Raw CCS values and Overriding with Explicit IM Values

Raw CCS values and Overriding with Explicit IM Values Premy  2023-01-05

Thanks so much for all the developments in Skyline. This tool has been an amazing support for my DDA and diaPASEF data!

I'm currently working with DDA-PASEF data (Bruker timsTOF) to build an ion mobility library for a set of lipid standards. I had a few questions regarding the 1/K0 and CCS values presented in the report.

  1. Is there a way to get the raw CCS values (in case there are slight shifts in CCS between replicates)?
  2. In the case that the IM extraction window needs to be corrected by overriding with "Explicit Ion Mobility Value", is there a way to also recalculate the CCS value in the report? It currently still reports the original CCS value and the newly corrected 1/K0 value.

I hope this makes sense and thank you in advance!


Brian Pratt responded:  2023-01-09

Hi Premy,

  1. As you know, Skyline converts the declared CCS value to 1/K0 then extracts chromatograms only from scans whose 1/K0 value is within a window around that. It sounds like you're asking whether we are looking within that ion mobility window to determine which scan contains the most intense signal at the RT peak, and noting the 1/K0 value there, and converting back to CCS for comparison to the declared CCS. That's a request that's in our list but we haven't implemented it yet, sorry.

  2. Generally in chromatogram extraction we're concerned with the effective 1/K0 value, usually derived from CCS but sometimes overridden by an explicit value. I don't think it occurred to us to do the reverse CCS calculation in the override case. Which report are you thinking of, by the way?

Thanks for using the Skyline support board,

Brian Pratt

Premy responded:  2023-01-13

Hi Brian,

Thanks for the help so far!

  1. Yes that was what I was asking, thank you!

  2. I was working with a customized report that exported the CCS and IM values for each sample. That makes sense, I will just clear the CCS value in the report, thanks.