{"content":[{"text":"Trying to Settle Ongoing Dispute, HUPO’s IAB <br>Finds 2D Gel Exp...","bbox":{"left":0.0,"top":-0.001958,"width":0.48325300000000004,"height":0.016877}},{"text":"http://www.proteomonitor.com/issues/7_44/features/143404-1.html?type=pf","bbox":{"left":0.497752,"top":-0.001958,"width":0.50169,"height":0.016877}},{"text":"Trying to Settle Ongoing Dispute, HUPO’s IAB \n Finds 2D Gel Experiments are Reproducible","bbox":{"left":0.068333,"top":0.200398,"width":0.4829120000000001,"height":0.04339599999999999}},{"text":"November 15, 2007 \n By Tony Fong","bbox":{"left":0.068333,"top":0.257362,"width":0.147228,"height":0.03245300000000001}},{"text":"In preliminary results \n from its first study aimed at addressing a longstanding problem associated with 2D gels, the Industry Advisory \n Board of the Human Proteome Organization has determined that experiments using the technology can be \n reproduced.","bbox":{"left":0.068333,"top":0.3122,"width":0.813304,"height":0.06228}},{"text":"The study, whose initial results were shared among IAB members during HUPO’s annual conference in Seoul last \n month, was meant to determine whether a widespread complaint about 2D gel work is valid.","bbox":{"left":0.068333,"top":0.386302,"width":0.8427310000000001,"height":0.032648999999999984}},{"text":"The lesson of the study is that protocols that have been proven to be robust should be followed even if they may not \n be “the best protocols in the world,” Jan van Oostrum, co-chairman of the IAB, told ProteoMonitor this week.","bbox":{"left":0.068333,"top":0.430848,"width":0.859179,"height":0.032647999999999955}},{"text":"Comparing scientists to chefs who experiment with recipes to enhance the flavor of dishes, he said researchers are \n notorious for doing the same with prescribed protocols, often with unwanted effects.","bbox":{"left":0.068333,"top":0.475318,"width":0.8542500000000001,"height":0.03264900000000004}},{"text":"“The minute you start tweaking, you get different results,” he said.","bbox":{"left":0.068333,"top":0.519864,"width":0.486395,"height":0.017800000000000038}},{"text":"“We didn’t know where the problems were before this, [but] we’ve now got a much, much better handle on the \n issues, and so we can actually to do something about them,” added Will Dracup, CEO of Nonlinear Dynamics, a \n member of the IAB.","bbox":{"left":0.068333,"top":0.549561,"width":0.8291120000000001,"height":0.047421000000000046}},{"text":"Because the results are preliminary, van Oostrum, who is also executive director of genome and proteome sciences \n at Novartis, which is not an IAB member, declined to publicly disclose them. Instead, he and his colleagues plan to \n present them at the HUPO USA meeting in March.","bbox":{"left":0.068333,"top":0.608879,"width":0.8586360000000001,"height":0.04749700000000012}},{"text":"What he would share is that experiments conducted by five laboratories involving more than 100 2D gels showed \n that if proper protocols are followed, reproducibility is not an issue with the technology. In particular, study \n organizers said they were surprised to discover that 1D separation, which has been assumed to be the “main \n culprit” to preventing 2D work from being reproduced, in fact turned out to be “extremely robust” regardless of the \n instrument that was used. By eliminating 1D separation as the source of reproducibility issues, the focus has now \n shifted to running temperatures and sample preparation as the problem.","bbox":{"left":0.068333,"top":0.668198,"width":0.838466,"height":0.09196800000000005}},{"text":"And by showing that researchers working with 2D gels can, in fact, duplicate each others’ results, the study has \n partially solved one of the largest issues dogging proteomics.","bbox":{"left":0.068333,"top":0.772063,"width":0.824411,"height":0.03264800000000001}},{"text":"“There has been a trend to basically state that 2D gels are not reproducible in the wider community, remarks which \n are mainly made by the people who use an LC-MS approach,” van Oostrum said. “Instead of entertaining an oral \n battle — ‘it’s reproducible, it’s not’ — why not just do a test and set up an experiment trying to see how we can \n make 2D gels reproducible, what is needed in order to make them reproducible if they are not in the first instance, \n and how can we solve this issue?”","bbox":{"left":0.068333,"top":0.816608,"width":0.850428,"height":0.07711900000000005}},{"text":"Credibility at Stake?","bbox":{"left":0.068333,"top":0.906067,"width":0.16117599999999999,"height":0.01783800000000002}},{"text":"Launched at HUPO’s 2006 conference, the IAB is designed to engage proteomics tools vendors to improve","bbox":{"left":0.068333,"top":0.936002,"width":0.794627,"height":0.017800000000000038}},{"text":"1 of 2","bbox":{"left":0.0,"top":0.983799,"width":0.038197,"height":0.01687699999999992}},{"text":"11/29/2007 5:31 PM","bbox":{"left":0.86402,"top":0.983799,"width":0.13554899999999992,"height":0.01687699999999992}}],"images_bbox":[{"left":0.068333,"top":0.052803,"width":0.859412,"height":0.100303}],"images_bbox_not_text_overlap":[{"left":0.068333,"top":0.052803,"width":0.859412,"height":0.100303}]}