How Do the Different Proteomic Strategies Cope with the Complexity of Biological Regulations in a Multi-Omic World? Critical Appraisal and Suggestions for Improvements

Abstract

In this second decade of the 21st century, we are lucky enough to have different types of proteomic analyses at our disposal. Furthermore, other functional omics such as transcriptomics have also undergone major developments, resulting in mature tools. However, choice equals questions, and the major question is how each proteomic strategy is fit for which purpose. The aim of this opinion paper is to reposition the various proteomic strategies in the frame of what is known in terms of biological regulations in order to shed light on the power, limitations, and paths for improvement for the different proteomic setups. This should help biologists to select the best-suited proteomic strategy for their purposes in order not to be driven by raw availability or fashion arguments but rather by the best fitness for purpose. In particular, knowing the limitations of the different proteomic strategies helps in interpreting the results correctly and in devising the validation experiments that should be made downstream of the proteomic analyses.

A proteomic-informed view of the changes induced by loss of cellular adherence: The example of mouse macrophages

“…We thus used this model to study the changes linked to the adherence status, using a proteomic screen to get a wider appraisal of the phenomena at play. To this purpose, we chose to perform 2D gel-based proteomics, as this proteomic setup is able to detect changes in post-translationally modified protein forms [ 39 ] and thus get closer to the cell physiology [ 40 ]. In the same trend, we chose to validate the proteomic results by functional assays rather than assays based on protein amounts [ 41 ].…”

Proteomes Are of Proteoforms: Embracing the Complexity

“…However, this is by far not a consensus definition considering that the bulk of current published research seeks to assesses or infer the presence of only canonical amino acid sequences as opposed to proteoforms. Nevertheless, with the working definition presented, the aims of proteomics as a discipline are to provide accurate, reliable, and detailed descriptions of the proteoforms present and their functions, thereby providing rational insight into the molecular mechanisms underlying biological systems in both health and disease [ 3 , 4 , 27 , 28 , 29 , 51 , 62 , 63 ].…”

“…However, it has also been used to describe a number of different approaches in the field, confusing matters to the point that its use becomes essentially meaningless [ 28 , 68 , 178 , 179 ]. Again, here is another area in which consensus would be useful and important, to move the field forward with a unified terminology and understanding of the genuine pros and cons of available analytical approaches [ 27 , 28 , 29 , 51 ].…”

“…While aspects of what we will discuss have been raised and reviewed over the years [ 1 , 3 , 27 , 28 , 29 , 48 , 49 , 50 , 51 , 52 , 53 ], here we seek to focus on the integrated assessment of proteomics as a whole—indeed, its need for integration—beginning with questions concerning terminology used. Our goal is to broadly consider the sheer complexity of proteomics and how this is addressed by current operating philosophies and associated analytical approaches.…”

A proteomic view of cellular responses of macrophages to copper when added as ion or as copper-polyacrylate complex

“…However, biology inference is made from amounts to function in most of the omics publications, either directly or indirectly through pathway analyses. This direct inference has been pointed as a potential issue [59], especially when confronted with the multiple layers of cellular regulations, as recently reviewed [60]. In this global frame, enzymes are one of the very few examples where the relevant biological outcome (i.e.…”