Adding a water loss product ion

Adding a water loss product ion joe.palandra  2019-06-11


Apologies if this has already been asked but I am developing a targeted assay on a triple quad and wanted to know if there was a way to select a -H2O product ion? I have a peptide that gives very good sensitivity using such a transition and I would like to add this to my other regular y and b ions. Essentially it is like a parent to parent transition.


Brendan MacLean responded:  2019-06-11

Hi Joe,
Absolutely. You need to add the modification "Water Loss (D, E, S, T)" to your document. Once you do this, all peptides with D, E, S, and T will allow the appropriate loss in their fragment ions. If you use a spectral library, Skyline will pick these ions from the library spectrum when they are the most intense. Otherwise, by default, you would need to pick the loss transitions manually.

If you need more detailed steps for how to achieve this, just ask and I can give them. If you already feel comfortable working with peptide modifications in Skyline, then this may be all you need.


joe.palandra responded:  2019-06-11

Hi Brendan,

Thanks for the prompt reply. I’ve done peptide modifications in the past but I’m not sure on how to go about adding the “water loss” modification.
Would this be added to the modifications tab under Peptide settings?


Brendan MacLean responded:  2019-06-11


  • On the Peptide Settings - Modifications tab, click Edit List beside the Structural modifications list.
  • Click the Add button.
  • Choose "Water Loss (D, E, S, T)" from the list of modification names.
  • Click OK.
  • Click OK.
  • Make sure the new modification is checked and click OK in the Peptide Settings form.

This will give you optional waters loss transitions wherever they are appropriate and it will cause Skyline to pick them automatically when you have a spectral library spectrum that indicates they are among the most intense ions. They will also show up as annotated ions in the "Spectrum Matches" plot, similar to the way phospho losses do in the MS1 Filtering tutorial.

Hope this helps.


joe.palandra responded:  2019-06-11

I did realize it already existed so it was simple to add. Thanks again Brendan.