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One of the primary challenges in the treatment of BC is the disease\u2019s heterogeneity, which can lead to ineffective therapies and poor patient outcomes. Spatial proteomics, which involves the study of protein localization within cells, offers a promising approach for understanding the biological processes that contribute to cellular heterogeneity within BC tissue. To fully leverage the potential of spatial proteomics, it is critical to identify early diagnostic biomarkers and therapeutic targets, and to understand protein expression levels and modifications. The subcellular localization of proteins is a key factor in their physiological function, making the study of subcellular localization a major challenge in cell biology. Achieving high resolution at the cellular and subcellular level is essential for obtaining an accurate spatial distribution of proteins, which in turn can enable the application of proteomics in clinical research. In this review, we present a comparison of current methods of spatial proteomics in BC, including untargeted and targeted strategies. Untargeted strategies enable the detection and analysis of proteins and peptides without a predetermined molecular focus, whereas targeted strategies allow the investigation of a predefined set of proteins or peptides of interest, overcoming the limitations associated with the stochastic nature of untargeted proteomics. By directly comparing these methods, we aim to provide insights into their strengths and limitations and their potential applications in BC research.<\/jats:p>","DOI":"10.3390\/proteomes11020017","type":"journal-article","created":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T01:33:36Z","timestamp":1683164016000},"page":"17","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Spatial Proteomics for the Molecular Characterization of Breast Cancer"],"prefix":"10.3390","volume":"11","author":[{"given":"Kl\u00e1ra","family":"Bro\u017eov\u00e1","sequence":"first","affiliation":[{"name":"Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria"},{"name":"Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria"},{"name":"Division of Molecular and Structural Preclinical Imaging, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1210 Vienna, Austria"},{"name":"Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9126-003X","authenticated-orcid":false,"given":"Brigitte","family":"Hantusch","sequence":"additional","affiliation":[{"name":"Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2184-1338","authenticated-orcid":false,"given":"Lukas","family":"Kenner","sequence":"additional","affiliation":[{"name":"Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria"},{"name":"Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria"},{"name":"CBmed GmbH\u2014Center for Biomarker Research in Medicine, 8010 Graz, Austria"},{"name":"Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, 1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0803-614X","authenticated-orcid":false,"given":"Klaus","family":"Kratochwill","sequence":"additional","affiliation":[{"name":"Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria"},{"name":"Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria"},{"name":"Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,5,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1586\/14789450.2015.1002474","article-title":"Proteomics reveals the importance of the dynamic redistribution of the subcellular location of proteins in breast cancer cells","volume":"12","author":"Pinto","year":"2015","journal-title":"Expert Rev. Proteom."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.trecan.2020.12.006","article-title":"Illuminating Non-genetic Cellular Heterogeneity with Imaging-Based Spatial Proteomics","volume":"7","author":"Gnann","year":"2021","journal-title":"Trends Cancer"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/s41580-018-0094-y","article-title":"Spatial proteomics: A powerful discovery tool for cell biology","volume":"20","author":"Lundberg","year":"2019","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_4","first-page":"176","article-title":"Genomic and proteomic biomarkers for cancer: A multitude of opportunities","volume":"1796","author":"Tainsky","year":"2009","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.semcancer.2017.08.010","article-title":"Prognostic and predictive biomarkers in breast cancer: Past, present and future","volume":"52","author":"Nicolini","year":"2018","journal-title":"Semin. Cancer Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1093\/annonc\/mdr160","article-title":"Death causes in breast cancer patients","volume":"23","author":"Riihimaki","year":"2012","journal-title":"Ann. Oncol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"783450","DOI":"10.3389\/fmolb.2022.783450","article-title":"Breast Cancer; Discovery of Novel Diagnostic Biomarkers, Drug Resistance, and Therapeutic Implications","volume":"9","author":"Afzal","year":"2022","journal-title":"Front. Mol. Biosci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1158\/1535-7163.MCT-12-0781","article-title":"Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities","volume":"12","author":"Craig","year":"2013","journal-title":"Mol. Cancer Ther."