  regulation largely unexplored, in part due to methodological limitations.
Indeed, we review evidence demonstrating that commonly used methods, such as
transcriptomics, are inadequate because the variability in mRNAs coding for
ribosomal proteins (RP) does not necessarily correspond to RP variability. Thus
protein remodeling of ribosomes should be investigated by methods that allow
direct quantification of RPs, ideally of isolated ribosomes. We review such
methods, focusing on mass spectrometry and emphasizing method-specific biases
and approaches to control these biases. We argue that using multiple
complementary methods can help reduce the danger of interpreting reproducible
systematic biases as evidence for ribosome remodeling.
