What is the total number of protein molecules per cell volume? A call to rethink some published values

Novel methods such as mass-spectrometry enable a view of the proteomes of cells in unprecedented detail. Recently, these efforts have culminated in quantitative measurements of the number of copies per cell for most expressed proteins in organisms ranging from bacteria to mammalian cells. Here, we estimate the expected total number of proteins per unit of cell volume using known parameters related to the composition of cells such as the fraction of cell mass that is protein, and the average protein length. Using simple arguments, we estimate a range of 2–4 million proteins per cubic micron (i.e. 1 fL) in bacteria, yeast, and mammalian cells. Interestingly, we find that measured values that are reported for fission yeast and mammalian cells are often about 3–10 times lower. We discuss this apparent discrepancy and how to use the estimate as benchmark to recalibrate proteome-wide quantitative censuses or to revisit assumptions about cell composition. We estimate the expected total number of proteins per unit cell volume as 2–4 million proteins per cubic micron. Some reported values for fission yeast and mammalian cells using mass spectrometry are 3–10 times lower than these estimates. We discuss this apparent discrepancy and how to recalibrate proteome-wide quantitative censuses.