002\/hep.31600"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/nm.3807","article-title":"Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps","volume":"21","author":"Guo","year":"2015","journal-title":"Nat. Med."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/978-1-61779-827-6_2","article-title":"Pressure cycling technology in systems biology","volume":"881","author":"Powell","year":"2012","journal-title":"Methods Mol. Biol."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Hallal, S., Azimi, A., Wei, H., Ho, N., Lee, M., Sim, H., Sy, J., Shivalingam, B., Buckland, M., and Alexander-Kaufman, K. (2020). A comprehensive proteomic swath-ms workflow for profiling blood extracellular vesicles: A new avenue for glioma tumour surveillance. Int. J. Mol. Sci., 21.","DOI":"10.1101\/2020.03.05.979716"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"129682","DOI":"10.1016\/j.bbagen.2020.129682","article-title":"Psmd11, ptprm and ptprb as novel biomarkers of pancreatic cancer progression","volume":"1864","author":"Sahni","year":"2020","journal-title":"Biochim. Biophys. Acta Gen. Subj."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"103581","DOI":"10.1016\/j.jprot.2019.103581","article-title":"Proteomic investigation on bio-corona of au, ag and fe nanoparticles for the discovery of triple negative breast cancer serum protein biomarkers","volume":"212","author":"Vence","year":"2020","journal-title":"J. Proteom."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"10438","DOI":"10.1021\/nn3052499","article-title":"Emerging techniques in proteomics for probing nano-bio interactions","volume":"6","author":"Lai","year":"2012","journal-title":"ACS Nano"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"e1900276","DOI":"10.1002\/pmic.201900276","article-title":"Data-independent acquisition mass spectrometry-based proteomics and software tools: A glimpse in 2020","volume":"20","author":"Zhang","year":"2020","journal-title":"Proteomics"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"5251","DOI":"10.1038\/s41467-020-18901-y","article-title":"Dialib-qc an assessment tool for spectral libraries in data-independent acquisition proteomics","volume":"11","author":"Midha","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/S1470-2045(21)00003-6","article-title":"Cancer moonshot 2.0","volume":"22","author":"Agus","year":"2021","journal-title":"Lancet Oncol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.cell.2018.04.008","article-title":"Revolutionizing precision oncology through collaborative proteogenomics and data sharing","volume":"173","author":"Rodriguez","year":"2018","journal-title":"Cell"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1038\/d41586-021-00182-0","article-title":"Cancer research needs a better map","volume":"589","author":"Boehm","year":"2021","journal-title":"Nature"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.1038\/nmeth.3144","article-title":"Proteogenomics: Concepts, applications and computational strategies","volume":"11","author":"Nesvizhskii","year":"2014","journal-title":"Nat. Methods"},{"key":"ref_75","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":"ref_76","doi-asserted-by":"crossref","first-page":"1962","DOI":"10.1016\/j.cell.2020.10.044","article-title":"Integrated proteogenomic characterization across major histological types of pediatric brain cancer","volume":"183","author":"Petralia","year":"2020","journal-title":"Cell"},{"key":"ref_77","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":"ref_78","doi-asserted-by":"crossref","first-page":"2707","DOI":"10.1021\/pr501254j","article-title":"The cptac data portal: A resource for cancer proteomics research","volume":"14","author":"Edwards","year":"2015","journal-title":"J. Proteome Res."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"D956","DOI":"10.1093\/nar\/gkx1090","article-title":"Linkedomics: Analyzing multi-omics data within and across 32 cancer types","volume":"46","author":"Vasaikar","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.cell.2020.05.043","article-title":"Integrative proteomic characterization of human lung adenocarcinoma","volume":"182","author":"Xu","year":"2020","journal-title":"Cell"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.celrep.2016.12.016","article-title":"Personalized proteome profiles of healthy and tumor human colon organoids reveal both individual diversity and basic features of colorectal cancer","volume":"18","author":"Cristobal","year":"2017","journal-title":"Cell Rep."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"604492","DOI":"10.3389\/fmolb.2020.604492","article-title":"Proteomics of colorectal cancer: Tumors, organoids, and cell cultures-a minireview","volume":"7","author":"Lindhorst","year":"2020","journal-title":"Front. Mol. Biosci."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"11401","DOI":"10.1038\/s41598-018-29837-1","article-title":"Improved phosphoproteomic analysis for phosphosignaling and active-kinome profiling in matrigel-embedded spheroids and patient-derived organoids","volume":"8","author":"Abe","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"68","DOI":"10.3389\/fonc.2020.00068","article-title":"Comprehensive review of web servers and bioinformatics tools for cancer prognosis analysis","volume":"10","author":"Zheng","year":"2020","journal-title":"Front. Oncol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"578345","DOI":"10.3389\/fgene.2020.578345","article-title":"Integration of online omics-data resources for cancer research","volume":"11","author":"Das","year":"2020","journal-title":"Front. Genet."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1007\/978-1-4939-7493-1_7","article-title":"Perseus: A bioinformatics platform for integrative analysis of proteomics data in cancer research","volume":"1711","author":"Tyanova","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/ng.2764","article-title":"The cancer genome atlas pan-cancer analysis project","volume":"45","author":"Weinstein","year":"2013","journal-title":"Nat. Genet."