ProAlanase is an effective alternative to trypsin for proteomics applications and disulfide bond mapping

ABSTRACT: Trypsin is the protease of choice in bottom-up proteomics. However, its application can be limited by the amino acid composition of target proteins and the pH of digestion solution. In this study we characterized ProAlanase, a protease from the fungus Aspergillus niger that cleaves primarily on the C-terminal side of proline and alanine residues. ProAlanase achieves high proteolytic activity and specificity when digestions are carried out at acidic pH (1.5) for relatively short (2 hr) time periods. To elucidate the potential of ProAlanase in proteomic applications, we conducted a series of investigations comprising digestion of proline-rich proteins, PTM analysis, de novo protein sequencing and disulfide bond mapping. The results demonstrated that digestion with ProAlanase improves protein sequence coverage and phosphosite localization for the proline-rich protein Notch3 intracellular domain and improves non-collagenous bone protein identification. Notably, cleavage also occurs at the C-terminus of hydroxyproline, facilitating efficient digestion of bone collagen. Finally, we demonstrate that ProAlanase is efficient in disulfide bond mapping, showing high coverage of disulfide-containing regions in monoclonal antibodies, as well as achieving nearly complete database-independent sequence reconstruction of endogenous protein by de novo sequencing.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Homo Sapiens (human) Loxodonta Africana (african Elephant)

TISSUE(S): Embryonic Cell, Epithelial Cell, Cell Culture, Long Bone, Hela Cell

DISEASE(S): Cervix Carcinoma

SUBMITTER: Diana Samodova  

LAB HEAD: Jesper Velgaard Olsen

PROVIDER: PXD019039 | Pride | 2020-10-19

REPOSITORIES: Pride