tag:blogger.com,1999:blog-3693238014525650573.post8321632351142106118..comments2024-03-28T08:46:55.598-07:00Comments on News in Proteomics Research: More isobaric mass tag comparisons!Unknownnoreply@blogger.comBlogger3125tag:blogger.com,1999:blog-3693238014525650573.post-55777385000503571382017-02-13T20:26:29.925-08:002017-02-13T20:26:29.925-08:00Does this help at all? http://proteomicsnews.blogs...Does this help at all? http://proteomicsnews.blogspot.com/2013/11/what-does-good-tmt-or-itraq-msms.html<br />Benhttps://www.blogger.com/profile/18385704761413487532noreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-23467875747498418882017-02-13T20:20:05.878-08:002017-02-13T20:20:05.878-08:00Todd, that is interesting. 33 seems a little high ...Todd, that is interesting. 33 seems a little high unless you are operating on lower N2 levels. You aren't running 80-100PSI into it by any chance? I only ask because I was somewhere that the whole place was rigged to 80 PSI. It totally works just fine, but the CE was a little different than I'd expect. Just a thought. Benhttps://www.blogger.com/profile/18385704761413487532noreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-13135626820557249872017-02-10T08:20:14.360-08:002017-02-10T08:20:14.360-08:00Hi Ben,
Thanks for the post, I too found it curiou...Hi Ben,<br />Thanks for the post, I too found it curious why such a large difference in peptide IDs. Though I actually had a question about your NCE comment with TMT peptides that you use the same NCE for both unlabeled and TMT peptides. We have a QE HF and for unlabeled peptides a NCE of 28 works well for us. However, if I use this same NCE for TMT peptides, the reporter ions are only about 5-10% of the base peak. Is this your experience? If I increase NCE by 5, then the reporter ions are 50-100% of the base peak. Intuitively, having a higher signal seems desirable, but the best comparison would probably be a S/N analysis across NCE values. Do you know if this has been done?Toddnoreply@blogger.com