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1101\/gad.242511.114","article-title":"Mammary stem cells and the differentiation hierarchy: Current status and perspectives","volume":"28","author":"Visvader","year":"2014","journal-title":"Genes Dev."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1002\/ame2.12077","article-title":"The promises and challenges of patient-derived tumor organoids in drug development and precision oncology","volume":"2","author":"Granat","year":"2019","journal-title":"Anim. Model. Exp. Med."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.ymeth.2016.06.023","article-title":"Applications of imaging flow cytometry in the diagnostic assessment of acute leukaemia","volume":"112","author":"Grimwade","year":"2017","journal-title":"Methods"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1093\/annonc\/mdv221","article-title":"Tailoring therapies--improving the management of early breast cancer: St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2015","volume":"26","author":"Coates","year":"2015","journal-title":"Ann. Oncol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/35021093","article-title":"Molecular portraits of human breast tumours","volume":"406","author":"Perou","year":"2000","journal-title":"Nature"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1200\/JOP.777003","article-title":"American society of clinical oncology\/college of american pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer","volume":"6","author":"Hammond","year":"2010","journal-title":"J. Oncol. Pract."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2105","DOI":"10.1200\/JCO.2018.77.8738","article-title":"Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer: American Society of Clinical Oncology\/College of American Pathologists Clinical Practice Guideline Focused Update","volume":"36","author":"Wolff","year":"2018","journal-title":"J. Clin. Oncol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1016\/S0140-6736(11)61178-1","article-title":"Cancer of unknown primary site","volume":"379","author":"Pavlidis","year":"2012","journal-title":"Lancet"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"4063","DOI":"10.1158\/1078-0432.CCR-10-2599","article-title":"Prospective gene signature study using microRNA to identify the tissue of origin in patients with carcinoma of unknown primary","volume":"17","author":"Varadhachary","year":"2011","journal-title":"Clin. Cancer Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1002\/pmic.201300430","article-title":"Imaging mass spectrometry to discriminate breast from pancreatic cancer metastasis in formalin-fixed paraffin-embedded tissues","volume":"14","author":"Casadonte","year":"2014","journal-title":"Proteomics"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1016\/j.breast.2016.07.009","article-title":"Validated biomarkers: The key to precision treatment in patients with breast cancer","volume":"29","author":"Duffy","year":"2016","journal-title":"Breast"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"10100","DOI":"10.1038\/s41598-017-10493-w","article-title":"Functional proteomics outlines the complexity of breast cancer molecular subtypes","volume":"7","author":"Selevsek","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1200\/JCO.2011.41.0902","article-title":"Prognostic and predictive value of tumor-infiltrating lymphocytes in a phase III randomized adjuvant breast cancer trial in node-positive breast cancer comparing the addition of docetaxel to doxorubicin with doxorubicin-based chemotherapy: BIG 02-98","volume":"31","author":"Loi","year":"2013","journal-title":"J. Clin. Oncol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1200\/JCO.2009.23.7370","article-title":"Tumor-Associated Lymphocytes As an Independent Predictor of Response to Neoadjuvant Chemotherapy in Breast Cancer","volume":"28","author":"Denkert","year":"2010","journal-title":"J. Clin. Oncol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/nrc1388","article-title":"Cancer