Can we put Humpty Dumpty back together again? What does protein quantification mean in bottom-up proteomics?

Plubell, Deanna L.; Käll, Lukas; Webb-Robertson, Bobbie-Jo; Bramer, Lisa; Ives, Ashley; Kelleher, Neil L.; Smith, Lloyd M.; Montine, Thomas J.; Wu, Christine C.; MacCoss, Michael J.

Bottom-up proteomics provides peptide measurements and has been invaluable for moving proteomics into large-scale analyses. In bottom-up proteomics, protein parsimony and protein inference derived from these measured peptides are important for determining which protein coding genes are present. However, given the complexity of RNA splicing processes, and how proteins can be modified post-translationally, it is overly simplistic to assume that all peptides that map to a singular protein coding gene will demonstrate the same quantitative response. Accordingly, by assuming all peptides from a protein coding sequence are representative of the same protein we may be missing out on detecting important biological differences. To better account for the complexity of the proteome we need to think of new or better ways of handling peptide data.