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.ebiom.2018.12.048","article-title":"Proteomic analysis discovers the differential expression of novel proteins and phosphoproteins in meningioma including nek9, hk2 and set and deregulation of rna metabolism","volume":"40","author":"Dunn","year":"2019","journal-title":"EBioMedicine"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1186\/s12935-020-01212-z","article-title":"Bioinformatics combined with quantitative proteomics analyses and identification of potential biomarkers in cholangiocarcinoma","volume":"20","author":"Da","year":"2020","journal-title":"Cancer Cell Int."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: The next generation","volume":"144","author":"Hanahan","year":"2011","journal-title":"Cell"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1586\/14789450.2015.1040770","article-title":"Recent findings from the human proteome project: Opening the mass spectrometry toolbox to advance cancer diagnosis, surveillance and treatment","volume":"12","author":"Cantor","year":"2015","journal-title":"Expert Rev. Proteom."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1016\/j.cca.2019.06.006","article-title":"Oncoproteomics: Current status and future opportunities","volume":"495","author":"He","year":"2019","journal-title":"Clin. Chim. Acta"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/j.ccell.2020.12.010","article-title":"Mat2a inhibition blocks the growth of mtap-deleted cancer cells by reducing prmt5-dependent mrna splicing and inducing DNA damage","volume":"39","author":"Kalev","year":"2021","journal-title":"Cancer Cell"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"3138","DOI":"10.7150\/thno.19506","article-title":"Rbfox3 promotes tumor growth and progression via htert signaling and predicts a poor prognosis in hepatocellular carcinoma","volume":"7","author":"Liu","year":"2017","journal-title":"Theranostics"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1126\/science.1219723","article-title":"Mms19 assembles iron-sulfur proteins required for DNA metabolism and genomic integrity","volume":"337","author":"Stehling","year":"2012","journal-title":"Science"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1038\/s41556-019-0404-4","article-title":"Tumour exosomal cemip protein promotes cancer cell colonization in brain metastasis","volume":"21","author":"Rodrigues","year":"2019","journal-title":"Nat. Cell Biol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1016\/j.cmet.2018.07.019","article-title":"Impairment of angiogenesis by fatty acid synthase inhibition involves mtor malonylation","volume":"28","author":"Bruning","year":"2018","journal-title":"Cell Metab."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"e1900026","DOI":"10.1002\/pmic.201900026","article-title":"Proteomics reveals cell-surface urokinase plasminogen activator receptor expression impacts most hallmarks of cancer","volume":"19","author":"Ahn","year":"2019","journal-title":"Proteomics"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1038\/cdd.2015.129","article-title":"Hbv-induced ros accumulation promotes hepatocarcinogenesis through snail-mediated epigenetic silencing of socs3","volume":"23","author":"Yuan","year":"2016","journal-title":"Cell Death Differ."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1016\/j.cell.2020.02.012","article-title":"A quantitative tissue-specific landscape of protein redox regulation during aging","volume":"180","author":"Xiao","year":"2020","journal-title":"Cell"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1038\/s41591-019-0368-8","article-title":"Combination of erk and autophagy inhibition as a treatment approach for pancreatic cancer","volume":"25","author":"Bryant","year":"2019","journal-title":"Nat. Med."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1007\/978-1-4939-9030-6_22","article-title":"The multifaceted s100a4 protein in cancer and inflammation","volume":"1929","author":"Ambartsumian","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Ghahremanifard, P., Chanda, A., Bonni, S., and Bose, P. (2020). Tgf-\u03b2 mediated immune evasion in cancer-spotlight on cancer-associated fibroblasts. Cancers, 12.","DOI":"10.3390\/cancers12123650"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s13073-016-0324-x","article-title":"Roles of telomeres and telomerase in cancer, and advances in telomerase-targeted therapies","volume":"8","author":"Jafri","year":"2016","journal-title":"Genome Med."},{"key":"ref_105","first-page":"357","article-title":"Adaptive mechanisms of tumor therapy resistance driven by tumor microenvironment","volume":"9","author":"Wu","year":"2021","journal-title":"Front. Cell Dev. Biol."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"E5900","DOI":"10.1073\/pnas.1706559114","article-title":"Delineation of an immunosuppressive gradient in hepatocellular carcinoma using high-dimensional proteomic and transcriptomic analyses","volume":"114","author":"Chew","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1016\/j.cell.2016.05.069","article-title":"Integrated proteogenomic characterization of human high-grade serous ovarian cancer","volume":"166","author":"Zhang","year":"2016","journal-title":"Cell"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1038\/s41586-019-1173-8","article-title":"Proteomics reveals nnmt as a master metabolic regulator of cancer-associated fibroblasts","volume":"569","author":"Eckert","year":"2019","journal-title":"Nature"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/s41375-019-0596-4","article-title":"Integrated nuclear proteomics and transcriptomics identifies s100a4 as a therapeutic target in acute myeloid leukemia","volume":"34","author":"Alanazi","year":"2020","journal-title":"Leukemia"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nrm3801","article-title":"Cellular mechanisms and physiological consequences of redox-dependent signalling","volume":"15","author":"Finkel","year":"2014","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"101047","DOI":"10.1016\/j.redox.2018.11.005","article-title":"Redox signaling and unfolded protein response coordinate cell fate decisions under er stress","volume":"25","author":"Zhang","year":"2019","journal-title":"Redox Biol."