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An important step in preventing such artefacts is to preserve the native, intact proteome as early as possible during sample preparation prior to proteomic analysis. Using the budding yeast <jats:italic>Saccharomyces cerevisiae<\/jats:italic>, we have evaluated the effects of trichloroacetic acid (TCA) and thermal treatments prior to protein extraction as a means to minimise proteolysis. TCA precipitation is commonly used to inactivate proteases; thermal stabilisation is used to heat samples to approximately 95\u00b0C to inactivate enzyme activity. The efficacy of these methods was also compared with that of protease inhibitors and lyophilisation. Sample integrity was assessed by 2\u2010D PAGE and a selection of spots was identified by MS\/MS. The analysis showed that TCA or thermal treatment significantly reduced the degree of degradation and that these pre\u2010treatment protocols were more effective than treatment with either protease inhibitors or lyophilisation. This study establishes standardised sample preparation methods for the reproducible analysis of protein patterns by 2\u2010D PAGE in yeast, and may also be applicable to other proteomic analyses such as gel\u2010free\u2010based quantitation methods.<\/jats:p>","DOI":"10.1002\/pmic.200800945","type":"journal-article","created":{"date-parts":[[2009,10,12]],"date-time":"2009-10-12T14:18:31Z","timestamp":1255357111000},"page":"4616-4626","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Preserving the yeast proteome from sample degradation"],"prefix":"10.1002","volume":"9","author":[{"given":"Julia","family":"Grassl","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jules A.","family":"Westbrook","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aisling","family":"Robinson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mats","family":"Bor\u00e9n","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael J.","family":"Dunn","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rosemary K.","family":"Clyne","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2009,10,12]]},"reference":[{"key":"e_1_2_6_2_2","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200700919"},{"key":"e_1_2_6_3_2","doi-asserted-by":"publisher","DOI":"10.1002\/yea.320050107"},{"key":"e_1_2_6_4_2","doi-asserted-by":"publisher","DOI":"10.1002\/yea.320110702"},{"key":"e_1_2_6_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/0003-2697(84)90394-4"},{"key":"e_1_2_6_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0143-4179(97)90072-X"},{"key":"e_1_2_6_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jneumeth.2003.12.006"},{"key":"e_1_2_6_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/0196-9781(90)90151-T"},{"key":"e_1_2_6_9_2","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200700142"},{"key":"e_1_2_6_10_2","doi-asserted-by":"publisher","DOI":"10.1021\/pr8006446"},{"key":"e_1_2_6_11_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.3727505"},{"issue":"546","key":"e_1_2_6_12_2","first-page":"563","article-title":"Life with 6000 genes","volume":"274","author":"Goffeau A.","year":"1996","journal-title":"Science (New York, NY)"},{"key":"e_1_2_6_13_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M400087-MCP200"},{"key":"e_1_2_6_14_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M400219-MCP200"},{"key":"e_1_2_6_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt0302-301"},{"key":"e_1_2_6_16_2","doi-asserted-by":"publisher","DOI":"10.1002\/yea.320101007"},{"key":"e_1_2_6_17_2","doi-asserted-by":"publisher","DOI":"10.1021\/pr700580m"},{"key":"e_1_2_6_18_2","first-page":"148","volume-title":"A Cold Spring Harbor Laboratory Course Manual","author":"Dickerson M. 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