and the chemokine network","volume":"4","author":"Balkwill","year":"2004","journal-title":"Nat. Rev. Cancer"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1016\/j.ccr.2014.03.021","article-title":"A Positive Feedback Loop between Mesenchymal-like Cancer Cells and Macrophages Is Essential to Breast Cancer Metastasis","volume":"25","author":"Su","year":"2014","journal-title":"Cancer Cell"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1330","DOI":"10.1016\/j.cell.2019.03.005","article-title":"A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer","volume":"177","author":"Wagner","year":"2019","journal-title":"Cell"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e696","DOI":"10.1002\/ctm2.696","article-title":"Spatial omics: Navigating to the golden era of cancer research","volume":"12","author":"Wu","year":"2022","journal-title":"Clin. Transl. Med."},{"key":"ref_27","first-page":"2435","article-title":"HER-2 tyrosine kinase pathway targets estrogen receptor and promotes hormone-independent growth in human breast cancer cells","volume":"10","author":"Pietras","year":"1995","journal-title":"Oncogene"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"6071","DOI":"10.1158\/0008-5472.CAN-04-0416","article-title":"Hedgehog signaling pathway is a new therapeutic target for patients with breast cancer","volume":"64","author":"Kubo","year":"2004","journal-title":"Cancer Res."},{"key":"ref_29","first-page":"302","article-title":"Pathway-based analysis of breast cancer","volume":"6","author":"Song","year":"2014","journal-title":"Am. J. Transl. Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"9258396","DOI":"10.1155\/2020\/9258396","article-title":"Signal Transduction Pathways in Breast Cancer: The Important Role of PI3K\/Akt\/mTOR","volume":"2020","author":"Ortega","year":"2020","journal-title":"J. Oncol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Schramm, G., Kannabiran, N., and Konig, R. (2010). Regulation patterns in signaling networks of cancer. BMC Syst. Biol., 4.","DOI":"10.1186\/1752-0509-4-162"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/nrc3261","article-title":"Intra-tumour heterogeneity: A looking glass for cancer?","volume":"12","author":"Marusyk","year":"2012","journal-title":"Nat. Rev. Cancer"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1111\/his.13334","article-title":"Altered glutamine metabolism in breast cancer; subtype dependencies and alternative adaptations","volume":"72","author":"McIntyre","year":"2018","journal-title":"Histopathology"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"602416","DOI":"10.3389\/fonc.2020.602416","article-title":"The Metabolic Mechanisms of Breast Cancer Metastasis","volume":"10","author":"Wang","year":"2020","journal-title":"Front. Oncol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"191","DOI":"10.4137\/BMI.S2557","article-title":"Protein modifications as potential biomarkers in breast cancer","volume":"4","author":"Jin","year":"2009","journal-title":"Biomark. Insights"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"10421","DOI":"10.1039\/D0SC02803G","article-title":"Post translational modification-assisted cancer immunotherapy for effective breast cancer treatment","volume":"11","author":"Theivendran","year":"2020","journal-title":"Chem. Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1158\/1541-7786.MCR-08-0299","article-title":"Specific activity of class II histone deacetylases in human breast cancer cells","volume":"6","author":"Duong","year":"2008","journal-title":"Mol. Cancer Res."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"113","DOI":"10.5483\/BMBRep.2019.52.2.017","article-title":"Regulation of post-translational modification in breast cancer treatment","volume":"52","author":"Heo","year":"2019","journal-title":"BMB Rep."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1080\/10409238.2020.1738332","article-title":"The implication of the SUMOylation pathway in breast cancer pathogenesis and treatment","volume":"55","author":"Rabellino","year":"2020","journal-title":"Crit. Rev. Biochem. Mol. Biol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Zhai, Q., Fan, J., Lin, Q., Liu, X., Li, J., Hong, R., and Wang, S. (2019). Tumor stromal type is associated with stromal PD-L1 expression and predicts outcomes in breast cancer. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0223325"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"216","DOI":"10.5694\/mja16.01020","article-title":"Radiation therapy and early breast cancer: Current controversies","volume":"207","author":"Boyages","year":"2017","journal-title":"Med. J. Aust."