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/s41590-020-0699-0","article-title":"Redox homeostasis maintained by gpx4 facilitates sting activation","volume":"21","author":"Jia","year":"2020","journal-title":"Nat. Immunol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.mam.2018.02.003","article-title":"Redox control in cancer development and progression","volume":"63","author":"Helfinger","year":"2018","journal-title":"Mol. Asp. Med."},{"key":"ref_114","first-page":"12","article-title":"Cancer a redox disease: Cancer cells are universally disturbed in their electronic energy balance, an understanding that potentially revolutionises cancer therapy and prevention","volume":"32","author":"Ho","year":"2013","journal-title":"J. Australas. Coll. Nutr. Environ. Med."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1021\/cr300073p","article-title":"Redox proteomics: Chemical principles, methodological approaches and biological\/biomedical promises","volume":"113","author":"Bachi","year":"2013","journal-title":"Chem. Rev."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.1038\/s41388-017-0046-6","article-title":"Dual role of autophagy in hallmarks of cancer","volume":"37","author":"Singh","year":"2018","journal-title":"Oncogene"},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/nrgastro.2016.185","article-title":"Autophagy in the liver: Functions in health and disease","volume":"14","author":"Ueno","year":"2017","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1177\/1535370217750088","article-title":"Biomarker definitions and their applications","volume":"243","author":"Califf","year":"2018","journal-title":"Exp. Biol. Med."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14740\/wjon1166","article-title":"Epidemiology of pancreatic cancer: Global trends, etiology and risk factors","volume":"10","author":"Rawla","year":"2019","journal-title":"World J. Oncol."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"9018","DOI":"10.1158\/0008-5472.CAN-04-3262","article-title":"Protein expression profiles in pancreatic adenocarcinoma compared with normal pancreatic tissue and tissue affected by pancreatitis as detected by two-dimensional gel electrophoresis and mass spectrometry","volume":"64","author":"Shen","year":"2004","journal-title":"Cancer Res."},{"key":"ref_121","doi-asserted-by":"crossref","unstructured":"Honda, K., Okusaka, T., Felix, K., Nakamori, S., Sata, N., Nagai, H., Ioka, T., Tsuchida, A., Shimahara, T., and Shimahara, M. (2012). Altered plasma apolipoprotein modifications in patients with pancreatic cancer: Protein characterization and multi-institutional validation. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0046908"},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"15921","DOI":"10.1038\/srep15921","article-title":"Plasma biomarker for detection of early stage pancreatic cancer and risk factors for pancreatic malignancy using antibodies for apolipoprotein-aii isoforms","volume":"5","author":"Honda","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.3389\/fonc.2019.01284","article-title":"Biomarkers in colorectal cancer: The role of translational proteomics research","volume":"9","author":"Cavalcanti","year":"2019","journal-title":"Front. Oncol."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"106935","DOI":"10.18632\/oncotarget.22149","article-title":"Successful identification of a predictive biomarker for lymph node metastasis in colorectal cancer using a proteomic approach","volume":"8","author":"Mori","year":"2017","journal-title":"Oncotarget"},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"17903","DOI":"10.1038\/srep17903","article-title":"Prognostic value of ezrin in various cancers: A systematic review and updated meta-analysis","volume":"5","author":"Li","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"2667","DOI":"10.1111\/cas.14093","article-title":"Clinicopathological significance of heterogeneic ezrin expression in poorly differentiated clusters of colorectal cancers","volume":"110","author":"Aikawa","year":"2019","journal-title":"Cancer Sci."},{"key":"ref_127","doi-asserted-by":"crossref","unstructured":"Pagliara, V., Donadio, G., De Tommasi, N., Amodio, G., Remondelli, P., Moltedo, O., and Dal Piaz, F. (2020). Bioactive ent-kaurane diterpenes oridonin and irudonin prevent cancer cells migration by interacting with the actin cytoskeleton controller ezrin. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21197186"},{"key":"ref_128","doi-asserted-by":"crossref","unstructured":"Sung, H., Ahn, J., Yoon, Y., Na, S., Choi, Y., Kim, Y., Lee, S., Lee, E., Cho, S., and Cho, J. (2018). Quiescin sulfhydryl oxidase 1 (qsox1) secreted by lung cancer cells promotes cancer metastasis. Int. J. Mol. Sci., 19.","DOI":"10.20944\/preprints201809.0586.v1"},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1172\/JCI93801","article-title":"Drug-perturbation-based stratification of blood cancer","volume":"128","author":"Dietrich","year":"2018","journal-title":"J. Clin. Investig."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"100720","DOI":"10.1016\/j.drup.2020.100720","article-title":"Surmounting cancer drug resistance: New insights from the perspective of n-methyladenosine rna modification","volume":"53","author":"Li","year":"2020","journal-title":"Drug Resist. Updates"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"205","DOI":"10.3389\/fphar.2015.00205","article-title":"Multi-target pharmacology: Possibilities and limitations of the \"skeleton key approach\" from a medicinal chemist perspective","volume":"6","author":"Talevi","year":"2015","journal-title":"Front. Pharmacol."