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const-ae / proDA

Protein Differential Abundance for Label-Free Mass Spectrometry https://const-ae.github.io/proDA/
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Why Intensity over iBAQ? #11

Open hukai916 opened 2 years ago

hukai916 commented 2 years ago

Hi there,

Can you clarify why Intensity column should be used over iBAQ column when importing the data according to: (https://www.bioconductor.org/packages/devel/bioc/vignettes/proDA/inst/doc/data-import.html?)

Thanks!

const-ae commented 2 years ago

Thanks for the question.

To expand on the explanation from the vignette that you linked:

iBAQ is short for intensity-based absolute quantification. It is an attempt to make intensity values comparable across proteins. Usually the intensity values are only relative, which means that they are only comparable within one protein. This is because differences in ionization and detection efficiency. It is usually better to just compare the Intensity columns to identify differentially abundant proteins

iBAQ is designed to make easier how the abundance of protein A is different from protein B. This is not a priority for proDA because it looks for differences across experimental conditions (and does not even try to compare proteins A and B).

Furthermore, the normalizations that Maxquant applies to calculate the iBAQ values may undermine the assumptions of proDA about how to calculate the dropout curves.

Yet, you are of course free to run proDA on the iBAQ values instead of the recommended intensity values. I am actually curious to hear what kind of differences you find for your analysis.

hukai916 commented 2 years ago

Thanks a lot for your prompt and detailed reply! I will try both way and see.