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The iTRAQ labeling method is a powerful technique; when combined with LC coupled to MS\/MS it allows relative quantitation of up to eight different samples simultaneously. Despite the usefulness of iTRAQ current software solutions have limited functionality and require the combined use of several software programs for analysis of the data from different MS vendors. We developed an integrated tool, now available in the virtual expert mass spectrometrist (VEMS) program, for database\u2010dependent search of MS\/MS spectra, quantitation and database storage for iTRAQ\u2010labeled samples. VEMS also provides useful alternative report types for large\u2010scale quantitative experiments. The implemented statistical algorithms build on quantitative algorithms previously used in proposed iTRAQ tools as described in detail herein. We propose a new algorithm, which provides more accurate peptide ratios for data that show an intensity\u2010dependent saturation. The accuracy of the proposed iTRAQ algorithm and the performance of VEMS are demonstrated by comparing results from VEMS, MASCOT and PEAKS Q obtained by analyzing data from a reference mixture of six proteins. Users can download VEMS and test data from \u201c<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.portugene.com\/software.html\">http:\/\/www.portugene.com\/software.html<\/jats:ext-link>\u201d.<\/jats:p>","DOI":"10.1002\/pmic.200900255","type":"journal-article","created":{"date-parts":[[2010,2,5]],"date-time":"2010-02-05T09:09:01Z","timestamp":1265360941000},"page":"1545-1556","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Virtual Expert Mass Spectrometrist: iTRAQ tool for database\u2010dependent search, quantitation and result storage"],"prefix":"10.1002","volume":"10","author":[{"given":"Eva","family":"Rodr\u00edguez\u2010Su\u00e1rez","sequence":"first","affiliation":[]},{"given":"Ewa","family":"Gubb","sequence":"additional","affiliation":[]},{"given":"Itziar Frades","family":"Alzueta","sequence":"additional","affiliation":[]},{"given":"Juan Manuel","family":"Falc\u00f3n\u2010P\u00e9rez","sequence":"additional","affiliation":[]},{"given":"Ant\u00f3nio","family":"Amorim","sequence":"additional","affiliation":[]},{"given":"Felix","family":"Elortza","sequence":"additional","affiliation":[]},{"given":"Rune","family":"Matthiesen","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2010,4,15]]},"reference":[{"key":"e_1_2_6_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/2211056a0"},{"key":"e_1_2_6_3_2","doi-asserted-by":"publisher","DOI":"10.1021\/pr060593y"},{"key":"e_1_2_6_4_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M600449-MCP200"},{"key":"e_1_2_6_5_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1522-2683(20000401)21:6<1104::AID-ELPS1104>3.0.CO;2-C"},{"key":"e_1_2_6_6_2","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200390006"},{"key":"e_1_2_6_7_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.T100007-MCP200"},{"key":"e_1_2_6_8_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja991063o"},{"key":"e_1_2_6_9_2","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200700127"},{"key":"e_1_2_6_10_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M500084-MCP200"},{"key":"e_1_2_6_11_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M600007-MCP200"},{"key":"e_1_2_6_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/13690"},{"key":"e_1_2_6_13_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M700072-MCP200"},{"key":"e_1_2_6_14_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M200025-MCP200"},{"key":"e_1_2_6_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2008.2"},{"key":"e_1_2_6_16_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.12.6591"},{"key":"e_1_2_6_17_2","doi-asserted-by":"publisher","DOI":"10.1021\/ac001487x"},{"key":"e_1_2_6_18_2","doi-asserted-by":"publisher","DOI":"10.1021\/ac001404c"},{"key":"e_1_2_6_19_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.T600029-MCP200"},{"key":"e_1_2_6_20_2","doi-asserted-by":"publisher","DOI":"10.1021\/pr070401e"},{"key":"e_1_2_6_21_2","doi-asserted-by":"publisher","DOI":"10.1021\/ac0262560"},{"key":"e_1_2_6_22_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M400129-MCP200"},{"key":"e_1_2_6_23_2","doi-asserted-by":"publisher","DOI":"10.1093\/bfgp\/eln007"},{"key":"e_1_2_6_24_2","doi-asserted-by":"publisher","DOI":"10.1021\/pr8001113"},{"key":"e_1_2_6_25_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jasms.2008.05.023"},{"key":"e_1_2_6_26_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M700370-MCP200"},{"key":"e_1_2_6_27_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M700251-MCP200"},{"key":"e_1_2_6_28_2","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M700500-MCP200"},{"key":"e_1_2_6_29_2","doi-asserted-by":"publisher","DOI":"10.1021\/pr800197z"},{"key":"e_1_2_6_30_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm467"},{"key":"e_1_2_6_31_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-6-145"},{"key":"e_1_2_6_32_2","doi-asserted-by":"publisher","DOI":"10.1021\/pr060132c"},{"key":"e_1_2_6_33_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm345"},{"key":"e_1_2_6_34_2","doi-asserted-by":"publisher","DOI":"10.1021\/pr050264q"},{"key":"e_1_2_6_35_2","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200800412"},{"key":"e_1_2_6_36_2","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.147.3.599"},{"key":"e_1_2_6_37_2","doi-asserted-by":"publisher","DOI":"10.1084\/jem.183.3.1161"},{"key":"e_1_2_6_38_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-1759(02)00330-7"},{"key":"e_1_2_6_39_2","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200402091"},{"key":"e_1_2_6_40_2","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200700116"},{"key":"e_1_2_6_41_2","doi-asserted-by":"publisher","DOI":"10.1351\/pac199870040993"},{"key":"e_1_2_6_42_2","first-page":"214","article-title":"Precise protein quantification based on peptide quantification using iTRAQ","volume":"8","author":"Boehm A. 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