Table I In vivo sumoylated proteins derived after immunoprecipitation from HeLa cells using anti-SUMO1 antibody (see “Experimental Procedures”)

The sequence of the sumoylated peptide and the positions of SUMO acceptor sites as determined by MS and MSMS using ChopNSpice in combination with MASCOT and SEQUEST as search engines are listed. For details, see supplemental Table_S4. Dashes (—) indicate that the corresponding sumoylated peptide or its actual conjugation position could not be identified and thus was not scored by the search engines.

Modification and conjugated protein	Swiss-Prot accession number	Sequence	Conjugated position	MASCOT score	SEQUEST XCorr
SUMO1
Ran GTPase-activating protein 1	P46060	⁵¹⁶LLVHMGLLKSEDKVK⁵³⁰	Lys⁵²⁴	70.29	6.10
Small ubiquitin-related modifier 1	P63165	¹⁷KEGEYIK²³	Lys¹⁷	92.87	5.60
Small ubiquitin-related modifier 2	P61956	⁸EGVKTENNDHINLK²¹	Lys¹¹	79.50	5.57
SUMO-conjugating enzyme UBC9	P63279	¹⁴²VEYEKR¹⁴⁷	Lys¹⁴⁶	59.84	5.18
E3 SUMO-protein ligase RanBP2	P49792	¹⁰⁰IAELLCKNDVTDGRAKYWLER¹²⁰	—	14.31	4.34
		¹⁴⁰⁸FALVTPKK¹⁴¹⁵	Lys¹⁴¹⁴	36.53	4.22
		¹⁷¹⁵SGFEGMFTKK¹⁷²⁴	Lys¹⁷²³	106.23	5.46
		²²⁵⁵KNLFR²²⁵⁹	Lys²²⁵⁵	35.55	2.86
		²⁴²⁴FKLQDVADSFKK²⁴³⁴	Lys²⁴³³	94.41	5.12
		²⁵⁰⁷AVVSPPKFVFGSESVK²⁵²²	Lys²⁵¹³	29.65	2.59
		²⁵⁸¹NSDIEQSSDSKVK²⁵⁹⁴	Lys²⁵⁹²	97.71	6.57
		²⁶¹⁷AKEK²⁶²⁰	Lys²⁶¹⁸	44.60	6.22
RanBP2-like and GRIP domain-containing protein 4	Q7Z3J3	⁶⁹¹KAEDIANDALSPEEQEECK⁷⁰⁹	Lys⁶⁹¹	7.29	—
Chromodomain-helicase-DNA-binding protein 8	Q9HCK8	⁵⁸¹YTEDLDIKITDDEEEEEVDVTGPIK⁶⁰⁹	Lys⁵⁹²	—	4.02
Cytoplasmic dynein 1 heavy chain 1	Q14204	³²⁰⁷KIKETVDQVEELR³²¹⁹	Lys³²⁰⁷	20.56	4.21
Very long-chain-specific acyl-CoA dehydrogenase	P49748	⁶³³NFKSISK⁶³⁹	Lys⁶³⁵	46.13	—
Bifunctional aminoacyl-tRNA synthetase	P07814	³¹⁴NPIEKNLQMWEEMK³²⁷	Lys³¹⁸	51.70	—
SUMO2
Small ubiquitin-related modifier 2	P61956	⁸EGVKTENNDHINLK²¹	Lys¹¹	37.99	7.31