Biological samples do not only show a high complexity in term of composition, but also have the property that they can span several orders of magnitude in concentration. Thus, a biological process does not simply result in presence or absence of proteins, but rather in regulations of entire systems.

On top of the identification of proteins and their attached PTMs, we are hence interested in estimating their abundance – and this is much more challenging. Several methods are well established in the field, each coming with advantages and shortcomings, notably in terms of data processing, and allowing you to answer different questions: it is therefore crucial to carefully select the optimal method at the very first stage of the project.

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