Determining error rate for DIA 2015 Oysterseed

Update on error rate peak picking - confusion as to how to categorize correct and incorrect picks by Skyline. Includes tips from Laura.

I moved computers from Swan to Woodpecker. In order to be able to continue a project on a different computer, you need to File > Share > Complete. It becomes a .zip file. Upload to OWL. Open zip on new computer, and all the libraries and everything is included.

I continued spot-checking the peaks. Skyline file (.zip): Xcel error-checking spreadsheet:

However, after going through roughly 50 today, I am having a hard time thinking about whether I’m error-checking correctly. Currently, I am going through peptides randomly - with an end goal of 100 peptides checked. I am assigning a “1” to peptide peaks that were correctly chosen by Skyline. A “0” to ones where the wrong peak was selected.

Laura says she views this process as having four categories:

  • There is a peak and Skyline chose the correct peak “1”
  • There is a peak and Skylinie chose the wrong peak “0”
  • There is not a peak and Skyline chose noise as a peak “0”
  • There is not a peak and Skyline did not select anything “1”

The two “1” options are correct because Skyline did the right thing. I am wondering if there should be a way to distinguish between the two options - use letters? I may be making this all too complicated. Getting thoughts out now and will update notebook post according to what I end up doing.

Here is an example of there being a peak, and Skyline making the correct selection:

Here is an example of there being peaks, and Skyline picking the wrong one…? Or is this considered all noise and Skyline just tried to pick something….?

Here is an example of noise:

Written on January 16, 2018