Table 2. A List of Quantified Proteins and Their Corresponding Ratios of Expression in WM-266-4 Cells with Respect to WM-115 Cells.
| NCBI accession | protein name | surface/membrane GOa | Ratio WM-266–4/115 mean ± SD (n = 3) | WM266-4 hitsb (H)c | WM115 hits (L)d |
|---|---|---|---|---|---|
| Up-Regulated Proteins | |||||
| NP_853509 | butyrophilin, subfamily 3, member A1 | Y | 2.37 ± 0.59 | 3 | 3 |
| NP_598000 | CD109 | Y | 3.65 ± 0.04 | 4 | 1 |
| NP_000102 | down-regulated in adenoma protein | Y | 5.97 ± 0.55 | 2 | 0 |
| NP_000203 | integrin beta chain, beta 3 precursor | Y | 2.38 ± 0.07 | 19 | 9 |
| NP_061984 | major histocompatibility complex, class II, DR alpha precursor | Y | >5 | 2 | 0 |
| NP_004986 | matrix metalloproteinase 14 preproprotein | Y | 2.18 ± 0.48 | 6 | 0 |
| NP_006491 | melanoma cell adhesion molecule | Y | 3.13 ± 0.69 | 19 | 6 |
| NP_005920 | melanoma-associated antigen p97 isoform 1, precursor | Y | 3.60 ± 1.05 | 2 | 0 |
| XP_933500 | PREDICTED: similar to immunoglobulin superfamily, member 3 isoform 1 | Y | 2.62 ± 0.10 | 2 | 0 |
| NP_005496 | scavenger receptor class B, member 1 isoform 1 | Y | 3.25 ± 0.35 | 6 | 0 |
| NP_001143 | solute carrier family 25, member 5 | Y | >20 | 3 | 0 |
| NP_001012679 | solute carrier family 3 | Y | 2.53 ± 0.18 | 9 | 6 |
| