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Table 4 Numbers of non-redundant cross-linked peptides identified by ProteinProspector, Kojak, and ECL, respectively. The database contains 5200 proteins

From: ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database

Data set

ProteinProspector

Kojak

ECL

1

20 (15)

5 (0)

36

2

32 (16)

6 (0)

39

3

24 (12)

4 (0)

39

4

23 (17)

2 (0)

57

  1. Values in the brackets are the numbers of overlapping cross-linked peptides identified by both ECL and the corresponding method. There is no result for intra-protein cross-linked peptides reported by Kojak because Percolator outputs errors in estimating q-value