Absolute protein quantification using mass spectrometry (MS)-based proteomics 
delivers protein concentrations or copy numbers per cell. Existing methodologies 
typically require a combination of isotope-labeled spike-in references, cell 
counting, and protein concentration measurements. Here we present a novel method 
that delivers similar quantitative results directly from deep eukaryotic 
proteome datasets without any additional experimental steps. We show that the MS 
signal of histones can be used as a "proteomic ruler" because it is proportional 
to the amount of DNA in the sample, which in turn depends on the number of 
cells. As a result, our proteomic ruler approach adds an absolute scale to the 
MS readout and allows estimation of the copy numbers of individual proteins per 
cell. We compare our protein quantifications with values derived via the use of 
stable isotope labeling by amino acids in cell culture and protein epitope 
signature tags in a method that combines spike-in protein fragment standards 
with precise isotope label quantification. The proteomic ruler approach yields 
quantitative readouts that are in remarkably good agreement with results from 
the precision method. We attribute this surprising result to the fact that the 
proteomic ruler approach omits error-prone steps such as cell counting or 
protein concentration measurements. The proteomic ruler approach is readily 
applicable to any deep eukaryotic proteome dataset-even in retrospective 
analysis-and we demonstrate its usefulness with a series of mouse organ 
proteomes.