International Scholarly Research Notices

Research Article

In Silico Proteome Cleavage Reveals Iterative Digestion Strategy for High Sequence Coverage

Table 1

Theoretical upper limits of coverage upon digestion with various cleavage agents using the iMED-FASP strategy. Iterative cleavage of the proteome starting with the rarest amino acids first results in the greatest theoretical proteome coverage of 92.9%. The reversed sequence of cleavage provides a minimal improvement to theoretical proteome coverage. Peptides were filtered after each digest keeping those with MW > 5 kDa for additional digestion. The final “flowthrough” peptides were filtered keeping only sequences with at least 7 residues.


Digestion strategy	Theoretical coverage limit (%)

Trypsin	74.0
LysC	69.6
GluC	64.9
AspN	64.9
ArgC	53.7
CNBr	22.7
NTCB	13.8
TrpC	11.0
LysC, trypsin	82.9
GluC, trypsin	84.2
CNBr, LysC, trypsin	86.3
NTCB, CNBr, LysC, trypsin	88.2
TrpC, NTCB, CNBr, ArgC, GluC, trypsin	92.4
TrpC, NTCB, CNBr, ArgC, AspN, GluC, trypsin	92.9
Trypsin, GluC, AspN, ArgC, CNBr, NTCB, TrpC^a	78.9

Reversed order of cleavage starting with the most common residues instead of the rarest residues.