ppm-level calculation

ppm-level calculation laura nieder  2020-11-23

Hi, thank’s for the great software and the really nice tutorials. Is there any way to let skyline calculate the ppm-levels of a certain protein (using for example 3 peptides for quantification) in sample A regarding to a housekeeping protein in the same sample?
I always have the same two Proteins in my samples. Protein X with a steady concentration, protein Y with changing levels. Usually we do absolute quantification with an external calibration curve. This time I would like to get the ppm levels of Y regarding the concentration of X within the same sample. Similar to HCP analysis.
Is there a possible way, that Skyline calculates this for me?
Thank you,

Nick Shulman responded:  2020-11-23
I am not sure I understand what you are asking for. Can you tell us what numbers would be multiplied or divided together?

What you are saying sounds a little like "Ratio to Global Standards". When you have peptides in your sample that were spiked in at a known amount, or which happen to be present in biological samples at constant amounts, you can right-click on those peptides in Skyline and say "Set Standard Type > Global Standard". Then, when you ask Skyline to use the normalization method "Ratio to Global Standards", Skyline will divide the peptide peak areas by the sum of the global standard peak areas in that Replicate.

In general, Skyline does not have any features for comparing the peak areas of different peptides to each other. Any comparisons like that would need to be done in a different tool like Excel, where you would have control over how the calculations are done.

If you want to learn more about exporting data from Skyline for use by other tools such as Excel, you can take a look at the Custom Reports tutorial:

-- Nick
laura nieder responded:  2020-11-23
Hi, sorry for the unclear question.

But you answered it anyway perfectly fine 😊
I wanted to compare the peak areas of different proteins within one sample, but multiply the ratio with a certain value. And all of that without the need of further manual processing in excel. I already did it with the ratio to the global standard, but that limits me a little bit…

thank you very much for the fast answer and have a nice day.