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.cell.2018.08.065","article-title":"Multi-level proteomics identifies ct45 as a chemosensitivity mediator and immunotherapy target in ovarian cancer","volume":"175","author":"Coscia","year":"2018","journal-title":"Cell"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1016\/j.ccell.2020.10.008","article-title":"Large-scale characterization of drug responses of clinically relevant proteins in cancer cell lines","volume":"38","author":"Zhao","year":"2020","journal-title":"Cancer Cell"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"14265","DOI":"10.1038\/s41598-017-14539-x","article-title":"Identification of mst1 as a potential early detection biomarker for colorectal cancer through a proteomic approach","volume":"7","author":"Yu","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_135","doi-asserted-by":"crossref","unstructured":"Zeng, L., Deng, X., Zhong, J., Yuan, L., Tao, X., Zhang, S., Zeng, Y., He, G., Tan, P., and Tao, Y. (2019). Prognostic value of biomarkers epcam and \u03b1b-crystallin associated with lymphatic metastasis in breast cancer by itraq analysis. BMC Cancer, 19.","DOI":"10.1186\/s12885-019-6016-3"},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1016\/j.cllc.2014.05.003","article-title":"Identification of eno1 as a potential sputum biomarker for early-stage lung cancer by shotgun proteomics","volume":"15","author":"Yu","year":"2014","journal-title":"Clin. Lung Cancer"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"36664","DOI":"10.18632\/oncotarget.17067","article-title":"Serological proteome analysis approach-based identification of eno1 as a tumor-associated antigen and its autoantibody could enhance the sensitivity of cea and cyfra 21-1 in the detection of non-small cell lung cancer","volume":"8","author":"Dai","year":"2017","journal-title":"Oncotarget"},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"47691","DOI":"10.18632\/oncotarget.17868","article-title":"Enolase 1 stimulates glycolysis to promote chemoresistance in gastric cancer","volume":"8","author":"Qian","year":"2017","journal-title":"Oncotarget"},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"5598","DOI":"10.18632\/oncotarget.6798","article-title":"Targeting the warburg effect in cancer cells through eno1 knockdown rescues oxidative phosphorylation and induces growth arrest","volume":"7","author":"Capello","year":"2016","journal-title":"Oncotarget"},{"key":"ref_140","doi-asserted-by":"crossref","unstructured":"Pellegrino, M., Rizza, P., Don\u00e0, A., Nigro, A., Ricci, E., Fiorillo, M., Perrotta, I., Lanzino, M., Giordano, C., and Bonofiglio, D. (2019). Foxo3a as a positive prognostic marker and a therapeutic target in tamoxifen-resistant breast cancer. Cancers, 11.","DOI":"10.3390\/cancers11121858"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1080\/14789450.2018.1523724","article-title":"Proteomics and the microbiome: Pitfalls and potential","volume":"16","author":"Lin","year":"2019","journal-title":"Expert Rev. Proteom."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"612202","DOI":"10.3389\/fimmu.2020.612202","article-title":"Exploring the emerging role of the gut microbiota and tumor microenvironment in cancer immunotherapy","volume":"11","author":"Qiu","year":"2020","journal-title":"Front. Immunol."},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1126\/science.aay9189","article-title":"The human tumor microbiome is composed of tumor type-specific intracellular bacteria","volume":"368","author":"Nejman","year":"2020","journal-title":"Science"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"e47638","DOI":"10.15252\/embr.201847638","article-title":"Fusobacterium nucleatum promotes colorectal cancer by inducing wnt\/\u03b2-catenin modulator annexin a1","volume":"20","author":"Rubinstein","year":"2019","journal-title":"EMBO Rep."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"3259","DOI":"10.1038\/s41467-020-16967-2","article-title":"Breast cancer colonization by fusobacterium nucleatum accelerates tumor growth and metastatic progression","volume":"11","author":"Parhi","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"eabc4218","DOI":"10.1126\/scisignal.abc4218","article-title":"Bacterial invaders drive crc progression","volume":"13","author":"Meyerson","year":"2020","journal-title":"Sci. Signal."},{"key":"ref_147","doi-asserted-by":"crossref","unstructured":"Guo, S., Chen, J., Chen, F., Zeng, Q., Liu, W., and Zhang, G. (2020). Exosomes derived from fusobacterium nucleatum-infected colorectal cancer cells facilitate tumour metastasis by selectively carrying mir-1246\/92b-3p\/27a-3p and cxcl16. Gut.","DOI":"10.1136\/gutjnl-2020-321187"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1016\/j.cell.2018.12.040","article-title":"Commensal microbiota promote lung cancer development via \u03b3\u03b4 t cells","volume":"176","author":"Jin","year":"2019","journal-title":"Cell"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"5","DOI":"10.3389\/fmicb.2018.00005","article-title":"Helicobacter pylori and gastric cancer: Adaptive cellular mechanisms involved in disease progression","volume":"9","author":"Bravo","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"12365","DOI":"10.1038\/ncomms12365","article-title":"Probiotic-derived ferrichrome inhibits colon cancer progression via jnk-mediated apoptosis","volume":"7","author":"Konishi","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_151","doi-asserted-by":"crossref","unstructured":"Chen, J., Zhao, K., and Vitetta, L. (2019). Effects of intestinal microbial-elaborated butyrate on oncogenic signaling pathways. Nutrients, 11.","DOI":"10.3390\/nu11051026"},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1086\/600885","article-title":"Ongoing revolution in bacteriology: Routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry","volume":"49","author":"Seng","year":"2009","journal-title":"Clin. Infect. Dis."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"1744","DOI":"10.3389\/fmicb.2018.01744","article-title":"Susceptibility testing of bacteria using maldi-tof mass spectrometry","volume":"9","author":"Burckhardt","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"8451728","DOI":"10.1155\/2016\/8451728","article-title":"Bacteria in cancer therapy: Renaissance of an old concept","volume":"2016","author":"Felgner","year":"2016","journal-title":"Int. J. Microbiol."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"S146","DOI":"10.1016\/j.juro.2016.10.083","article-title":"Intracavitary bacillus calmette-gu\u00e9rin for superficial bladder tumors","volume":"197","author":"Droller","year":"2017","journal-title":"J. Urol."},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.juro.2007.08.122","article-title":"History of bacillus calmette-guerin and bladder cancer: An immunotherapy success story","volume":"179","author":"Herr","year":"2008","journal-title":"J. Urol."