tag:blogger.com,1999:blog-3693238014525650573.post4851568863644762608..comments2024-03-28T08:46:55.598-07:00Comments on News in Proteomics Research: Process DIA data directly in Proteome Discoverer 2.0 with DIA UmpireUnknownnoreply@blogger.comBlogger3125tag:blogger.com,1999:blog-3693238014525650573.post-78255518526745111112016-06-03T04:12:13.622-07:002016-06-03T04:12:13.622-07:00Thanks, Ben. Yes, MGF looks similar, but it is mis...Thanks, Ben. Yes, MGF looks similar, but it is missing the scan number line. Not sure if this matters? In the Spectrum Selector parameters tab pf PD2.0 I have parameters defined for QE data (mostly default values except mass analyzer and activation type), but am unsure which line items are critical to interpreting the mgf file. I'm also wondering if there is something about SE params file for DIAUmpire v2 that make a difference? I used default values for that with the exception of setting mass tolerances to 10 ppm for parent and fragment. <br />Thanks!<br /><br />GundryLabhttps://www.blogger.com/profile/05787637305059810921noreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-90270250422019727022016-06-01T13:22:02.539-07:002016-06-01T13:22:02.539-07:00Wow. That's weird. Normally MGFs are straight-...Wow. That's weird. Normally MGFs are straight-forward and go into PD no problem. Since the MGF loses all the scan header functions you may need to go into the Scan selector and tell it what its looking at. Otherwise, I'm not sure what to suggest. <br />If you open the MGF file does it look normal? http://proteomicsnews.blogspot.com/2012/08/what-is-in-mgf-file.htmlBenhttps://www.blogger.com/profile/18385704761413487532noreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-59409555657759788902016-06-01T13:11:16.187-07:002016-06-01T13:11:16.187-07:00Hi Ben,
What versions of software did you use? I&...Hi Ben,<br /><br />What versions of software did you use? I"m not having any luck getting any output (mzML or mzXML) from MSConvert to work in PD 2.0. I am able to use MSConvert to generate files for DIA-Umpire just fine. But I cannot get from the .MGF to a file format that I can put into PD 2.0 successfully. Thanks!Anonymoushttps://www.blogger.com/profile/10778773429068937159noreply@blogger.com