TABLE 1.

List of identified human caspase-2, caspase-3, and caspase-7 cleavage sites

Processing sites are ordered by decreasing relative cleavage efficiency of caspase-2 (C2), caspase-3 (C3), and caspase-7 (C7). Columns from the left to right contain the Swiss-Prot accession number, protein name, start and end position of the identified (neo-N-terminal) peptide in the protein sequence, sequence of the identified peptide, residues surrounding the cleavage site from P6 to P4′, relative cleavage efficiency by each caspase compared to the most efficient cleavage, cleavage ratios of caspase-2/caspase-3 (C2/C3), caspase-2/caspase-7 (C2/C7), and caspase-7/caspase-3 (C7/C3), number of identified MS/MS spectra, Mascot score and threshold of the highest scoring spectrum, and possible protein isoforms in which the same peptide sequence can be found. The last two columns indicate whether the identified site was previously reported to be cleaved by caspases, in which case the name of caspase(s) involved and reference is provided.

Accession	Protein name	Start	End	Peptide sequence	Cleavage site	C2	C3	C7	C2/C3	C2/C7	C7/C3	No. spectra	Score	Threshold	Isoforms	Known caspase cleavage	References
P23588	Eukaryotic translation initiation factor 4B	564	571	GKKDQDSR	ESDRKD↓GKKD	100	33.17	73.45	3.01	1.36	2.21	2	57	47
P09496	Clathrin light chain A	77	102	GVMNGEYYQESNGPTDSYAAISQVDR	GPDAVD↓GVMN	16.74	100	94.85	0.17	0.18	0.95	4	77	41		Caspase-3	59
Q13263	Transcription intermediary factor 1-β	686	702	GADSTGVVAKLSPANQR	GSLSLD↓GADS	0	100	92.48	0	0	0.92	3	110	46
Q15046	Lysyl-tRNA synthetase	13	25	GSEPKLSKNELKR	AEVKVD↓GSEP	7.34	100	92.04	0.07	0.08	0.92	2	53	46		Caspase-3	59
Q8WU90	Zinc finger CCCH domain-containing protein 15	325	340	DSVSVNDIDLSLYIPR	GGDEVD↓DSVS	8.35	100	89.55	0.08	0.09	0.9	1	82	46
Q7Z406	Myosin-14	1178	1186	STNAQQELR	LEDTLD↓STNA	15.84	100	85.17	0.16	0.19	0.85	1	63	47
Q96IZ0	PRKC apoptosis WT1 regulator protein	132	145	GVPEKGKSSGPSAR	DEEEPD↓GVPE	9.03	100	82.33	0.09	0.11	0.82	2	72	47		Caspase-3	59
Q13148	TAR DNA-binding protein 43	90	98	ASSAVKVKR	KmDETD↓ASSA	12.42	100	81.76	0.12	0.15	0.82	2	53	47		Caspase-3	59
P46821	Microtubule-associated protein 1B	1197	1220	GKDYNASASTISPPSSMEEDKFSR	KTDATD↓GKDY	8.55	100	81.73	0.09	0.1	0.82	2	52	44		Caspase-3, -7	38
P23588	Eukaryotic translation initiation factor 4B	532	545	GMNAPKGQTGNSSR	DENKVD↓GMNA	4.87	100	77.77	0.05	0.06	0.78	2	62	47		Caspase-3	59
P35579	Myosin-9	1154	1162	STAAQQELR	LEDTLD↓STAA	5.99	100	75.64	0.06	0.08	0.76	3	55	47		Caspase-3	59
P05783	Keratin, type I cytoskeletal 18	398	411	SSNSMQTIQKTTTR	LGDALD↓SSNS	9.46	100	74.24	0.09	0.13	0.74	4	137	46		Caspase-3, -7	71
Q15056	Eukaryotic translation initiation factor 4H	94	109	SLKEALTYDGALLGDR	EFDEVD↓SLKE	5.04	100	73.35	0.05	0.07	0.73	3	105	46		Caspase-3	59
P14625	Endoplasmin	29	39	GTVEEDLGKSR	DEVDVD↓GTVE	0	100	54.35	0	0	0.54	2	61	47
P45974	Ubiquitin carboxyl-terminal hydrolase 5	768	778	AEAAMDISEGR	HIDDLD↓AEAA	0	100	48.67	0	0	0.49	1	54	47
