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The present study demonstrates an in\u2010depth gel\u2010based proteome optimization survey to approach more appropriate and efficient systems in various situations such as normal and dry\u2010eye syndromes. Therefore, systematic and statistical evaluations were performed on different preparation methods, including acetone, acetone\u2013methanol, chloroform\u2013methanol\u2013water, trichloroacetic acid (TCA)\u2013acetone, tri\u2010<jats:italic>n<\/jats:italic>\u2010butylphosphate\u2013acetone\u2013methanol precipitations and ammonium sulfate fractionation at three different percentages of saturations (50, 70 and 90%). Methods were compared quantitatively on both one\u2010 and two\u2010dimensional patterns. Some important parameters such as total protein recovery yield, densitometric analysis of some protein contaminants, banding patterns and total spot numbers along with statistical models for proper clustering were considered. Findings revealed noticeable impacts of preparation methods on all aspects of gel\u2010based separations as well as recovery yield (ranging from 5.29\u2009\u00b1\u20090.96 to 22.56\u2009\u00b1\u20091.77\u2009\u00b5g\/mm) and banding and pattern resolution. In addition to all these, the most important point is that the total protein spot number on the final two\u2010dimensional patterns (varied from 528.00\u2009\u00b1\u200919.00 to 657.00\u2009\u00b1\u200921.52 for different methods) were also noticeably increased in comparison with previously published reports (maximum of 250 spots), which is essential for a more comprehensive analysis. Increasing the proteome coverage in the present study is supposed to originate from improved solubility and effective rehydration during the sample application and isoelectric focusing (IEF) procedure along with proper sample preparation. Copyright \u00a9 2014 John Wiley &amp; Sons, Ltd.<\/jats:p>","DOI":"10.1002\/bmc.3392","type":"journal-article","created":{"date-parts":[[2014,12,2]],"date-time":"2014-12-02T02:14:03Z","timestamp":1417486443000},"page":"1056-1067","source":"Crossref","is-referenced-by-count":8,"title":["Increasing proteome coverage for gel\u2010based human tear proteome maps: towards a more comprehensive profiling"],"prefix":"10.1002","volume":"29","author":[{"given":"Neda","family":"Saraygord\u2010Afshari","sequence":"first","affiliation":[{"name":"Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University  Tehran Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hossein","family":"Naderi\u2010Manesh","sequence":"additional","affiliation":[{"name":"Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University  Tehran Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mostafa","family":"Naderi","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology Bina eye hospital  Tehran Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2014,12,2]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.exer.2011.03.002"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cbpc.2004.02.012"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.exer.2011.12.010"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jchromb.2006.10.040"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201200121"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0076-6879(09)63020-2"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/1522-2683(200202)23:2<292::AID-ELPS292>3.0.CO;2-5"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200401222"},{"key":"e_1_2_6_10_1","volume-title":"Basic and Clinical Science Course; 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