Request about Heavy/Light Peptides

Request about Heavy/Light Peptides philip remes  2023-08-22 17:47

We have a question similar to this one:

The situation is we have 800 peptides spiked into a sample. We wanted to find the RT's of the heavy/light peptide pairs and have a Skyline document with heavy/light pairs defined for all of the heavy peptides we could find.

Trial 1
In the initial peptide search, we included heavy K/R as a dynamic modification and imported this to Skyline. Using Accept Peptides, one could reduce to the list of peptides of interest, but not all of them would have both heavy and light in the document, because some peptides would just have an ID for the light, some just for the heavy.

Trial 2
We did a peptide search with static K/R modifications for just the heavies, and imported these to Skyline. Use Accept Peptides to make sure they are the ones we want. Now, how to add the lights? What we ended up doing was exporting the heavy transition list, appending the light transitions, and reimporting. We could make an external tool to enable this, but perhaps there is a better way already, or perhaps it would be a feature useful enough for the Skyline team to implement?

all_trans = []
for heavy in heavy_trans:
    light = deepcopy(heavy)
    seq = light['peptide_modified_sequence']
    light['precursor_mz'] = get_subtracted_mz(light['precursor_mz'], light['precursor_charge'], seq)
    if 'y' in light['fragment_ion']:
        light['product_mz'] = get_subtracted_mz(light['product_mz'], light['product_charge'], seq)


Nick Shulman responded:  2023-08-22 18:22
If you want to add a bunch of heavy or light precursors to the peptides that you already have in your document, the way to do that is with the menu item:
Refine > Advanced

In the Refine dialog, there is a thing that says "Remove label type" but there is a checkbox next to that which says "Add" and if you check the checkbox then the "Remove label type" will change to "Add label type" and then you can tell Skyline to add all the heavy or light precursors.

Does that answer your question?

If this does not answer your question then you should send us your Skyline document: "File > Share" and you can upload it to

-- Nick
philip remes responded:  2023-08-22 23:06
Yes, that's exactly what we needed, thanks for that.