International Scholarly Research Notices / 2014 / Article / Tab 1

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 strategyTheoretical coverage limit (%)

Trypsin74.0
LysC69.6
GluC64.9
AspN64.9
ArgC53.7
CNBr22.7
NTCB13.8
TrpC11.0
LysC, trypsin82.9
GluC, trypsin84.2
CNBr, LysC, trypsin86.3
NTCB, CNBr, LysC, trypsin88.2
TrpC, NTCB, CNBr, ArgC, GluC, trypsin92.4
TrpC, NTCB, CNBr, ArgC, AspN, GluC, trypsin92.9
Trypsin, GluC, AspN, ArgC, CNBr, NTCB, TrpCa78.9

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