Table 1.

Proteomic analysis of unprenylated small GTPases in J774 cells following treatment with 50 nM or 500nM ZOL (or saline control) for 7 days. Proteins were identified and quantitated by nano-LC-MS/MS using SILAC. The fold change in abundance of each protein after ZOL treatment was calculated as a ratio of protein abundance in whole cell lysates of 500 nM ZOL-treated/control cells in a single experiment (see Table S1 for additional proteins and details). After in vitro prenylation of cell lysates and enrichment of biotinylated proteins, the relative abundance of each protein was calculated as a percentage of all of the enriched Rab GGTase substrates or all of the GGTase 1 substrates identified. The average fold change in unprenylated small GTPases was calculated as a ratio of abundance of in vitro-prenylated protein in ZOL-treated/control cells from 2 biological replicates (ie inversely labeled by SILAC), +/− SD where the protein was detected in both replicates (see Table S2 for details). NR = No Ratio could be calculated (ie undetectable in either the treated or the control cells)

Name	Relative % abundance	Fold Change with 500 nM ZOL ± SD	Fold Change with 50 nM ZOL ± SD	Fold Change in Abundance
Rab GGTase substrates
Rab1B	14.32	9.5±6.7	1.6±0.03	NR
Rab14	13.41	7.0±3.5	1.2±0.04	−1.1
Rab7A	11.67	7.7±2.6	1.5±<0.01	−1.1
Rab21	7.32	8.8±4.2	1.5±0.05	−1.1
Rab6A/Rab6B	7.27	7.0±3.5	1.1±0.04	1.0
Rab18	5.75	4.9±0.4	1.3±0.2	−1.1
Rab5C	5.20	6.7±1.8	1.3±0.04	−1.1
Rab11B/Rab11A	5.16	8.3±4.5	1.3±0.2	−1.1
Rab2A	4.95	5.3±0.3	1.2±0.07	1.3
Rab1A	3.95	7.9±3.8	1.5±0.02	1.0
Rab10	3.17	4.9±0.8	1.1±0.3	1.0
Rab39A	2.36	2.4±2.3	NR	No ID
Rab3A	1.91	6.2±0.5	NR	No ID
Rab5B	1.88	5.9	−1.1	1.0
Rab5A	1.87	7.0±2.2	NR	−1.3
Rab31	1.51	4.4±2.9	−1.1±0.1	−1.3
Rab9A	1.19	4.3	NR	1.0
Rab43/Rab19	1.08	3.0	NR	No ID
GGTase I substrates
Rac1/Rac3	58.25	2.6±1.2	−1.3±0.01	NR
Rac2	21.58	1.8±0.6	1.0±0.2	1.0
RhoA	3.94	2.1	NR	1.0