Hi Skyline team,
Actually I am trying to analyze the DIA data using the targeted extraction strategy i.,e, by using the assay library generated based on the DDA data.
During assay library generation I used the CiRT peptides for the RT normalization. Though I have used the Biognosys Standard peptides in the samples during the DDA data acquisition, but only one peptide was present in my DDA data after the statistical validation with iProphet. So, I could not used the Biognosys peptides for the RT normalization.
Now I am trying to import this library in the skyline, but as it contains the iRT information, skyline is asking for the iRT calculator.
I have few doubts now:
- Can I use the Biognosys iRT peptides for this purpose, by using the assay library for these peptides provided by your team alongwith the tutorial of Import assay library?
- If I could not use above option, can I use the CiRT calculator inbuilt in the skyline?
- Else I need to built a new calculator by using the CiRT peptides? If so, should I use only those CiRT which are related to human, as I have only human data?
Also, should I use the CIRT_All or CiRT_SW only provided alongwith the paper of Sarah Parker on CiRT?
I will be very grateful for your help.
Thanks in advance.