Acc. #i. Protein Name Gene Peptide (% Cov)ii. Ratio (p-value)iii. IPiv. SDGv. Primary localisationvi. Modificationsvi. Proteins involved in signal transduction P33241 Lymphocyte-specific protein 1 LSP1 15(50.4) 0.20 (0.01) + + Plasma membrane Acetylation B1AH80 Ras-related C3 botulinum toxin substrate 2 RAC2 3 (17.3) 0.40 (0.04) + + Plasma membrane Acetylation/ prenylation P01919 HLA class II histocompatibility antigen, DQ(W1.1) beta chain HLA-DQB1 8 (36.8) 0.54 (0.04) + + Plasma membrane Glycosylation P01903 HLA class II histocompatibility antigen, DR alpha chain HLA-DRA 6 (11.4) 0.30 (0.00) + + Plasma membrane Glycosylation P05536 HLA class II histocompatibility antigen, DQ(W3) alpha chain HLA-DQA1 2 (7.9) 0.54 (0.01) - + Plasma membrane Glycosylation Q96SB3 Neurabin II PPP1R9B 4 (10.2) 0.52 (0.01) - + Plasma membrane Acetylation Q9Y4H4 G-protein-signaling modulator 3 GPSM3 2 (23.1) 0.50 (0.03) - + Plasma membrane Phosphorylation Q8WU40 Calcium/calmodulin-dependent protein kinase type II subunit gamma CAMK2G 1 (5.3) 0.30 (0.03) - + Plasma membrane Phosphorylation Q92928 Putative Ras-related protein Rab-1C RAB1C 2 (12.4) 0.62 (0.02) - + Plasma membrane Prenylation/ acetylation Q8TBC3 SH3KBP1-binding protein 1 SHKBP1 1 (7.6) 0.40 (0.05) - + Plasma membrane Phosphorylation Q01518 Adenylyl cyclase-associated protein 1 CAP1 3 (12.0) 0.51 (0.01) - + Plasma membrane Acetylation P01871 Ig mu chain C region IGHM 8 (19.1) 0.48 (0.05) - + Plasma membrane Glycosylation P15907 Beta-galactoside alpha-2,6-sialyltransferase 1, B-cell antigen CD75 ST6GAL1 1 (5.4) 0.46 (0.04) - + Plasma membrane Glycosylation Q96FS4 Signal-induced proliferation-associated protein 1 SIPA1 1 (3.5) 0.24 (0.01) - - Cytoplasm Phosphorylation Q7LGA3 Heparan sulfate 2-O-sulfotransferase 1 HS2ST1 1 (10.4) 0.54 (0.04) - - Plasma membrane Glycosylation P61952 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-11 GNG11 1 (28.8) 0.28 (0.00) - - Plasma membrane Prenylation/ lipid anchor P09486 Basement-membrane protein 40 SPARC 1 (8.5) 0.50 (0.05) - - Plasma membrane Glycosylation Proteins involved in immune response A9YLN4 Tyrosine-protein kinase receptor CD74/ROS fusion 2 (4.8) 0.65 (0.01) - - Plasma membrane Phosphorylation P06314 Ig kappa chain V-IV region B17   2 (13.4) 0.69 (0.05) + + Plasma membrane - Q7YPT8 MHC class II antigen HLA-DQA1/DRA 6 (11.4) 0.39 (0.00) + + Plasma membrane Glycosylation Q0KKI6 Immunoglobulin kappa light chain IGKC 4 (28.9) 0.61 (0.03) - + Plasma membrane - P13284 Gamma-interferon-inducible lysosomal thiol reductase IFI30 1 (5.2) 0.24 (0.00) - - Plasma membrane Glycosylation P04440 HLA class II histocompatibility antigen, DP(W4) beta chain HLA-DPB1 3 (26.4) 0.29 (0.00) - - Plasma membrane Glycosylation Proteins involved in protein metabolism Q6NYC8 Phostensin PPP1R18 2 (6.7) 0.43 (0.02) - + Plasma membrane Phosphorylation Q8WWI1 LIM domain only protein 7 LMO7 3 (4.1) 0.28 (0.01) - + Cytoplasm Phosphorylation P29144 Tripeptidyl-peptidase 2 TPP2 2 (2) 0.35 (0.04) - - Plasma membrane Acetylation Transport proteins Q10567 AP-1 complex subunit beta-1 AP1B1 1 (4.3) 0.46 (0.00) - - Plasma membrane Acetylation Q9H0X9 Oxysterol-binding protein-related protein 5 OSBPL5 1 (1.4) 0.30 (0.04) - + Cytoplasm Phosphorylation ATP-binding protein Q6S8J3 POTE ankyrin domain family member E POTEE 9 (8.6) 0.46 (0.01) - + Plasma membrane Phosphorylation Protein involved in cisplatin resistance Q6UW68 Transmembrane protein 205 TMEM205 1 (13.8) 0.42 (0.03) - - Plasma membrane Acetylation i. Accession numbers retrieved from UniProt database. ii. Number of peptides identified with >95% confidence, protein sequence coverage percentage in brackets. iii. Protein level ratio (all proteins depleted after MβCD treatment) with p-value in brackets. iv. ‘+’ denotes identification of protein in immuno-precipitation MS/MS analysis. v. ‘+’ denotes identification of protein in sucrose density gradient MS/MS analysis. vi. Primary sub-cellular localisation and post-translational modifications were obtained from the Human Protein Reference Database (http://www.hprd.org/)

Table 1: Novel lipid raft proteins identified in MEC1 cells by cholesterol depletion using MβCD (1 mM, 1 h).