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"2796","DOI":"10.1016\/S0140-6736(16)30512-8","article-title":"Bladder cancer","volume":"388","author":"Kamat","year":"2016","journal-title":"Lancet"},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"137ra172","DOI":"10.1126\/scitranslmed.3003586","article-title":"Preexisting bcg-specific t cells improve intravesical immunotherapy for bladder cancer","volume":"4","author":"Biot","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.3109\/00016489.2010.483480","article-title":"Effects and mechanism of ok-432 therapy in various neck cystic lesions","volume":"130","author":"Ohta","year":"2010","journal-title":"Acta Oto-Laryngol."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"2193","DOI":"10.1002\/lary.21141","article-title":"Treatments of various otolaryngological cystic diseases by ok-4321: Its indications and limitations","volume":"120","author":"Ohta","year":"2010","journal-title":"Laryngoscope"},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.joms.2016.08.013","article-title":"Evaluation of ok-432 injection therapy as possible primary treatment of intraoral ranula","volume":"75","author":"Kono","year":"2017","journal-title":"J. Oral Maxillofac. Surg."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1016\/j.pedneo.2013.06.011","article-title":"Complete resolution of retroperitoneal lymphangioma with a single trial of ok-432 in an infant","volume":"57","author":"Olivieri","year":"2016","journal-title":"Pediatrics Neonatol."},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.molmed.2012.05.006","article-title":"Bioengineered microbes in disease therapy","volume":"18","author":"Paton","year":"2012","journal-title":"Trends Mol. Med."},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"2359","DOI":"10.3892\/ol.2014.2525","article-title":"Tumor-targeting bacterial therapy: A potential treatment for oral cancer (review)","volume":"8","author":"Liu","year":"2014","journal-title":"Oncol. Lett."},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.gendis.2016.01.003","article-title":"Clostridium novyi-nt in cancer therapy","volume":"3","author":"Staedtke","year":"2016","journal-title":"Genes Dis."},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"4183","DOI":"10.1016\/j.vaccine.2007.03.008","article-title":"Improving tumor targeting and therapeutic potential of salmonella vnp20009 by displaying cell surface cea-specific antibodies","volume":"25","author":"Bereta","year":"2007","journal-title":"Vaccine"},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"e1303584","DOI":"10.1080\/2162402X.2017.1303584","article-title":"A phase 1 trial extension to assess immunologic efficacy and safety of prime-boost vaccination with vxm01, an oral t cell vaccine against vegfr2, in patients with advanced pancreatic cancer","volume":"7","author":"Hohmann","year":"2018","journal-title":"OncoImmunology"},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1038\/nnano.2016.137","article-title":"Magneto-aerotactic bacteria deliver drug-containing nanoliposomes to tumour hypoxic regions","volume":"11","author":"Felfoul","year":"2016","journal-title":"Nat. Nanotechnol."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"301","DOI":"10.4155\/tde-2016-0088","article-title":"Targeting active cancer cells with smart bullets","volume":"8","author":"Martel","year":"2017","journal-title":"Ther. Deliv."},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"41","DOI":"10.4142\/jvs.2004.5.1.41","article-title":"Immunomodulatory and antitumor effects in vivo by the cytoplasmic fraction of lactobacillus casei and bifidobacterium longum","volume":"5","author":"Lee","year":"2004","journal-title":"J. Vet. Sci."},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"G1025","DOI":"10.1152\/ajpgi.90227.2008","article-title":"Secreted bioactive factors from bifidobacterium infantis enhance epithelial cell barrier function","volume":"295","author":"Ewaschuk","year":"2008","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"1595","DOI":"10.1016\/j.ajpath.2013.01.013","article-title":"Bifidobacteria stabilize claudins at tight junctions and prevent intestinal barrier dysfunction in mouse necrotizing enterocolitis","volume":"182","author":"Bergmann","year":"2013","journal-title":"Am. J. Pathol."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1126\/science.aac4255","article-title":"Commensal bifidobacterium promotes antitumor immunity and facilitates anti-pd-l1 efficacy","volume":"350","author":"Sivan","year":"2015","journal-title":"Science"},{"key":"ref_174","doi-asserted-by":"crossref","unstructured":"Uccello, M., Malaguarnera, G., Basile, F., D\u2019agata, V., Malaguarnera, M., Bertino, G., Vacante, M., Drago, F., and Biondi, A. (2012). Potential role of probiotics on colorectal cancer prevention. BMC Surg., 12.","DOI":"10.1186\/1471-2482-12-S1-S35"},{"key":"ref_175","doi-asserted-by":"crossref","unstructured":"Flickinger, J., Rodeck, U., and Snook, A. (2018). Listeria monocytogenes as a vector for cancer immunotherapy: Current understanding and progress. Vaccines, 6.","DOI":"10.3390\/vaccines6030048"},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"46","DOI":"10.2174\/156652310790945539","article-title":"Listeria monocytogenes as a vector for anti-cancer therapies","volume":"10","author":"Tangney","year":"2010","journal-title":"Curr. Gene Ther."},{"key":"ref_177","first-page":"1389","article-title":"Prospects and progress of listeria-based cancer vaccines","volume":"17","author":"Bolhassani","year":"2017","journal-title":"Expert Opin. Biol. Ther."},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1186\/s13036-019-0189-9","article-title":"Intestinal probiotics e. Coli nissle 1917 as a targeted vehicle for delivery of p53 and tum-5 to solid tumors for cancer therapy","volume":"13","author":"He","year":"2019","journal-title":"J. Biol. Eng."},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1089\/hum.1997.8.14-1637","article-title":"In vivo gene therapy of cancer with e. Coli purine nucleoside phosphorylase","volume":"8","author":"Parker","year":"1997","journal-title":"Hum. Gene Ther."