Yaamini’s Notebook: Skyline Test 2

I can now analyze my full .blib!

Emma sent my .blib file generated using all of my oyster samples. I uploaded it to OWL here.

Well, maybe not all my sample files. For some reason, pecanpie was unable to analyze files 8, 11, 17, 21, 22, and 23. Files 11 and 17 had bubbles in them and did not produce any usable data, so their exclusion makes sense. However, files 8, 21, 22, and 23 had data in them. I confirmed this during data collection by looking at the .raw files. Emma said she’ll ask Brian, but apparently he’s really busy right now and may not be able to solve the problem yet.

To analyze my .blib file, I opened up the Skyline document I created earlier. The settings I used in that document can be found here.

Step 1: Use my new .blib instead of my old one.

Under Peptide Settings » Library, I created a library for my new .blib.

imageimage 1image 2image 3

Step 2: Remove the heavy/light isotope distinction.

Because our data does not have any marked heavy or light signatures, we do not need this setting. Under Peptide Settings » Modifications, I unchecked all isotope label distinctions.


My Skyline document looks like this:

image 1

Over the next week, I’ll spot check about 100 different peptides to see if Skyline correctly identified the peak signature and peak width. This will give me an error rate for the program.

from the responsible grad student http://ift.tt/2qEio6Y