Sequential protein extraction analysis

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Sequential protein extraction analysis francescodemetrio lofaro  2020-11-30
 

Hi,

I would like to performe a DDA analysis on three sequential protein extraction on each sample comparing two different conditions. My idea is to import DDA search from Mascot engine merging all technical replicates of all fractions together and import the dda search on Skyline.

  1. How i can specify that .raw files are fractions of the same sample?
  2. Is it possible to consider the total amount of the same protein combaning peaks of the three fractions of the same sample?

Thank you for your help

Francesco

 
 
Nick Shulman responded:  2020-11-30
If you want to attach extra information to your replicates such as which sample that they came from, you can use the "Annotations" feature, which you get to at:
Settings > Document Settings > Annotations

The Group Comparison tutorial talks a lot about using annotations to group your replicates and then do comparisons between those groups:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_grouped

If you want to export data from Skyline to analyze in another tool such as Excel, you can look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

-- Nick