},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1016\/j.ccr.2012.02.007","article-title":"Promotion of hepatocellular carcinoma by the intestinal microbiota and tlr4","volume":"21","author":"Dapito","year":"2012","journal-title":"Cancer Cell"},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1038\/nature11465","article-title":"Adenoma-linked barrier defects and microbial products drive il-23\/il-17-mediated tumour growth","volume":"491","author":"Grivennikov","year":"2012","journal-title":"Nature"},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/j.cell.2016.03.001","article-title":"Microbiome and anticancer immunosurveillance","volume":"165","author":"Zitvogel","year":"2016","journal-title":"Cell"},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1053\/j.gastro.2015.01.040","article-title":"Helicobacter pylori update: Gastric cancer, reliable therapy, and possible benefits","volume":"148","author":"Graham","year":"2015","journal-title":"Gastroenterology"},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1038\/nrc703","article-title":"Helicobacter pylori and gastrointestinal tract adenocarcinomas","volume":"2","author":"Peek","year":"2002","journal-title":"Nat. Rev. Cancer"},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/nature12347","article-title":"Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome","volume":"499","author":"Yoshimoto","year":"2013","journal-title":"Nature"},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1038\/nm.2015","article-title":"A human colonic commensal promotes colon tumorigenesis via activation of t helper type 17 t cell responses","volume":"15","author":"Wu","year":"2009","journal-title":"Nat. Med."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.chom.2013.07.007","article-title":"Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment","volume":"14","author":"Kostic","year":"2013","journal-title":"Cell Host Microbe"},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.chom.2013.07.012","article-title":"Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating e-cadherin\/\u03b2-catenin signaling via its fada adhesin","volume":"14","author":"Rubinstein","year":"2013","journal-title":"Cell Host Microbe"},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.immuni.2015.01.010","article-title":"Binding of the fap2 protein of fusobacterium nucleatum to human inhibitory receptor tigit protects tumors from immune cell attack","volume":"42","author":"Gur","year":"2015","journal-title":"Immunity"},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1126\/science.1224820","article-title":"Intestinal inflammation targets cancer-inducing activity of the microbiota","volume":"338","author":"Arthur","year":"2012","journal-title":"Science"},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1016\/j.jsps.2017.05.007","article-title":"Prediction of chlamydia pneumoniae protein localization in host mitochondria and cytoplasm and possible involvements in lung cancer etiology: A computational approach","volume":"25","author":"Alshamsan","year":"2017","journal-title":"Saudi Pharm. J."},{"key":"ref_192","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1016\/j.chom.2013.05.010","article-title":"Chlamydia infection promotes host DNA damage and proliferation but impairs the DNA damage response","volume":"13","author":"Chumduri","year":"2013","journal-title":"Cell Host Microbe"},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/ismej.2008.108","article-title":"Shotgun metaproteomics of the human distal gut microbiota","volume":"3","author":"Verberkmoes","year":"2009","journal-title":"ISME J."},{"key":"ref_194","doi-asserted-by":"crossref","first-page":"855","DOI":"10.7326\/M17-1068","article-title":"Novel stool-based protein biomarkers for improved colorectal cancer screening: A case-control study","volume":"167","author":"Bosch","year":"2017","journal-title":"Ann. Intern. Med."},{"key":"ref_195","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1038\/s41522-020-0123-4","article-title":"Metaproteomics characterizes human gut microbiome function in colorectal cancer","volume":"6","author":"Long","year":"2020","journal-title":"NPJ Biofilms Microbiomes"},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.lungcan.2016.10.016","article-title":"Characterization of microbiome in bronchoalveolar lavage fluid of patients with lung cancer comparing with benign mass like lesions","volume":"102","author":"Lee","year":"2016","journal-title":"Lung Cancer"},{"key":"ref_197","doi-asserted-by":"crossref","first-page":"2401","DOI":"10.3109\/10428194.2016.1144879","article-title":"Butyrate production from high-fiber diet protects against lymphoma tumor","volume":"57","author":"Wei","year":"2016","journal-title":"Leuk. Lymphoma"},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"3053","DOI":"10.1038\/onc.2014.234","article-title":"Immune-dependent antineoplastic effects of cisplatin plus pyridoxine in non-small-cell lung cancer","volume":"34","author":"Aranda","year":"2015","journal-title":"Oncogene"},{"key":"ref_199","doi-asserted-by":"crossref","first-page":"1010428317711311","DOI":"10.1177\/1010428317711311","article-title":"Ferrichrome identified from lactobacillus casei atcc334 induces apoptosis through its iron-binding site in gastric cancer cells","volume":"39","author":"Ijiri","year":"2017","journal-title":"Tumour Biol."},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"1186","DOI":"10.3349\/ymj.2013.54.5.1186","article-title":"Growth inhibition of hepatocellular carcinoma huh7 cells by lactobacillus casei extract","volume":"54","author":"Han","year":"2013","journal-title":"Yonsei Med. J."},{"key":"ref_201","doi-asserted-by":"crossref","first-page":"721","DOI":"10.3892\/ijo.2020.5096","article-title":"Probiotic-derived ferrichrome inhibits the growth of refractory pancreatic cancer cells","volume":"57","author":"Kita","year":"2020","journal-title":"Int. J. Oncol."},{"key":"ref_202","doi-asserted-by":"crossref","first-page":"2021","DOI":"10.1002\/ijc.32003","article-title":"Fecal microbiota transplantation in cancer management: Current status and perspectives","volume":"145","author":"Chen","year":"2019","journal-title":"Int. J. Cancer"},{"key":"ref_203","doi-asserted-by":"crossref","first-page":"8941340","DOI":"10.1155\/2018\/8941340","article-title":"Protocol for fecal microbiota transplantation in inflammatory bowel disease: A systematic review and meta-analysis","volume":"2018","author":"Fang","year":"2018","journal-title":"BioMed Res. Int."