Several issues with iRT standards in Skyline have come up recently:
1. Cambridge Isotope Lab, the supplier of the APOA1 standard has requested it be renamed to "ProteusQC CIL-14 (iRT-C18)" or possibly create a second set of standards for this QC standard if it is different. We need to talk with Sandi about this.
2. It was recently pointed out on Slack qc forum that the LSSEAPALFQFDLK peptide in the PRTC standard is too variable for use in an iRT standard. (Sandi also chimed in on this)
3. Sandi has pointed out that the iRT-C18 values we have for Sigma-Aldrich may need adjusting.

I have added Sandi to the "Notify List" for this issue. Let's make sure all these issues get resolved to her satisfaction.

Sandi, can you comment on what should be done for these issues?

1. If we need a second set of standards, can you share with me the list of peptides and their iRT values?
2. I guess we should just remove this peptide from the list, leaving the iRT values of the remaining peptides unchanged?
3. If the iRT values need to be adjusted, can you share with me a list of the new values?

Oh, sorry, I didn't realize I was holding this up!

1. I'd like to defer to Mike about how to handle the ProteusQC set of standards. Mike, as per Andrew's earlier e-mail he said that "we wish to have the name changed to reflect our product (Sigma, Pierce, Biognosys, and others clearly listed). The name Brendan and I discussed was -- ProteusQC CIL-14 (iRT-C18)." I think the only confusion here is that if someone is using just ApoA1 they won't necessarily know that this is the thing they should use. I can see a couple solutions here:
a. Using the trademarked name for it
b. Having two apo-a1 lists, one named apoA1 and one named ProteusQC
c. In keeping with the format of Sigma/Pierce/Biognosys, updating the name to be the company name in the list rather than the product name and maybe indicate that it's for 2 products, something like "CIL ApoA1/ProteusQC (iRT-C18)"
Do you have a preference?

2. As far as the variability of the LSS peptide and a few others, this variability is in the peak area, not the retention time. I think they're fine to stay as iRT standards, they're just not great for global normalization.

3. The sigma peptides... I haven't convinced myself that my issues with this weren't because of my own confusion caused by my mediocre abilities with Skyline. I can say that I have recently re-analyzed a mixture of PRTC, Sigma, Biognosis, and ApoA1 and the results are attached here. As I'm writing this up for the ProteusQC manuscript I've just used this data and calibrated everything to Biognosys. It might be useful as a check for what we have?

I think we decided what we have now is acceptable.