The DIA pipeline has been quite a #strugglebus

It’s unfortunate that the strugglebus website no longer works :/ Let’s go through our current struggle:

• I showed Emma my error checking results
• She said my error rate was pretty high (and I agreed)
• She looked at my blib and Laura’s blib with people from her lab (a.k.a. the Skyline creators)
• They found asterisks at the end of some of the blib sequences that could affect Skyline’s ability to peak peaks
• Another problem may be that brecan reports the same peptide multiple times, and Skyline doesn’t like that

Overall, this means that my current Skyline output isn’t valid anymore. I can’t work on MSstats or target identification using Skyline data, but I can still look through the literature for proteins of interest. Emma and her team are working on fixing Skyline for our files, so I just have to wait! After everything’s fixed, I will need to check error rates again for the same peptides.