{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T03:15:19Z","timestamp":1790046919024,"version":"4.0.1"},"reference-count":160,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2023,4,3]],"date-time":"2023-04-03T00:00:00Z","timestamp":1680480000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Cancer Institute of the National Institutes of Health","award":["R15CA260126"],"award-info":[{"award-number":["R15CA260126"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteomes"],"abstract":"<jats:p>Invasive ductal carcinoma (IDC) is the most common histological subtype of malignant breast cancer (BC), and accounts for 70\u201380% of all invasive BCs. IDC demonstrates great heterogeneity in clinical and histopathological characteristics, prognoses, treatment strategies, gene expressions, and proteomic profiles. Significant proteomic determinants of the progression from intraductal pre-invasive malignant lesions of the breast, which characterize a ductal carcinoma in situ (DCIS), to IDC, are still poorly identified, validated, and clinically applied. In the era of \u201c6P\u201d medicine, it remains a great challenge to determine which patients should be over-treated versus which need to be actively monitored without aggressive treatment. The major difficulties for designating DCIS to IDC progression may be solved by understanding the integrated genomic, transcriptomic, and proteomic bases of invasion. In this review, we showed that multiple proteomics-based techniques, such as LC\u2013MS\/MS, MALDI-ToF MS, SELDI-ToF-MS, MALDI-ToF\/ToF MS, MALDI-MSI or MasSpec Pen, applied to in-tissue, off-tissue, BC cell lines and liquid biopsies, improve the diagnosis of IDC, as well as its prognosis and treatment monitoring. Classic proteomics strategies that allow the identification of dysregulated protein expressions, biological processes, and interrelated pathway analyses based on aberrant protein\u2013protein interaction (PPI) networks have been improved to perform non-invasive\/minimally invasive biomarker detection of early-stage IDC. Thus, in modern surgical oncology, highly sensitive, rapid, and accurate MS-based detection has been coupled with \u201cproteome point sampling\u201d methods that allow for proteomic profiling by in vivo \u201cproteome point characterization\u201d, or by minimal tissue removal, for ex vivo accurate differentiation and delimitation of IDC. For the detection of low-molecular-weight proteins and protein fragments in bodily fluids, LC\u2013MS\/MS and MALDI-MS techniques may be coupled to enrich and capture methods which allow for the identification of early-stage IDC protein biomarkers that were previously invisible for MS-based techniques. Moreover, the detection and characterization of protein isoforms, including posttranslational modifications of proteins (PTMs), is also essential to emphasize specific molecular mechanisms, and to assure the early-stage detection of IDC of the breast.<\/jats:p>","DOI":"10.3390\/proteomes11020013","type":"journal-article","created":{"date-parts":[[2023,4,3]],"date-time":"2023-04-03T02:32:27Z","timestamp":1680489147000},"page":"13","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Proteomics-Based Identification of Dysregulated Proteins and Biomarker Discovery in Invasive Ductal Carcinoma, the Most Common Breast Cancer Subtype"],"prefix":"10.3390","volume":"11","author":[{"given":"Anca-Narcisa","family":"Neagu","sequence":"first","affiliation":[{"name":"Laboratory of Animal Histology, Faculty of Biology, \u201cAlexandru Ioan Cuza\u201d University of Iasi, Carol I bvd. No. 20A, 700505 Iasi, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4799-8096","authenticated-orcid":false,"given":"Danielle","family":"Whitham","sequence":"additional","affiliation":[{"name":"Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Logan","family":"Seymour","sequence":"additional","affiliation":[{"name":"Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-9357-6636","authenticated-orcid":false,"given":"Norman","family":"Haaker","sequence":"additional","affiliation":[{"name":"Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabella","family":"Pelkey","sequence":"additional","affiliation":[{"name":"Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6402-2311","authenticated-orcid":false,"given":"Costel C.","family":"Darie","sequence":"additional","affiliation":[{"name":"Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,4,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2523","DOI":"10.1091\/mbc.e03-11-0786","article-title":"Different Gene Expression Patterns in Invasive Lobular and Ductal Carcinomas of the Breast","volume":"15","author":"Zhao","year":"2004","journal-title":"Mol. 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