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.cell.2011.05.040","article-title":"Biomechanical remodeling of the microenvironment by stromal caveolin-1 favors tumor invasion and metastasis","volume":"146","author":"Goetz","year":"2011","journal-title":"Cell"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1007\/s10549-012-1984-x","article-title":"Podoplanin-expressing cancer-associated fibroblasts are associated with poor prognosis in invasive breast cancer","volume":"134","author":"Schoppmann","year":"2012","journal-title":"Breast Cancer Res. Treat."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1038\/ng1596","article-title":"Distinct epigenetic changes in the stromal cells of breast cancers","volume":"37","author":"Hu","year":"2005","journal-title":"Nat. Genet."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1021\/jasms.0c00439","article-title":"Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics","volume":"32","author":"Taylor","year":"2021","journal-title":"J. Am. Soc. Mass. Spectr."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/nrc1804","article-title":"Mapping normal and cancer cell signalling networks: Towards single-cell proteomics","volume":"6","author":"Irish","year":"2006","journal-title":"Nat. Rev. Cancer"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1038\/nature08012","article-title":"Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis","volume":"459","author":"Spencer","year":"2009","journal-title":"Nature"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/nature22794","article-title":"Rare cell variability and drug- induced reprogramming as a mode of cancer drug resistance","volume":"546","author":"Shaffer","year":"2017","journal-title":"Nature"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1016\/j.jaci.2013.03.015","article-title":"Mechanisms underlying helper T-cell plasticity: Implications for immune-mediated disease","volume":"131","author":"Hirahara","year":"2013","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1016\/j.celrep.2017.06.074","article-title":"Proteomic and Metabolomic Characterization of a Mammalian Cellular Transition from Quiescence to Proliferation","volume":"20","author":"Lee","year":"2017","journal-title":"Cell Rep."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/j.tibs.2021.01.013","article-title":"Single-Cell Proteomics","volume":"46","author":"Vistain","year":"2021","journal-title":"Trends Biochem. Sci."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1007\/s10911-020-09470-3","article-title":"Methodological Advancements for Investigating Intra-tumoral Heterogeneity in Breast Cancer at the Bench and Bedside","volume":"25","author":"Baek","year":"2020","journal-title":"J. Mammary Gland. Biol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/nature19949","article-title":"Mass-spectrometric exploration of proteome structure and function","volume":"537","author":"Aebersold","year":"2016","journal-title":"Nature"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1586\/14789450.2014.899469","article-title":"Proteomic analysis of tissue samples in translational breast cancer research","volume":"11","author":"Gromov","year":"2014","journal-title":"Expert. Rev. Proteom."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Foss, E.J., Radulovic, D., Shaffer, S.A., Goodlett, D.R., Kruglyak, L., and Bedalov, A. (2011). Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms. PLoS Biol., 9.","DOI":"10.1371\/journal.pbio.1001144"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"5626","DOI":"10.1111\/febs.12502","article-title":"Proteomics methods for subcellular proteome analysis","volume":"280","author":"Drissi","year":"2013","journal-title":"FEBS J."},{"key":"ref_57","first-page":"251","article-title":"Comparative Proteomics of Tumor and Paired Normal Breast Tissue Highlights Potential Biomarkers in Breast Cancer","volume":"12","author":"Gomig","year":"2015","journal-title":"Cancer Genom. Proteom."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1002\/bmb.21516","article-title":"Applications of western blot technique: From bench to bedside","volume":"49","author":"Meftahi","year":"2021","journal-title":"Biochem. Mol. Biol. Educ."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1002\/adma.201503939","article-title":"Hydrogel Pore-Size Modulation for Enhanced Single-Cell Western Blotting","volume":"28","author":"Duncombe","year":"2016","journal-title":"Adv. Mater."