While top-down proteomics provides direct identification of a protein species including all of its PTMs, assigning peptide identifications from shotgun analyses to specific protein species remains problematic. However, as exemplified in Figure 2b for a TopFIND analysis of HMGB1 (http://clipserve.clip.ubc.ca/topfind/proteins/P17096), knowledge of the terminal peptides of the species present in the sample provides boundaries drastically reducing the search space. Modification of a protein by limited proteolysis can be divided into two general

classes: first, BMS-354825 purchase sequential maturation and second, protein partitioning. During sequential maturation the removal of, for example, a propeptide that maintains enzyme PD-0332991 supplier latency, enables enzymatic activity of the

major chain, but the propeptide, its task done, is most often then degraded (Figure 3a). Similarly, chemokine functions are frequently altered by truncation of few amino acids at their N-terminus or C-terminus (Figure 3b and c). CCL2 and CCL7, for example, become antagonists after N-terminal truncation [11]. In contrast, partitioning leads to the formation of two new protein species with usually unrelated properties thereby increasing the complexity of the proteome and potential for functional diversity (Figure 3d). HARP cleavage by MMP2 generates two bioactive species having opposing activity — the N-terminal species increases mitogenesis whereas the C-terminal species is antagonistic [13]. Irrespective of its mode of formation each new protein species is characterized by one ‘neo’ terminus. New functionality can be introduced by further modification of the new terminus including the recent recognition of post-translational acetylation [29••] thereby increasing the functional repertoire of the new protein species. However, as the species inherits only a subset of its progenitors features, such as active sites, binding regions

and PTM sites, the potential functional complexity is limited. In the following we use the amyloid beta A4 protein (APP) to illustrate how protein termini identified by Cyclic nucleotide phosphodiesterase terminomics can serve as markers for the functionality a protein species. We refer to this as the ‘functional competence’ of a protein species which can be obtained by ‘positional cross correlation’ of a species’ termini with prior functional knowledge [31•]. APP is well known for its role in Alzheimer’s disease [51]. APP is a single pass type-I transmembrane protein that undergoes a series of partitioning processing steps leading to multiple bioactive species (Figure 4). Comparing the normal nonamyloidogenic with disease causing amyloidogenic situations, the participation of different proteases in different subcellular compartments and facing changing physicochemical conditions translate to minute differences in species length and dramatic changes in systemic effect.