rdopt meaning hwang2  2017-04-26
 
I'm trying to explain the rdopt value in a manuscript for publication. is the following statement correctly explain the rdopt?

The result dot product (rdotp) ( i.e. the dot-product between the analyte precursor and the isotope labeled standard precursor) that determines the spectral similarity between the native and the labeled peptide for these two peptide markers was 0.94 and 0.99 respectively.
 
 
Nick Shulman responded:  2017-04-26
Title: rdotp meaning
It stands for "ratio dot product".
Skyline calculates the Ratio To Heavy by dividing the sum of the light transition peak areas by the sum of the heavy transition peak areas.

The Ratio Dot Product is the normalized dot product of the light transition peak areas with the heavy transition peak areas.
The Ratio Dot Product is a measure of whether the transition peak areas in the two label types are in the same ratio to each other.
That is, if the y7 ion, for instance, was the most intense ion from the light precursor, was y7 also the most intense ion from the heavy precursor?
 
mmeyer responded:  2021-03-17
How exactly is the ratio dot product calculated in Skyline?

Can you point me toward the source code?

Thanks,
Matt
 
Nick Shulman responded:  2021-03-17
The ratio dot product gets calculated here:
https://github.com/ProteoWizard/pwiz/blob/master/pwiz_tools/Skyline/Model/Results/RatioValue.cs#L73

That function "Statistics.Angle" is calculating the dot product of two lists of transition peak areas. The code for that Angle function is here:
https://github.com/ProteoWizard/pwiz/blob/master/pwiz_tools/Skyline/Util/Statistics.cs#L1412

Note that the ratio dot product really is the dot product of the lists of transition areas. The other dot products in Skyline (isotope dot product, library dot product) are actually "Normalized Contrast Angles".

-- Nick