Mimicking LysC Proteolysis by ‘Arginine Modification-cum-Trypsin Digestion’: Comparison of Bottom-up & Middle-down Proteomic Approaches by ESI Q-TOF MS

Middle-down (MD) proteomics is an emerging approach for reliable identification of post-translational modifications and isoforms, as this approach focuses on proteolytic peptides containing > 25-30 amino acid residues (a.a.r.), which are longer than typical tryptic peptides. Such longer peptides can be obtained by AspN, GluC, and LysC proteases. Additionally, some special proteases were developed specifically to effect MD approach, e.g., OmpT, Sap9, etc. However, these proteases are expensive. Herein we report a cost-effective strategy 'arginine modification- cum trypsin digestion', which can produce longer tryptic peptides resembling LysC peptides derived from proteins.The aim of this study is to obtain proteolytic peptides that resemble LysC peptides by using 'trypsin', which is a less expensive protease.This strategy is based on the simple principle that trypsin cannot act at the C-termini of those arginines in proteins, whose sidechain guanidine groups are modified by 1,2-cyclohexanedione or phenylglyoxal.As a proof of concept, we demonstrate this strategy on four models: β-casein (bovine), β- lactoglobulin (bovine), ovalbumin (chick) and transferrin (human), by electrospray ionization-mass spectrometry (ESI-MS) involving hybrid quadrupole time-of-flight. From the ESI-MS of these models, we obtained several arginine modified tryptic peptides, whose lengths are in the range of 30-60 a.a.r. The collision induced dissociation MS/MS characteristics of some of the arginine modified longer tryptic peptides are compared with the unmodified standard tryptic peptides.The strategy demonstrated in this proof-of-concept study is not only useful to obtain longer tryptic peptides that mimic LysC proteolytic peptides, but also facilitates in enhancing the probability of missed cleavages by the trypsin. Hence, this method aids in evading the possibility of obtaining very short peptides that are <5-10 a.a.r. Therefore, this is indeed a cost-effective alternative/ substitute for LysC proteolysis and, in turn, for those MD proteomic studies that utilize LysC. Additionally, this methodology can be fruitful for mass spectrometry-based de novo protein and peptide sequencing.