A ‘proteomic ruler’ for protein copy number and concentration estimation without spike-in standards

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 concept 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 is proportional to the amount of DNA in the sample, which in turn depends of the number of cells. As a result, our proteomic ruler approach adds an absolute scale to the MS readout and allows the estimation of the copy numbers of individual proteins per cell. We compare our protein quantifications with values derived from the SILAC-PrEST method, which 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 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 retrospect analysis – and we demonstrate its usefulness on a series of mouse organ proteomes.