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"2379","DOI":"10.1021\/acs.jproteome.0c00061","article-title":"Improved Alignment and Quantification of Protein Signals in Two-Dimensional Western Blotting","volume":"19","author":"Herzog","year":"2020","journal-title":"J. Proteome Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"101556","DOI":"10.1016\/j.tranon.2022.101556","article-title":"Recent advances in the field of single-cell proteomics","volume":"27","author":"Petrosius","year":"2023","journal-title":"Transl. Oncol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1080\/10408363.2021.1942781","article-title":"Molecular tissue profiling by MALDI imaging: Recent progress and applications in cancer research","volume":"58","author":"Lee","year":"2021","journal-title":"Crit. Rev. Clin. Lab. Sci."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1126\/science.2675315","article-title":"Electrospray ionization for mass spectrometry of large biomolecules","volume":"246","author":"Fenn","year":"1989","journal-title":"Science"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0168-1176(87)87041-6","article-title":"Matrix-Assisted Ultraviolet-Laser Desorption of Nonvolatile Compounds","volume":"78","author":"Karas","year":"1987","journal-title":"Int. J. Mass. Spectrom."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1038\/s41587-022-01302-5","article-title":"Deep Visual Proteomics defines single-cell identity and heterogeneity","volume":"40","author":"Mund","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"161","DOI":"10.12688\/f1000research.10851.1","article-title":"The challenges with the validation of research antibodies","volume":"6","author":"Voskuil","year":"2017","journal-title":"F1000Res"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1586\/14789450.5.4.603","article-title":"Complementary methods to assist subcellular fractionation in organellar proteomics","volume":"5","author":"Gauthier","year":"2008","journal-title":"Expert. Rev. Proteom."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"e1900029","DOI":"10.1002\/pmic.201900029","article-title":"Targeted and Untargeted Proteomics Approaches in Biomarker Development","volume":"20","author":"Sobsey","year":"2020","journal-title":"Proteomics"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1038\/labinvest.3700343","article-title":"Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS\/MS","volume":"85","author":"Crockett","year":"2005","journal-title":"Lab. Investig."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/nmeth.2369","article-title":"Proteoform: A single term describing protein complexity","volume":"10","author":"Smith","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1136\/mp.53.2.64","article-title":"Laser capture microscopy","volume":"53","author":"Curran","year":"2000","journal-title":"Mol. Pathol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1080\/14789450.2021.1984886","article-title":"Laser Capture Proteomics: Spatial tissue molecular profiling from the bench to personalized medicine","volume":"18","author":"Liotta","year":"2021","journal-title":"Expert. Rev. Proteom."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/s00418-013-1127-4","article-title":"Qualitative and quantitative mass spectrometry imaging of drugs and metabolites in tissue at therapeutic levels","volume":"140","author":"Sun","year":"2013","journal-title":"Histochem. Cell Biol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1021\/pr060549i","article-title":"Direct analysis and MALDI imaging of formalin-fixed, paraffin-embedded tissue sections","volume":"6","author":"Lemaire","year":"2007","journal-title":"J. Proteome Res."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"2622","DOI":"10.1002\/pmic.200800364","article-title":"Sample preparation issues for tissue imaging by imaging MS","volume":"9","author":"Kaletas","year":"2009","journal-title":"Proteomics"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1002\/jms.505","article-title":"Direct tissue analysis using matrix-assisted laser desorption\/ionization mass spectrometry: Practical aspects of sample preparation","volume":"38","author":"Schwartz","year":"2003","journal-title":"J. Mass. Spectrom."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1089\/bio.2012.0052","article-title":"Archived formalin-fixed paraffin-embedded (FFPE) blocks: A valuable underexploited resource for extraction of DNA, RNA, and protein","volume":"11","author":"Kokkat","year":"2013","journal-title":"Biopreserv. Biobank"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1039\/b800098k","article-title":"Mining the archival formalin-fixed paraffin-embedded tissue proteome: Opportunities and challenges","volume":"4","author":"Nirmalan","year":"2008","journal-title":"Mol. Biosyst."