Table 1. Differential presentation of peptides on HLA-DR molecules and corresponding mRNA data
6 h of starvation 24 h of starvation
Source protein Entrez gene ID Peptide sequence Peptide ratio mRNA ratio Peptide ratio mRNA ratio
Membrane proteins
    HLA-A*0201 3105 FVRFDSDAASQR 0.64 NC 1.53 NC
3105 FVRFDSDAASQRME 0.68 NC 1.30 NC
3105 DTQFVRFDSDAASQRME 1.58 NC 0.36 NC
3105 VDDTQFVRFDSDAASQR 1.15 NC 0.82 NC
3105 KHKWEAAHVAEQLR 1.09 NC 1.23 NC
3105 DDTQFVRFDSDAASQRME 1.18 NC 0.95 NC
    HLA-B*4402 3106 EDLSSWTAADTAAQITQRKWE 1.18 NC 0.42 NC
3106 LSSWTAADTAAQITQR 1.11 NC 1.07 NC
    HLA-Cw*0501 3107 VDDTQFVQFDSDAASPRGEPR 1.20 NC 0.50 NC
3107 KDYIALNEDLRSWTA 1.11 NC NC
3107 DGKDYIALNEDLRSWTA 1.01 NC 0.61 NC
3107 FVQFDSDAASPRGEPR 0.76 NC 1.12 NC
    HLA-E 3133 DLRSWTAVDTAAQISEQ 0.97 1.87 0.70 2.46
    HLA-DQB1*0301 3119 DVEVYRAVTPLGPPD 1.25 NC NC
    Lymphocyte antigen Ly-6E 4061 KPTICSDQDNYCVT 1.18 NC 0.54
4061 LKPTICCSDQDNYCVT 1.40 NC 0.97 0.54
    Immunoglobulin heavy chain 3492 YLQMNSLKTEDT 0.75 1.33
3492 TLYLQMNSLKTEDT 1.38
    Immunoglobulin λ chain 3537 SHKSYSCQVTHEGSTVE 1.02 1.45
    B-lymphocyte antigen CD 20 931 INIYNCEPANPSEK 1.16 NC 1.53 NC
    Class I cytokine receptor 9466 VGVPYRITVTAVSASG 1.20 NC NC
    Transferrin receptor protein 1 7037 FTYINLDKAVLGTSN 1.18 NC 0.85 NC
    Carboxypeptidase D 1362 VPGTYKITASARGYNPV 1.27 1.23 1.37 1.52
1362 VPGTYKITASARGYN 1.13 1.23 1.52
Extracellular proteins
    Serotransferrin (bovine) FVKDQTVIQNTD 0.66 1.37
DVAFVKDQTVIQNTD 1.13
DVAFVKDQTVIQ 1.24
    Serum albumin (bovine) SPDLPKLKPDPNTLCDEF 1.24 1.01
    Apolipoprot B-100 (bovine) SASYKADTVAKVQGT 1.08 1.02
SASYKADTVAKVQGTE 0.98 0.44
Intracellular proteins
    Heat shock 70-kDa protein 1 3303 NVLRIINEPTAAAIAYG 1.50 3.48 1.48 NC
3303 VLRIINEPTAAAIAY 1.03 3.48 1.24 NC
3303 RIINEPTAAAIA 1.49 3.48 2.25 NC
3303 VLRIINEPTAAAIAYG 1.12 3.48 1.30 NC
    Heat shock cognate 71-kDa protein 3312 GILNVSAVDKSTGKE 1.67 NC 1.51 NC
3312 ERAMTKDNNLLGKFE 1.19 NC 1.50 NC
3312 GERAMTKDNNLLGKFE 1.48 NC 1.30 NC
    Elongation factor 1-α 1 1917 IEKFEKEAAEMGKGSF 1.49 NC 2.87 NC
    TNF, α-induced protein 3 7128 EIIHKALIDRNIQ 1.32 2.14 2.64
    RAD23 homolog B 5887 LLQQISQHQEHF 1.88 NC 1.79 NC
    Actin, cytoplasmic 2 71 TDYLMKILTERGYS 1.30 NC 1.09 NC
    NEDD4La 23327 DGRTFYIDHNSKITQ 1.26 NC 1.51 NC
    T complex protein 1, β subunit 10576 SLMVTNDGATILKN 1.15 NC NC
    Ubiquitin 7311 SDYNIQKESTLHLV 1.05 1.42
    α enolase 2023 VPLYRHIADLAGNSEV 1.50 NC 1.14 NC
    syntaxin 6 10228 NPRKFNLDATELSIRK 1.60 NC NC
    tubulin β-5 chain 10382 EPYNATLSVHQL 1.50 NC 1.23 NC
Lysosomal proteins
    Cathepsin C 1075 YDHNFVKAINAIQKSWT 1.31 NC 1.28 NC
1075 YDHNFVKAINAIQKSW 1.28 NC 1.27 NC
1075 YDHNFVKAINAIQKS 1.56 NC 1.40 NC
    Cathepsin D 1509 LSRDPDAQPGGE 0.83 NC 2.30 NC
    Cathepsin S 1520 TTAFQYIIDNKGIDSD 1.61 2.30 4.92
1520 TTAFQYIIDNKGID 1.90 2.30 1.56 4.92
    Lysosomal α-mannosidase 4125 VDYFLNVATAQGRYY 1.64 NC NC
  • The given peptide and mRNA ratios refer to the comparison of cells grown under starvation with control cells. For peptides, ratios were calculated from the signal intensities in LC-MS experiments. mRNA ratios were calculated from the signal log ratios given by the microarray analysis. No change (NC) is displayed if no significant change in the expression level was observed according to the change algorithm.