On normalizing protein intensity data

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On normalizing protein intensity data

Postby woa » Mon Oct 14, 2013 7:45 pm

Hello All,

I'm working on intensity based absolute quantification(iBAQ) for a couple of experimental conditions with replicates. However, the number of cells used to derive the samples is not known for many of the replicates. The cell counts where available is not accurate either.

I wish to to normalize the sample/replicate protein intensities with respect to the cell numbers. However as the cell count data is not reliable, how to proceed in this case? I've noted that the total number of protein identified vs. the sum of log(ibaq-intensity) of identified proteins is highly linear. Can the total number of protein identified act as a surrogate for cell count for normalizing the ibaq intensities across sample?

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