P22102	Trifunctional purine biosynthetic protein adenosine-3	952	965	AGQIILQEAVPVKR	VAEDVD↓AGQI	0	100	46.48	0	0	0.46	1	62	46
P08670	Vimentin	86	100	FSLADAINTEFKNTR	LQDSVD↓FSLA	9.39	100	45.84	0.09	0.2	0.46	1	71	46		Caspase-3, -7	72
Q9UIL1	Short coiled-coil protein	88	99	AENQVELEEKTR	DMDAVD↓AENQ	0	100	42.62	0	0	0.43	1	66	47
P25705	ATP synthase subunit α, mitochondrial	160	169	GKGPIGSKTR	LGNAID↓GKGP	4.47	100	40.28	0.04	0.11	0.4	1	53	47		Caspase-3	59
P60709	Actin, cytoplasmic 1	12	28	NGSGMCKAGFAGDDAPR	AALVVD↓NGSG	0	100	40.23	0	0	0.4	3	90	45	A5A3E0, AP0CG38, AP0CG39, AP63261, AQ6S8J3	Caspase-1	58
Q6P996	Pyridoxal-dependent decarboxylase domain-containing protein 1	585	597	AAELVETIAATAR	ASDNVD↓AAEL	0	100	38.75	0	0	0.39	1	52	47
P63313	Thymosin β-10	7	40	MGEIASFDKAKLKKTETQEKNTLPTKETIEQEKR	MADKPD↓MGEI	27.95	100	37.07	0.28	0.75	0.37	1	64	42
Q5SNT6	Protein FAM21B	1044	1059	SGDIFSTGTGSQSVER	EADLFD↓SGDI	0	100	35.55	0	0	0.36	1	87	46	Q5SRD0, AQ641Q2, AQ9Y4E1
O95801	Tetratricopeptide repeat protein 4	16	27	SFLEKFQSQPYR	SDDVMD↓SFLE	0	100	34.61	0	0	0.35	1	61	47
P06454	Prothymosin α	8	31	TSSEITTKDLKEKKEVVEEAENGR	SDAAVD↓TSSE	0	100	33.31	0	0	0.33	2	77	45		Caspase-3	59
P14625	Endoplasmin	60	67	GLNASQIR	EAIQLD↓GLNA	6.86	100	32.41	0.07	0.21	0.32	1	64	48
Q9BWU0	Kanadaptin	538	554	AFMSEMKSGSTLDGVSR	SQDSLD↓AFMS	0	100	28.91	0	0	0.29	2	56	46		Caspase-3	59
P21333	Filamin-A	2319	2333	SPFVVPVASPSGDAR	EEHIPD↓SPFV	0	100	28.39	0	0	0.28	1	56	47
P21333	Filamin-A	1505	1515	GTQTVNYVPSR	VVDNAD↓GTQT	13.92	100	28.39	0.14	0.49	0.28	1	54	47
P21333	Filamin-A	1502	1515	NADGTQTVNYVPSR	PVDVVD↓NADG	4.74	100	23.13	0.05	0.2	0.23	1	101	47
Q14203	Dynactin subunit 1	111	119	SSASKVLKR	SPETPD↓SSAS	0	100	21.09	0	0	0.21	1	78	47
Q12797	Aspartyl/asparaginyl β-hydroxylase	238	247	SSEPVVEDER	EQENPD↓SSEP	8.73	100	18.98	0.09	0.46	0.19	1	61	47
P52888	Thimet oligopeptidase	14	25	AASPCSVVNDLR	AGDMAD↓AASP	12.93	100	15.5	0.13	0.83	0.15	1	57	47		Caspase-3	59
P62877	RING-box protein 1	9	21	TPSGTNSGAGKKR	AAMDVD↓TPSG	0	100	15.5	0	0	0.15	1	62	47		Caspase-3	59
P53990	Uncharacterized protein KIAA0174	198	211	VGFTDDVKKGGPGR	ETDLID↓VGFT	7.68	100	14.65	0.08	0.52	0.15	1	82	47
Q9P265	Disco-interacting protein 2 homolog B	61	68	SAVQKELR	QTQETD↓SAVQ	0	100	13.34	0	0	0.13	1	57	47		caspase-3	59
Q13263	Transcription intermediary factor 1-β	689	702	STGVVAKLSPANQR	SLDGAD↓STGV	5.47	100	9.31	0.05	0.59	0.09	2	77	47		Caspase-3	59
Q5UIP0	Telomere-associated protein RIF1	1524	1531	KSSEKLVR	TQDIVD↓KSSE	0	100	0	0	Single C3	0	1	56	47
O75369	Filamin-B	1447	1458	SSKAGLAPLEVR	QSFTVD↓SSKA	0	100	0	0	Single C3	0	1	57	47
P62269	40 S ribosomal protein S18	93	108	GKYSQVLANGLDNKLR	QKDVKD↓GKYS	7	0	100	0	0.07	0	1	69	46
P39687	Acidic leucine-rich nuclear phosphoprotein 32 family member A	217	233	GEVDDEEDEEELGEEER	EEGYND↓GEVD	5.3	0	100	0	0.05	0	1	92	41
P47712	Cytosolic phospholipase A2	523	533	AAVADPDEFER	DDDELD↓AAVA	0	99.55	100	0	0	1	1	48	47		Caspase-3, -8	73, 74
