tag:blogger.com,1999:blog-3693238014525650573.post8540208524508957105..comments2024-03-28T08:46:55.598-07:00Comments on News in Proteomics Research: Is there any reason to skip low mass fragment ions?Unknownnoreply@blogger.comBlogger2125tag:blogger.com,1999:blog-3693238014525650573.post-58532713228781907822016-05-12T04:37:02.800-07:002016-05-12T04:37:02.800-07:00Dear Ben,
I was quite interested by this setting ...Dear Ben,<br /><br />I was quite interested by this setting "Fixed First Mass at 100.0 (m/z)" some time ago because I noticed that Mann's lab were using it in several publications.<br /><br />We made some tests injecting several times some Hela from Piere using 300 ng on a 2 Hours LC-MS/MS . In the method, we only modified the Fixed First Mass at 100.0 (m/z)parameter.<br /><br />We performed a basic MaxQuant analysis and we noticed a slight reduction of the overall ID rate for a normal proteome analysis.<br /><br />Am I the only who have the feeling that this paramenter doesn't help so much ?<br /><br />best,<br /><br /><br /><br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-69870819449698978652016-05-06T13:15:01.827-07:002016-05-06T13:15:01.827-07:00I remember hearing from one of the orbi tech guys ...I remember hearing from one of the orbi tech guys saying that there beyond 1.5 times the lowest mass, you really take a hit in analyzing larger m/z. when you start at 50 m/z you'll see that your high m/z fragments are much worse then if you put it at 100 or 120. So you may reduce the number of sequence fragments in favor or immonium ions and internal fragments. Anonymousnoreply@blogger.com