tag:blogger.com,1999:blog-3693238014525650573.post1321996541432840003..comments2024-03-28T08:46:55.598-07:00Comments on News in Proteomics Research: HYPER-Sol -- Crazy reproducible data from FFPE Tissues! Unknownnoreply@blogger.comBlogger1125tag:blogger.com,1999:blog-3693238014525650573.post-5173848092411096072019-06-21T08:23:38.141-07:002019-06-21T08:23:38.141-07:00I absolutely love Ruedi's work--like all of it...I absolutely love Ruedi's work--like all of it, and Tiannan has done great stuff as well--and as an author of the HYPERsol article, I want to highlight some key differences between these papers:<br />1) HYPERsol uses AFA which can be done in a 96-well format or single tubes. In contrast, we inherently cannot do PCT in an automated high-throughput format.<br />2) HYPERsol protein yields per mg FFPE are in general higher (avg. 80 ug/mg vs. avg. 60 ug/mg).<br />3) HYPERsol resulted in deeper proteome coverage of tumor samples (~4000 vs. ~3000).<br />4) HYPERsol resulted in a higher Pearson correlation with flash frozen tissue (0.94 vs. 0.91).<br />5) HYPERsol examined the oldest sample (17 vs. 15 year old).<br />6) HYPERsol uses *zero* organic solvents for deparaffinization. It's really a one-pot solution with SDS.<br />7) HYPERsol uses two solvents: SDS then digestion buffer. The more recently released work uses eight (heptane, heptane, ethanol, 90% ethanol, 75% ethanol, 0.1% formic acid, 0.1 M tris pH 10, digestion buffer).<br />8) In HYPERsol, the AFA time is 11 min total vs. 95 min processing (plus sample handling time) for this newer paper. Both digestions are 60 min.<br /><br />I look forward to comparisons of these methods.<br /><br />JPW [Those who wish to email can find it.]John P. Wilsonhttp://www.protifi.comnoreply@blogger.com