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1021\/acs.analchem.6b04185","article-title":"Precast Gelatin-Based Molds for Tissue Embedding Compatible with Mass Spectrometry Imaging","volume":"89","author":"Gill","year":"2017","journal-title":"Anal. Chem."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"6352","DOI":"10.1038\/s41598-017-06583-4","article-title":"Mass Spectrometry Imaging proves differential absorption profiles of well-characterised permeability markers along the crypt-villus axis","volume":"7","author":"Nilsson","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"4788","DOI":"10.1021\/acs.analchem.6b00165","article-title":"Inflation-Fixation Method for Lipidomic Mapping of Lung Biopsies by Matrix Assisted Laser Desorption\/Ionization-Mass Spectrometry Imaging","volume":"88","author":"Carter","year":"2016","journal-title":"Anal. Chem."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"2309","DOI":"10.1021\/cr3004295","article-title":"Analysis of tissue specimens by matrix-assisted laser desorption\/ionization imaging mass spectrometry in biological and clinical research","volume":"113","author":"Norris","year":"2013","journal-title":"Chem. Rev."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1021\/acs.jproteome.7b00713","article-title":"Mapping Extracellular Matrix Proteins in Formalin-Fixed, Paraffin-Embedded Tissues by MALDI Imaging Mass Spectrometry","volume":"17","author":"Angel","year":"2018","journal-title":"J. Proteome Res."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/S1044-0305(98)00135-4","article-title":"Investigations of matrix-assisted laser desorption\/ionization sample preparation by time-of-flight secondary ion mass spectrometry","volume":"10","author":"Hanton","year":"1999","journal-title":"J. Am. Soc. Mass. Spectr."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"2299","DOI":"10.1021\/ac00171a028","article-title":"Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons","volume":"60","author":"Karas","year":"1988","journal-title":"Anal. Chem."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"3946","DOI":"10.1016\/j.chroma.2010.01.033","article-title":"A concise review of mass spectrometry imaging","volume":"1217","author":"Smith","year":"2010","journal-title":"J. Chromatogr. A"},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Chen, K., Baluya, D., Tosun, M., Li, F., and Maletic-Savatic, M. (2019). Imaging Mass Spectrometry: A New Tool to Assess Molecular Underpinnings of Neurodegeneration. Metabolites, 9.","DOI":"10.3390\/metabo9070135"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1038\/nrd1011","article-title":"The basics of mass spectrometry in the twenty-first century","volume":"2","author":"Glish","year":"2003","journal-title":"Nat. Rev. Drug. Discov."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"1510","DOI":"10.1039\/D2NP00011C","article-title":"Image to insight: Exploring natural products through mass spectrometry imaging","volume":"39","author":"Dong","year":"2022","journal-title":"Nat. Prod. Rep."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"e13063","DOI":"10.1200\/JCO.2020.38.15_suppl.e13063","article-title":"A novel proteomic mass spectrometry-based approach to reveal functionally heterogeneous tumor clones in breast cancer metastases and identify clone-specific drug targets","volume":"38","author":"Hajjaji","year":"2020","journal-title":"J. Clin. Oncol."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/j.jasms.2009.09.016","article-title":"On-tissue protein identification and imaging by MALDI-ion mobility mass spectrometry","volume":"21","author":"Stauber","year":"2010","journal-title":"J. Am. Soc. Mass. Spectrom."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1089\/gtmb.2020.0086","article-title":"HnRNPA2\/B1 Is a Novel Prognostic Biomarker for Breast Cancer Patients","volume":"24","author":"Ma","year":"2020","journal-title":"Genet. Test. Mol. Biomark."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1080\/13102818.2021.1985611","article-title":"Filamin-A expression in triple-negative breast cancer and its clinical significance","volume":"35","author":"Ouban","year":"2021","journal-title":"Biotechnol. Biotechnol. Equip."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1126\/science.aaa1051","article-title":"Mass spectrometry imaging with laser-induced postionization","volume":"348","author":"Soltwisch","year":"2015","journal-title":"Science"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1002\/jms.3108","article-title":"Direct imaging of single cells and tissue at sub-cellular spatial resolution using transmission geometry MALDI MS","volume":"47","author":"Zavalin","year":"2012","journal-title":"J. Mass Spectrom."