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However, because the proteome of most organisms are significantly more complex than the genome, the comprehensive analysis of protein expression changes will require an analytical effort beyond the capacity of standard laboratory equipment. We describe the first high\u2010throughput proteomic analysis of human breast infiltrating ductal carcinoma (IDCA) using OCT (optimal cutting temperature) embedded biopsies, two\u2010dimensional difference gel electrophoresis (2\u2010D DIGE) technology and a fully automated spot handling workstation. Total proteins from four breast IDCAs (Stage\u00a0I, IIA, IIB and IIIA) were individually compared to protein from non\u2010neoplastic tissue obtained from a female donor with no personal or family history of breast cancer. We detected differences in protein abundance that ranged from 14.8% in stage\u00a0I IDCA <jats:italic>versus<\/jats:italic> normal, to 30.6% in stage IIB IDCA <jats:italic>versus<\/jats:italic> normal. A total of 524 proteins that showed \u2265\u00a0three\u2010fold difference in abundance between IDCA and normal tissue were picked, processed and identified by mass spectrometry. Out of the proteins picked, \u223c\u200980% were unambiguously assigned identities by matrix\u2010assisted laser desorbtion\/ionization\u2010time of flight mass spectrometry or liquid chromatography\u2010tandem mass spectrometry in the first pass. Bioinformatics tools were also used to mine databases to determine if the identified proteins are involved in important pathways and\/or interact with other proteins. Gelsolin, vinculin, lumican, alpha\u20101\u2010antitrypsin, heat shock protein\u201060, cytokeratin\u201018, transferrin, enolase\u20101 and \u03b2\u2010actin, showed differential abundance between IDCA and normal tissue, but the trend was not consistent in all samples. Out of the proteins with database hits, only heat shock protein\u201070 (more abundant) and peroxiredoxin\u20102 (less abundant) displayed the same trend in all the IDCAs examined. This preliminary study demonstrates quantitative and qualitative differences in protein abundance between breast IDCAs and reveals 2\u2010D DIGE portraits that may be a reflection of the histological and pathological status of breast IDCA.<\/jats:p>","DOI":"10.1002\/pmic.200300560","type":"journal-article","created":{"date-parts":[[2003,11,14]],"date-time":"2003-11-14T17:52:22Z","timestamp":1068832342000},"page":"1863-1873","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":149,"title":["High\u2010throughput proteomic analysis of human infiltrating ductal carcinoma of the breast"],"prefix":"10.1002","volume":"3","author":[{"given":"Richard I.","family":"Somiari","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony","family":"Sullivan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Russell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stella","family":"Somiari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hai","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rick","family":"Jordan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alisha","family":"George","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Katenhusen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alicja","family":"Buchowiecka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cletus","family":"Arciero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henry","family":"Brzeski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeff","family":"Hooke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Craig","family":"Shriver","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2003,10,9]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1002\/1615-9861(200110)1:10<1205::AID-PROT1205>3.0.CO;2-X"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1002\/1522-2683(20000601)21:11<2099::AID-ELPS2099>3.0.CO;2-N"},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0014-5793(00)01771-3"},{"key":"e_1_2_1_5_2","doi-asserted-by":"publisher","DOI":"10.1002\/3527600175"},{"key":"e_1_2_1_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1097-2765(00)00132-5"},{"key":"e_1_2_1_7_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1522-2683(20000401)21:6<1202::AID-ELPS1202>3.0.CO;2-I"},{"key":"e_1_2_1_8_2","first-page":"69","volume":"7","author":"Bichsel V. 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