Table 1. Quantitative SILAC analysis reveals increased accumulation of unprenylated Rab proteins in MKD2 cells cultured at 40 °C compared with 37 °C.

Name	Relative abundance (%)	Ratio 40 °C/37 °C (H/L)	Ratio 40 °C/37 °C (L/H)
Rab11A/11B	8.7	2.1	1.8
Rab6A/6B/39A	23.4	1.6	1.4
Rab1A	0.8	ND	2.9
Rab1B/1C	12.6	1.6	1.5
Rab5C	4.6	1.4	0.8
Rab7A	10.0	3.0	2.7
Rab2A/2B	5.6	1.4	1.4
Rab5B	19.8	1.7	1.7
Rab14	1.0	2.7	ND
Rab21	13.5	2.4	1.3

Abbreviations: LC/MS, liquid chromatography–mass spectrometry; MKD2, mevalonate kinase deficiency; SILAC, stable isotope labelling with amino acids in cell culture.

Cells labelled in ‘heavy' (H) or ‘light' (L) medium were cultured for 7 days at 40 °C or 37 °C, respectively. As an inverse labelling control, cells labelled in ‘heavy' (H) or ‘light' (L) medium were cultured for 7 days at 37 °C or 40 °C, respectively. Equal amounts of protein from cell lysates were mixed prior to in vitro prenylation, then biotinylated proteins were enriched with streptavidin beads and analysed by LC/MS. The amount of individual Rab proteins was expressed as a ratio of levels in cells at 40 or 37 °C (either H/L or L/H). For the 10 Rab proteins identified, the average relative abundance was calculated from the analysis of whole-cell lysates of H- or L-labelled cells cultured at 37 °C. Rab1A and Rab14 could not be detected (ND) in one of the pair of H- or L-labelled samples.