Selecting SRM Targets Part 7


After looking at my work from yesterday, Steven suggested that I hit 150 transitions and max out our capacity. However, I’ve already pored over both the short and long protein lists. He offered to help me search for proteins in the full Skyline output. I merged my full Skyline output with annotations to get this list. I evaluated the following proteins that Steven identified as interesting:

screen shot 2017-07-12 at 11 00 12 pm

screen shot 2017-07-12 at 11 00 25 pm

Most of the peaks had interference or missing data, but there were a handful I added to my protein list. Just to recap, here’s what I was looking for.



Figures 1-2. A noisy transition in Figure 1 (highlighted in red) that when deleted, produces a much better looking peak in Figure 2.


Figure 3. A peak showing slight interference. I avoided this when possible. When interference was more extreme, I deleted the peptide.


Figure 4. An example of an ideal peak.

I then evaluated all of my proteins one last time:

screen shot 2017-07-12 at 11 01 59 pm

And I finally had a list of 146 targets from 16 proteins!

screen shot 2017-07-12 at 11 09 31 pm

Aside from some last-minute lab preparation, I’m all set for starting my mass spectrometry runs tomorrow! cue happy dance

Written on July 9, 2017