Using OD(Optical Densisty)for Normalization

Using OD(Optical Densisty)for Normalization ka79422  2022-07-11

I am working on bacterial samples and want to use skyline to process my data.I am trying to normalize my samples using the optical density readings.Is there a way I can import these OD readings into skyline for normalizing my data before processing?

Thanks in Advance,

Nick Shulman responded:  2022-07-11
I am not sure I understand your question, but if you have figured out a number for each of your Result Files that you would like Skyline to divide things by, then you can specify that number in the "Explicit Global Standard Area" column in the Document Grid.
Then, after you have done that, you can go to:
Settings > Peptide Settings > Quantification
and change the "Normalization Method" to "Ratio to Global Standards".
Skyline will then use the Explicit Global Standard Area value that you have provided when Skyline calculates things such as the "Normalized Area" on the Peptide Result.

If you would like to learn more about the Document Grid you should look at the Custom Reports tutorial:

By the way, do not try to set the Explicit Global Standard Area to a number which is less than 1. We recently discovered a bug in Skyline that when the Global Standard Area is less than 1, Skyline treats it as 1. If you were planning on setting the Explicit Global Standard Area to a number which is less than 1, you should choose a higher number, and scale up the Explicit Global Standard Area values that you are setting on all of your Result File's by the same scaling factor.

I hope this helps. Let me know if I have not understood your question correctly.
-- Nick
ka79422 responded:  2022-07-11
Thank you Nick for responding.
May be I wasn't clear.I have biological replicates and want to normalize them according to the OD readings.I have different readings for different samples.So my question is : Is there a way I can add the OD readings as a new column in the transition list or import the OD readings any other way?