Table IV. Intraprotein identifications by Protein Prospector from E. coli dataset. Shaded identifications were also reported by pLink (14).

Peptide 1	Peptide 2	Xlink Res 1	Xlink Res 2	Protein 1	Protein 2
WLGGMLTNWK*TVR	Acetyl-AHIEK*QAGELQEK	105	6	30S ribosomal protein S2	30S ribosomal protein S5
K*ILPDPK	K*AGFVTR	11	100	30S ribosomal protein S7	30S ribosomal protein S9
LLSLFK*LTETDQR	VDEIATDVDK*TPHAWYFQQAGNGIFAR	34	280	Aspartate carbamoyltransferase regulatory chain	Aspartate carbamoyltransferase
SSAQK*VR	K*PELDAK	16	108	50S ribosomal protein L22	30S ribosomal protein S3
ANDIALK*CK	TVHSLTQALAK*FDGNR	137	179	Aspartate carbamoyltransferase regulatory chain	Aspartate carbamoyltransferase
FWVESEK*R	K*NIEFFEAR	44	42	50S ribosomal protein L28	50S ribosomal protein L9
SSAQK*VR	K*HNASR	16	19	50S ribosomal protein L22	30S ribosomal protein S20
EK*VAGQVAYR	K*LLDEGR	177	264	Ribosomal RNA small subunit methyltransferase D	Elongation factor Tu 1