We have a question similar to this one:

https://skyline.ms/announcements/home/support/thread.view?entityId=cc72af62-72f6-1034-b804-da202582a216&_docid=thread%3Acc72af62-72f6-1034-b804-da202582a216

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)
    all_trans.append(heavy)
    all_trans.append(light)

Thanks
Philip