Table 1.
Parameters used in each analysis with Kojak.
| Parameter1 | SCF(FBXL3) ubiquitin ligase complex |
Cop9 signalosome | 26S proteasome |
|---|---|---|---|
| cross-linked modification mass2 | 138.0680742 (a-a) | 138.0680742 (a-a) 150.1434042 (a-a) |
138.09055 (b-b) 146.14076 (b-b) −18.010595 (a-b) |
| differential amino acid modification mass (Da) | K=14.015894 K=28.031788 K=42.047682 M=15.9949 N-term=42.01055 |
K=14.015894 K=28.031788 K=42.047682 M=15.9949 |
K=14.015894 K=28.031788 K=42.047682 M=15.9949 |
| enzyme specificity | trypsin | trypsin | trypsin |
| maximum number of missed cleavages (includes linkage site) | 4 | 4 | 3 |
| maximum peptide mass (Da) | 8000 | 8000 | 8000 |
| minimum peptide mass (Da) | 500 | 500 | 500 |
| mono-linked modification mass2 | 155.0946 (a) 156.0786 (a) |
155.0946 (a) 156.0786 (a) 167.16993 (a) 168.15393 (a) |
156.10111 (b) 164.15132 (b) |
| precursor mass prediction | yes | yes | no |
| precursor mass tolerance (ppm) | 15 | 10 | 15 |
| scoring algorithm bin offset (Th)3 | 0 | 0.4 | 0.4 |
| scoring algorithm bin size (Th)3 | 0.03 | 1.0005 | 1.0005 |
| spectral processing | yes | no | no |
| static amino acid modification mass (Da) | C=57.02146 | C=57.02146 | C=57.02146 |
| top number of single peptides | 250 | 250 | 250 |
1
Parameters listed here are relevant to the differences for each analysis. Detailed description of these and other Kojak parameters are provided in Supplementary Table 5.
2
‘a’ designates linkage to primary amines (K or protein N-terminus). ‘b’ designates linkage to carboxyl groups (D, E, or C-terminus). For example ‘a–b’ indicates the cross-linker binds an amine to a carboxyl-terminating side chain.
3
bin offset and bin size are set to match the resolution of the data set. High resolution data analysis requires smaller bins and no offset.