Table 3. Unique Cross-Linked Sites Corresponding to the 132 Intraprotein and 84 Interprotein PSMs Identified at 1% FDR (at the Unique Peptide Pair Level) by Searching against the E. coli Ribosomal Proteins (See Table 4)^a.

proteins	linkage	distance (Å)	PSMs
intraprotein cross-links
L1–L1	K14–K6	NA	2
L1-L1	K205–K54	NA	3
L1–L1	K54–K167	NA	5
L14–L14	K44–K54	5.5	8
L14–L14	K54–K111	25.6	1
L17–L17	K78–K121	NA	1
L18–L18	K63–K76	16.5	2
L19–L19	K63–K87	14.2	1
L2–L2	K59–K207	20.1	1
L20–L20	K85–K78	10.2	9
L25–L25	K25–K10	13.3	3
L33–L33	K10–K50	8.8	1
L33–L33	K37–K50	9.0	1
L33–L33	K50–K33	7.4	7
L4–L4	K166–K132	14.3	1
L6–L6	K44–K6	11.9	1
L7–L7	K108–K60	NA	3
L9–L9	K42–K57	NA	8
S14–S14	K19–K47	17.9	2
S14–S14	K23–K47	16.0	3
S17–S17	K39–K30	9.0	1
S19–S19	K17–K21	5.9	8
S19–S19	K17–K28	13.5	1
S20–S20	K16–K19	5.3	11
S20–S20	K49–K34	10.1	2
S20–S20	K69–K76	11.3	2
S3–S3	K108–K147	14.3	2
S3–S3	K49–K86	16.8	20
S3–S3	K86–K45	14.0	4
S3–S3	K86–K79	11.3	3
S4–S4	K167–K156	16.1	10
S7–S7	K149–K171	NA	5
interprotein cross-links
L14–L31B	K114–K30	NA	1
L17–L32	K35–K53	16.7	1
L25–L16	K83–K127	12.5	3
L27–L18	K62–K17	15.7	1
L28–L9	K44–K35	15.8	2
L28–L9	K44–K42	22.7	15
L28–L9	K44–K57	NA	8
L28–L9	K62–K42	12.5	5
L6–L7	K29–K71	NA	2
L6–L7	K86–K60	NA	2
L7–L11	K71–K100	NA	1
S1–L2	K150–K68	NA	1
S14–L3	K12–K106	148.4	1
S14–S10	K76–K11	17.8	2
S15–S17	K71–K81	17.6	2
S17–S8	K30–K87	12.3	20
S19–S14	K17–K47	12.1	4
S21–S12	K40–K44	46.4	1
S6–S18	K106–K30	NA	8
S7–S1	K149–K279	NA	1
S8–S2	K69–K26	15.9	1
S9–S1	K100–K279	NA	1
S9–S12	K100–K44	85.0	1

^aThe “Linkage” column indicates the indices of the lysine residues in the protein sequences.