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1038\/s41592-019-0536-2","article-title":"Transmission-mode MALDI-2 mass spectrometry imaging of cells and tissues at subcellular resolution","volume":"16","author":"Niehaus","year":"2019","journal-title":"Nat. Methods"},{"key":"ref_97","first-page":"71","article-title":"Recent Advances of MALDI-Mass Spectrometry Imaging in Cancer Research","volume":"10","author":"Jung","year":"2019","journal-title":"Mass Spectrom. Lett."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.jprot.2018.02.008","article-title":"Application of targeted mass spectrometry in bottom-up proteomics for systems biology research","volume":"189","author":"Manes","year":"2018","journal-title":"J. Proteom."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"2160","DOI":"10.1002\/pmic.201500449","article-title":"Advances in targeted proteomics and applications to biomedical research","volume":"16","author":"Shi","year":"2016","journal-title":"Proteomics"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.1351\/PAC-REC-06-04-06","article-title":"Definitions of terms relating to mass spectrometry (IUPAC Recommendations 2013)","volume":"85","author":"Murray","year":"2013","journal-title":"Pure Appl. Chem."},{"key":"ref_101","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_102","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1016\/1044-0305(92)85001-Z","article-title":"Principles of collisional activation in analytical mass spectrometry","volume":"3","author":"McLuckey","year":"1992","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1002\/(SICI)1096-9888(199604)31:4<339::AID-JMS322>3.0.CO;2-L","article-title":"Surface-induced dissociation: An effective tool to probe structure, energetics and fragmentation mechanisms of protonated peptides","volume":"31","author":"Dongre","year":"1996","journal-title":"J. Mass Spectrom."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1002\/pmic.201100517","article-title":"Electron transfer dissociation mass spectrometry in proteomics","volume":"12","author":"Kim","year":"2012","journal-title":"Proteomics"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"100416","DOI":"10.1016\/j.mcpro.2022.100416","article-title":"Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays","volume":"21","author":"Steiner","year":"2022","journal-title":"Mol. Cell Proteomics"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1200\/EDBK_351207","article-title":"Protein Profiling of Breast Cancer for Treatment Decision-Making","volume":"42","author":"Badve","year":"2022","journal-title":"Am. Soc. Clin. Oncol. Educ. Book"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1002\/cac2.12023","article-title":"Overview of multiplex immunohistochemistry\/immunofluorescence techniques in the era of cancer immunotherapy","volume":"40","author":"Tan","year":"2020","journal-title":"Cancer Commun."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"16079","DOI":"10.1038\/micronano.2016.79","article-title":"Subcellular western blotting of single cells","volume":"3","author":"Yamauchi","year":"2017","journal-title":"Microsyst. Nanoeng."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1007\/978-1-4939-8935-5_26","article-title":"An Introduction to Performing Immunofluorescence Staining","volume":"1897","author":"Im","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"960734","DOI":"10.3389\/fonc.2022.960734","article-title":"Automated multimodal fluorescence microscopy for hyperplex spatial-proteomics: Coupling microfluidic-based immunofluorescence to high resolution, high sensitivity, three-dimensional analysis of histological slides","volume":"12","author":"Furia","year":"2022","journal-title":"Front. Oncol."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/s41698-020-0114-1","article-title":"Multiplex bioimaging of single-cell spatial profiles for precision cancer diagnostics and therapeutics","volume":"4","author":"Allam","year":"2020","journal-title":"NPJ Precis. Oncol."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"11982","DOI":"10.1073\/pnas.1300136110","article-title":"Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue","volume":"110","author":"Gerdes","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"e31657","DOI":"10.7554\/eLife.31657","article-title":"Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes","volume":"7","author":"Lin","year":"2018","journal-title":"Elife"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1038\/modpathol.2017.143","article-title":"Single-cell heterogeneity in ductal carcinoma in situ of breast","volume":"31","author":"Gerdes","year":"2018","journal-title":"Mod. Pathol."