Table 1. Mass spectrometric identifications from all three AP-1γ IPs.

Protein	Experiment 1				Experiment 2				Experiment 3
	Score		Peptides		Score		Peptides		Score		Peptides
	Soft	Std	Soft	Std	Soft	Std	Soft	Std	Soft	Std	Soft	Std
AP-1γ1	726	635	28	37	2757	1737	118	77	2582	3450	86	147
AP-1β	2072	1779	92	109	3792	2655	160	111	5854	4996	244	212
AP-1µ1a	495	1348	44	96	2906	1754	148	100	3124	3650	145	178
AP-1σ1a	901	1406	14	26	839	383	25	11	777	978	24	24
AP-1σ1b	74	62	5	6	141	68	9	3	162	224	15	11
AP-1σ1c	98	-	2	-	31	-	1	-	141	91	11	3
Aftiphilin	332	241	20	9	1235	519	34	20	2622	2644	88	83
γ-Synergin	1052	549	21	18	1068	404	29	16	5596	3881	188	138
p200	282	354	13	12	903	494	39	17	4116	4074	161	165
KIF13a	745	524	29	21	1386	851	59	30	280	191	12	11
p34	63	50	2	2	330	269	19	14	105	83	3	3

This table shows AP-1 constituents and associated proteins identified in three independent AP1-γ immunoprecipitations. In each experiment, samples (ie Protein A sepharose beads with bound antigen) were split into two equal aliquots prior to elution. Aliquots were either subjected to the soft elution protocol (“Soft”) reported in this study, or to standard elution conditions (“Std”). Eluates were subjected to tryptic solution digest without further fractionation, and analyzed by LC-MSMS. Mascot scores reflecting the confidence of identification [8], and the number of peptides identified for each protein are indicated. Please note that the AP-1σ1c subunit was not identified in experiments 1 and 2 using standard elution conditions.

Experiments 1 and 2 were performed in MES-D buffer; experiment 3 was performed in PBS-T buffer (see File S1 for details).