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Among the hundreds of posttranslational modifications, limited proteolysis, also known as processing, is special: It is irreversible, near ubiquitous, and by trimming peptide chains from their ends or cutting proteins into two, proteolysis forms shorter chains displaying new termini. The unique chemistry and location of α-amino-termini and carboxyl-termini in a protein engender special chemical and physical properties to a protein. Hence, modification of protein termini is often associated with new biological activities of a protein. We highlight recent proteomic developments enabling high throughput identification of protein termini. This has revolutionized degradomics and protein characterization by mapping the specificity of terminal modifications and of proteases, and has been used to directly identify new protease substrates and molecular pathways altered by proteolysis. [ABSTRACT FROM AUTHOR]

Background: Murine xenografts of pediatric leukemia accurately recapitulate genomic aberrations. How this translates to the functional capacity of cells remains unclear. Here, we studied global protein abundance, phosphorylation, and protein maturation by proteolytic processing in 11 pediatric B- and T- cell ALL patients and 19 corresponding xenografts. Methods: Xenograft models were generated for each pediatric patient leukemia. Mass spectrometry-based methods were used to investigate global protein abundance, protein phosphorylation, and limited proteolysis in paired patient and xenografted pediatric acute B- and T- cell lymphocytic leukemia, as well as in pediatric leukemia cell lines. Targeted next-generation sequencing was utilized to examine genetic abnormalities in patients and in corresponding xenografts. Bioinformatic and statistical analysis were performed to identify functional mechanisms associated with proteins and protein post-translational modifications. Results: Overall, we found xenograft proteomes to be most equivalent with their patient of origin. Protein level differences that stratified disease subtypes at diagnostic and relapse stages were largely recapitulated in xenografts. As expected, PDXs lacked multiple human leukocyte antigens and complement proteins. We found increased expression of cell cycle proteins indicating a high proliferative capacity of xenografted cells. Structural genomic changes and mutations were reflected at the protein level in patients. In contrast, the post-translational modification landscape was shaped by leukemia type and host and only to a limited degree by the patient of origin. Of 201 known pediatric oncogenic drivers and drug-targetable proteins, the KMT2 protein family showed consistently high variability between patient and corresponding xenografts. Comprehensive N terminomics revealed deregulated proteolytic processing in leukemic cells, in particular from caspase-driven cleavages found in patient cells. Conclusion: Genomic and host factors shape protein and post-translational modification landscapes differently. This study highlights select areas of diverging biology while confirming murine patient-derived xenografts as a generally accurate model system. [ABSTRACT FROM AUTHOR]