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1016\/j.cell.2018.07.010","article-title":"Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging","volume":"174","author":"Goltsev","year":"2018","journal-title":"Cell"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/s13046-021-02221-0","article-title":"cPLA2 blockade attenuates S100A7-mediated breast tumorigenicity by inhibiting the immunosuppressive tumor microenvironment","volume":"41","author":"Mishra","year":"2022","journal-title":"J. Exp. Clin. Cancer Res."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1007\/978-1-4939-8935-5_25","article-title":"An Introduction to the Performance of Immunohistochemistry","volume":"1897","author":"Magaki","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1038\/bjc.2016.204","article-title":"Non-canonical NF-kappaB pathway activation predicts outcome in borderline oestrogen receptor positive breast carcinoma","volume":"115","author":"Rojo","year":"2016","journal-title":"Br. J. Cancer"},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"1911","DOI":"10.1038\/s41598-022-05841-4","article-title":"MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors","volume":"12","author":"Kinkhabwala","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.aca.2019.04.064","article-title":"High-resolution imaging and single-cell analysis via laser ablation-inductively coupled plasma-mass spectrometry for the determination of membranous receptor expression levels in breast cancer cell lines using receptor-specific hybrid tracers","volume":"1074","author":"Buckle","year":"2019","journal-title":"Anal. Chim. Acta"},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1002\/cyto.a.23053","article-title":"Imaging Mass Cytometry","volume":"91","author":"Chang","year":"2017","journal-title":"Cytometry A"},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"6813","DOI":"10.1021\/ac901049w","article-title":"Mass cytometry: Technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry","volume":"81","author":"Bandura","year":"2009","journal-title":"Anal. Chem."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.2869","article-title":"Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry","volume":"11","author":"Giesen","year":"2014","journal-title":"Nat. Methods"},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1002\/mas.20124","article-title":"Imaging mass spectrometry","volume":"26","author":"McDonnell","year":"2007","journal-title":"Mass Spectrom. Rev."},{"key":"ref_125","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_126","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/nm.3488","article-title":"Multiplexed ion beam imaging of human breast tumors","volume":"20","author":"Angelo","year":"2014","journal-title":"Nat. Med."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1038\/s41587-020-0472-9","article-title":"Multiplex digital spatial profiling of proteins and RNA in fixed tissue","volume":"38","author":"Merritt","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1007\/s00428-020-02821-9","article-title":"Digital spatial profiling application in breast cancer: A user's perspective","volume":"477","author":"Bennett","year":"2020","journal-title":"Virchows Arch."},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1021\/jasms.0c00473","article-title":"Highly Multiplexed Immunohistochemical MALDI-MS Imaging of Biomarkers in Tissues","volume":"32","author":"Yagnik","year":"2021","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"ref_130","doi-asserted-by":"crossref","unstructured":"Alexandrov, T. (2012). MALDI imaging mass spectrometry: Statistical data analysis and current computational challenges. BMC Bioinform., 13.","DOI":"10.1186\/1471-2105-13-S16-S11"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1002\/mas.21527","article-title":"Signal preprocessing, multivariate analysis and software tools for MA(LDI)-TOF mass spectrometry imaging for biological applications","volume":"37","author":"Rafols","year":"2018","journal-title":"Mass Spectrom. Rev."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.bbapap.2013.01.040","article-title":"2D and 3D MALDI-imaging: Conceptual strategies for visualization and data mining","volume":"1844","author":"Thiele","year":"2014","journal-title":"Biochim. Biophys Acta"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"2803","DOI":"10.1007\/s00216-021-03179-w","article-title":"Spatially aware clustering of ion images in mass spectrometry imaging data using deep learning","volume":"413","author":"Zhang","year":"2021","journal-title":"Anal. Bioanal. 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