tag:blogger.com,1999:blog-3693238014525650573.post1082230901495958498..comments2024-03-28T08:46:55.598-07:00Comments on News in Proteomics Research: Dynamic exclusion mass windows -- and why they matter.Unknownnoreply@blogger.comBlogger7125tag:blogger.com,1999:blog-3693238014525650573.post-24499477052217378112014-11-19T01:37:18.658-08:002014-11-19T01:37:18.658-08:00Ian,
Welcome to the field! I certainly wish that...Ian,<br /> Welcome to the field! I certainly wish that what you were describing was a problem. In virtually every case we are fragmenting far too many things. For example, even on the Q Exactive HF, the best efficiency comes with fragmenting everything within a 1.4Da window. According to the newest Max Planck article, even with a window this narrow, between 6 and 20% of the fragment ions within that window are actually peptides other than the one that we tried to target. We can tell the Mass spec to ignore within narrow windows, but that doesn't mean that we can fragment windows that narrow. We get around that with sophisticated algorithms such as MIPS (also called peptide match) because the MS1 mass assigned to a fragmentation event is weighted much heavier during the search engine run than any of the fragment ions. <br />I'm running to the airport now and don't have time to elaborate. I would look up MIPS and peptide match for a more clear understanding of these functions (I should have some awesome pics from Tara Schroeder up on this blog somewhere that I hope will clarify.<br />Benhttps://www.blogger.com/profile/18385704761413487532noreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-12746953249680526112014-11-18T01:31:14.941-08:002014-11-18T01:31:14.941-08:00Hi,
very nice article. I am still a greenhorn in M...Hi,<br />very nice article. I am still a greenhorn in MS so I have a question. In case of very narrow window, in some cases only izotopes of the same peptide will be isolated for fragmentation. How to overcome this issue?<br />Thanks for awesome blog!<br />Ian<br />Iannoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-2221604380587494502014-11-07T15:05:09.840-08:002014-11-07T15:05:09.840-08:00Ben, thank you so much! I'm a new bird in mass...Ben, thank you so much! I'm a new bird in mass spec and what you wrote is really helpful! Anonymoushttps://www.blogger.com/profile/01993135313721316077noreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-23561188185730614382014-09-30T04:45:44.072-07:002014-09-30T04:45:44.072-07:00Sure!
On QE software up to 2.2, the DE windows ar...Sure!<br /> On QE software up to 2.2, the DE windows are locked at 10ppm. On 2.3 and up, however, you have complete control. You'll just have to download the software from the Omics portal and upgrade. Now...that being said, 2.3 requires Foundation 3.0. This may require you to update Proteome Discoverer to 1.4 SP1.<br /> Hope this helps!<br />Benhttps://www.blogger.com/profile/18385704761413487532noreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-47885497894651015102014-09-29T17:00:27.379-07:002014-09-29T17:00:27.379-07:00Thank you for these valuable informations. I have ...Thank you for these valuable informations. I have a question quite specific about Q-Exactive and XCalibur software and I would appreciate whether you could help me. How can I change the DE mass window? Are DE window and MS/MS isolation window the same parameter? If yes, the resolution reached by the quadrupole (QExactive) isn't enough to select ions in a window narrower than 0.4Da. <br /><br />Thank you again!Leandro X Nevesnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-51548791320090104902014-07-04T06:41:24.562-07:002014-07-04T06:41:24.562-07:00Thanks for your comments. It is a little instrume...Thanks for your comments. It is a little instrument specific, but you should be able to go into your instrument configuration and change it to accept PPM. Close all Thermo programs, open instrument config, go to the device that Xcalibur is connected to (or thinks that it is!) and go through the tabs. You should be able to either add PPM or change from % to ppm. Hope this helps! Benhttps://www.blogger.com/profile/18385704761413487532noreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-69891609675848368382014-06-30T08:11:52.932-07:002014-06-30T08:11:52.932-07:00Congratulations (and thanks) for keeping this grea...Congratulations (and thanks) for keeping this great blog, Ben.<br />Just one question here: Do you know how do I set the DE window to 10 ppm in Xcalibur 2.2? My dialog box is limited to Da and % options and in % I can't go below 0.01.<br />I heard from a friend that this happens only in this new version.<br />In more details, the version is 2.2 SP1.48<br /><br />Thanks!<br />Wagnerhttps://www.blogger.com/profile/06242722850006724971noreply@blogger.com