P63261	Actin, cytoplasmic 2	245	254	GQVITIGNER	SYELPD↓GQVI	20.69	98.79	100	0.21	0.21	1.01	5	55	47	P60709, AP62736, AP63261, AP63267, AP68032, AP68133, AQ562R1, AQ6S8J3, AQ9BYX7
P61011	Signal recognition particle 54-kDa protein	392	402	GAKVFSKQPGR	ELDSTD↓GAKV	51.73	95.75	100	0.54	0.52	1.04	1	51	47		Caspase-3	59
Q92917	G patch domain and KOW motif-containing protein	342	353	GPAAKSEKAAPR	LPDRQD↓GPAA	10.68	71.97	100	0.15	0.11	1.39	1	66	47
Q13151	Heterogeneous nuclear ribonucleoprotein A0	74	81	GNTVELKR	SPHAVD↓GNTV	7.69	67.1	100	0.11	0.08	1.49	2	51	47
Q86V48	Leucine zipper protein 1	443	454	SGTQETKKTEDR	MGVSTD↓SGTQ	0	55.04	100	0	0	1.82	1	56	47
P63241	Eukaryotic translation initiation factor 5A-1	12	26	AGASATFPMQCSALR	DFETGD↓AGAS	0	54.76	100	0	0	1.83	1	57	46	Q6IS14
P55209	Nucleosome assembly protein 1-like 1	58	72	GLVETPTGYIESLPR	LQERLD↓GLVE	7.19	53.9	100	0.13	0.07	1.86	2	85	47
Q7Z6Z7	E3 ubiquitin-protein ligase HUWE1	2360	2371	GGSGNSTIIVSR	ELLERD↓GGSG	15.6	53.54	100	0.29	0.16	1.87	1	82	47
P30419	Glycylpeptide N- tetradecanoyltransferase 1	73	88	SAQDQPVKMNSLPAER	KGSETD↓SAQD	0	47.04	100	0	0	2.13	1	52	46		Caspase-3	59
Q15233	Non-POU domain-containing octamer-binding protein	423	434	GTLGLTPPTTER	ATMMPD↓GTLG	5.63	35.09	100	0.16	0.06	2.85	1	48	47		Caspase-3	75
O94992	Protein HEXIM1	220	228	LKTGLYSKR	DQEEPD↓LKTG	5.13	34.66	100	0.15	0.05	2.89	1	68	47
P46777	60 S ribosomal protein L5	137	152	GQPGAFTCYLDAGLAR	NVESID↓GQPG	0	32.48	100	0	0	3.08	1	49	46
Q13435	Splicing factor 3B subunit 2	777	791	GSETPQLFTVLPEKR	IEEAMD↓GSET	4.35	31.89	100	0.14	0.04	3.14	1	94	46
Q6PKG0	La-related protein 1	496	508	FSQLLNCPEFVPR	DYSQTD↓FSQL	0	28.54	100	0	0	3.5	1	66	47
O60664	Mannose 6-phosphate receptor-binding protein 1	10	28	GSTQVTVEEPVQQPSVVDR	DGAEAD↓GSTQ	0	26.79	100	0	0	3.73	1	70	46
Q04637	Eukaryotic translation initiation factor 4γ1	754	762	GSKTQDLFR	GEEDAD↓GSKT	8.73	22.98	100	0.38	0.09	4.35	1	53	47
Q13442	28-kDa heat- and acid-stable phosphoprotein	25	35	AQLQAEKQKAR	SPEEID↓AQLQ	0	20.67	100	0	0	4.84	2	68	47		Caspase-3	59
Q32MZ4	Leucine-rich repeat flightless-interacting protein 1	679	690	FEDDTVQSSGPR	DGDTLD↓FEDD	0	16.42	100	0	0	6.09	1	79	47
P06454	Prothymosin α	77	90	GDEDEEAESATGKR	DGEEED↓GDED	18.54	16.31	100	1.14	0.19	6.13	1	66	46
P14618	Pyruvate kinase isozymes M1/M2	355	376	GADCIMLSGETAKGDYPGADCIMLSGETAKGDYPLELEAVR	ANAVLD↓GADC	4.37	14.11	100	0.31	0.04	7.09	1	72	45
P06454	Prothymosin α	72	90	GEEEDGDEDEEAESATGKR	EEEEGD↓GEEE	8.51	10.48	100	0.81	0.09	9.54	1	115	42
Q8N1G4	Leucine-rich repeat-containing protein 47	526	554	AVSGQLPDPTTNPSAGKDGPSLLVVEQVR	SDTEAD↓AVSG	0	0	100	0	0	Single C7	1	62	44
P05455	Lupus La protein	375	384	ENGATGPVKR	EHDEHD↓ENGA	0	0	100	0	0	Single C7	2	49	47		Caspase-3	76
P26599	Polypyrimidine tract-binding protein 1	3	14	GIVPDIAVGTKR	MD↓GIVP	0	0	100	0	0	Single C7	2	59	47
Q00839	Heterogeneous nuclear ribonucleoprotein U	233	244	GKTEQKGGDKKR	GAPAGD↓GKTE	0	0	100	0	0	Single C7	1	68	46
Q9NX24	H/ACA ribonucleoprotein complex subunit 2	10	22	GPEAQAEACSGER	IKADPD↓GPEA	0	0	100	0	0	Single C7	1	67	46		Caspase-3	59