},{"key":"ref_204","doi-asserted-by":"crossref","first-page":"e00137-18","DOI":"10.1128\/mSystems.00137-18","article-title":"Fecal microbiota transplantation beneficially regulates intestinal mucosal autophagy and alleviates gut barrier injury","volume":"3","author":"Cheng","year":"2018","journal-title":"mSystems"},{"key":"ref_205","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/s41398-017-0078-2","article-title":"Metabolite identification in fecal microbiota transplantation mouse livers and combined proteomics with chronic unpredictive mild stress mouse livers","volume":"8","author":"Li","year":"2018","journal-title":"Transl. Psychiatry"},{"key":"ref_206","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1126\/science.abb5920","article-title":"Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients","volume":"371","author":"Baruch","year":"2021","journal-title":"Science"},{"key":"ref_207","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1126\/science.abf3363","article-title":"Fecal microbiota transplant overcomes resistance to anti-pd-1 therapy in melanoma patients","volume":"371","author":"Davar","year":"2021","journal-title":"Science"},{"key":"ref_208","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/nature12352","article-title":"Insights into the phylogeny and coding potential of microbial dark matter","volume":"499","author":"Rinke","year":"2013","journal-title":"Nature"},{"key":"ref_209","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1111\/1469-0691.12023","article-title":"Microbial culturomics: Paradigm shift in the human gut microbiome study","volume":"18","author":"Lagier","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_210","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.critrevonc.2019.06.004","article-title":"The microbiome and cancer for clinicians","volume":"141","author":"Picardo","year":"2019","journal-title":"Crit. Rev. Oncol. Hematol."},{"key":"ref_211","doi-asserted-by":"crossref","first-page":"2006","DOI":"10.1074\/mcp.RA117.000023","article-title":"High sensitivity quantitative proteomics using automated multidimensional nano-flow chromatography and accumulated ion monitoring on quadrupole-orbitrap-linear ion trap mass spectrometer","volume":"16","author":"Cifani","year":"2017","journal-title":"Mol. Cell. Proteom."},{"key":"ref_212","doi-asserted-by":"crossref","first-page":"3793","DOI":"10.1038\/s41467-020-17641-3","article-title":"Strategies to enable large-scale proteomics for reproducible research","volume":"11","author":"Poulos","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_213","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1038\/nmeth.3995","article-title":"A proposal for validation of antibodies","volume":"13","author":"Uhlen","year":"2016","journal-title":"Nat. Methods"},{"key":"ref_214","doi-asserted-by":"crossref","first-page":"eaal3321","DOI":"10.1126\/science.aal3321","article-title":"A subcellular map of the human proteome","volume":"356","author":"Thul","year":"2017","journal-title":"Science"},{"key":"ref_215","doi-asserted-by":"crossref","first-page":"2028","DOI":"10.1074\/mcp.M800264-MCP200","article-title":"Antibodypedia, a portal for sharing antibody and antigen validation data","volume":"7","year":"2008","journal-title":"Mol. Cell. Proteom."},{"key":"ref_216","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1080\/14789450.2020.1855982","article-title":"Top-down proteomics: Challenges, innovations, and applications in basic and clinical research","volume":"17","author":"Brown","year":"2020","journal-title":"Expert Rev. Proteom."},{"key":"ref_217","doi-asserted-by":"crossref","first-page":"eaax8978","DOI":"10.1126\/sciadv.aax8978","article-title":"Beyond mass spectrometry, the next step in proteomics","volume":"6","author":"Timp","year":"2020","journal-title":"Sci. Adv."},{"key":"ref_218","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1016\/j.tibtech.2018.07.018","article-title":"Differential ion mobility-mass spectrometry for detailed analysis of the proteome","volume":"37","author":"Winter","year":"2019","journal-title":"Trends Biotechnol."},{"key":"ref_219","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s12127-019-00251-1","article-title":"Possible strategy to use differential mobility spectrometry in real time applications","volume":"23","author":"Anttalainen","year":"2020","journal-title":"Int. J. Ion Mobil. Spectrom."},{"key":"ref_220","doi-asserted-by":"crossref","first-page":"2657","DOI":"10.3389\/fimmu.2019.02657","article-title":"Mass cytometry imaging for the study of human diseases-applications and data analysis strategies","volume":"10","author":"Baharlou","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_221","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s43018-020-0026-6","article-title":"Imaging mass cytometry and multiplatform genomics define the phenogenomic landscape of breast cancer","volume":"1","author":"Ali","year":"2020","journal-title":"Nat. Cancer"},{"key":"ref_222","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.3389\/fimmu.2019.01515","article-title":"Meeting the challenges of high-dimensional single-cell data analysis in immunology","volume":"10","author":"Palit","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_223","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1016\/j.bios.2018.09.051","article-title":"Fluorescence-based kinetic analysis of miniaturized protein microarrays","volume":"122","author":"Gheber","year":"2018","journal-title":"Biosens. Bioelectron."},{"key":"ref_224","doi-asserted-by":"crossref","unstructured":"Sauer, U. (2017). Analytical protein microarrays: Advancements towards clinical applications. Sensors, 17.","DOI":"10.3390\/s17020256"},{"key":"ref_225","unstructured":"(2017). Integrated genomic characterization of pancreatic ductal adenocarcinoma. Cancer Cell, 32, 185\u2013203."