MS1attributes of SILAC pairs

MS1attributes of SILAC pairs Tobi  2018-11-28

Dear Skyline team,

thank you for providing such a helpful software, it means a lot. There are few things in terms of chromatograms and document grid I would wish to ask.

screenshot 1

  1. While DotProductLightToHeavy is identical for both light and heavy of a SILAC pair, the ratio dotp always shows #N/A for the heavy, shouldnt it also have the identical value as the respective light peptide? (for better filtering of results for silac pairs, at least it should not hurt or would it?) Is it possible to filter the documents grid for silac pairs where both isotope patterns of a silac pair fulfill certain filtering criteria (e.g. both of a pair having idotp>0.9), is it essential to use pivot isotope label for this?

  2. The Ratio dotp is always the dotp displayed in the target list (one silac pair) while the DotProductLightToHeavy seems to be the average of all charge states of one peptide (multiple silac pairs in a way). Just want to mention its easy for users to mix them up unintentionally, similar with average mass error and peak apex mass error.

  3. The Coelution feature says: "similar apex and extents as the other transitions within the peak group" but how is that peak group defined (all quantitative transitions? light and heavy silac pair in one group) ?

The coelution was partially explained here, but i dont find the coelution count feature, was it removed? :

screenshot 2
The document grid precursor serves as a link which moves the displayed single chromatogram to the peak, but it stays within one and the same raw file even if the selected precursor was from another file. Is it possible to have a link in the document grid which always directs you to the exact chromatogram you want to see, even across loaded raw files?

not on screenshot
When working with quantitative PRM, does skyline consider if a single specific fragment ion can be theoretically interfered by signals from other fragment ions (with ammonia/ water loss). How is it when applied to a silac pair, also when multiplexing light and heavy fragments into one measurement ( i know this sounds bit weird but its implemented in mascot and i would like to try translating it to skyline)

Sorry to post so much text here but i hope it also helps other users as well. Thank you for your support, its highly appreciated.

Best regards,