},{"key":"ref_226","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.ccell.2017.01.005","article-title":"Characterization of human cancer cell lines by reverse-phase protein arrays","volume":"31","author":"Li","year":"2017","journal-title":"Cancer Cell"},{"key":"ref_227","doi-asserted-by":"crossref","first-page":"140560","DOI":"10.1016\/j.bbapap.2020.140560","article-title":"Translating proteomics big data into biomedical applications with computational modeling","volume":"1869","author":"Cai","year":"2021","journal-title":"Biochim. Biophys. Acta Proteins Proteom."},{"key":"ref_228","doi-asserted-by":"crossref","unstructured":"Moldogazieva, N., Mokhosoev, I., Zavadskiy, S., and Terentiev, A. (2021). Proteomic profiling and artificial intelligence for hepatocellular carcinoma translational medicine. Biomedicines, 9.","DOI":"10.3390\/biomedicines9020159"},{"key":"ref_229","doi-asserted-by":"crossref","unstructured":"Giulietti, M., Cecati, M., Sabanovic, B., Scir\u00e8, A., Cimadamore, A., Santoni, M., Montironi, R., and Piva, F. (2021). The role of artificial intelligence in the diagnosis and prognosis of renal cell tumors. Diagnostics, 11.","DOI":"10.3390\/diagnostics11020206"},{"key":"ref_230","doi-asserted-by":"crossref","unstructured":"Tunali, I., Gillies, R., and Schabath, M. (2021). Application of radiomics and artificial intelligence for lung cancer precision medicine. Cold Spring Harb. Perspect. Med., 039537.","DOI":"10.1101\/cshperspect.a039537"},{"key":"ref_231","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1038\/s41592-019-0426-7","article-title":"Prosit: Proteome-wide prediction of peptide tandem mass spectra by deep learning","volume":"16","author":"Gessulat","year":"2019","journal-title":"Nat. Methods"},{"key":"ref_232","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/d41586-020-03348-4","article-title":"\u2018It will change everything\u2019: Deepmind\u2019s ai makes gigantic leap in solving protein structures","volume":"588","author":"Callaway","year":"2020","journal-title":"Nature"},{"key":"ref_233","doi-asserted-by":"crossref","first-page":"2565","DOI":"10.1021\/acs.jproteome.8b00257","article-title":"Transformative opportunities for single-cell proteomics","volume":"17","author":"Specht","year":"2018","journal-title":"J. Proteome Res."},{"key":"ref_234","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/s41570-020-0162-7","article-title":"Single-cell analysis targeting the proteome","volume":"4","author":"Labib","year":"2020","journal-title":"Nat. Rev. Chem."},{"key":"ref_235","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1186\/s13045-019-0818-2","article-title":"Emerging insights of tumor heterogeneity and drug resistance mechanisms in lung cancer targeted therapy","volume":"12","author":"Lim","year":"2019","journal-title":"J. Hematol. Oncol."},{"key":"ref_236","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1158\/2159-8290.CD-17-0256","article-title":"Tcr repertoire intratumor heterogeneity in localized lung adenocarcinomas: An association with predicted neoantigen heterogeneity and postsurgical recurrence","volume":"7","author":"Reuben","year":"2017","journal-title":"Cancer Discov."},{"key":"ref_237","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1016\/j.cell.2017.04.014","article-title":"Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses","volume":"169","author":"Lavin","year":"2017","journal-title":"Cell"},{"key":"ref_238","doi-asserted-by":"crossref","first-page":"1076","DOI":"10.1038\/nbt.4278","article-title":"Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures","volume":"36","author":"Swaminathan","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref_239","doi-asserted-by":"crossref","first-page":"3338","DOI":"10.1073\/pnas.1707207115","article-title":"Single-molecule peptide fingerprinting","volume":"115","author":"Filius","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_240","doi-asserted-by":"crossref","unstructured":"Ohayon, S., Girsault, A., Nasser, M., Shen-Orr, S., and Meller, A. (2019). Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification. PLoS Comput. Biol., 15.","DOI":"10.1371\/journal.pcbi.1007067"},{"key":"ref_241","first-page":"79","article-title":"Bayesian hierarchical models for protein networks in single-cell mass cytometry","volume":"13","author":"Mitra","year":"2014","journal-title":"Cancer Inform."},{"key":"ref_242","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/nbt.2594","article-title":"Visne enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia","volume":"31","author":"Amir","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref_243","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s13059-020-1926-6","article-title":"Eleven grand challenges in single-cell data science","volume":"21","author":"Szczurek","year":"2020","journal-title":"Genome Biol."},{"key":"ref_244","doi-asserted-by":"crossref","first-page":"4838","DOI":"10.1002\/cncr.33205","article-title":"Clinical trial design: Past, present, and future in the context of big data and precision medicine","volume":"126","author":"Li","year":"2020","journal-title":"Cancer"},{"key":"ref_245","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1002\/1878-0261.12465","article-title":"New clinical trial designs in the era of precision medicine","volume":"13","author":"Garralda","year":"2019","journal-title":"Mol. Oncol."},{"key":"ref_246","doi-asserted-by":"crossref","first-page":"S13","DOI":"10.1038\/d41586-020-02678-7","article-title":"Health-care inequality could deepen with precision oncology","volume":"585","author":"Madhusoodanan","year":"2020","journal-title":"Nature"}],"container-title":["Cancers"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2072-6694\/13\/11\/2512\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:05:08Z","timestamp":1760162708000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2072-6694\/13\/11\/2512"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,21]]},"references-count":246,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2021,6]]}},"alternative-id":["cancers13112512"],"URL":"https:\/\/doi.org\/10.3390\/cancers13112512","relation":{},"ISSN":["2072-6694"],"issn-type":[{"value":"2072-6694","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,21]]}}}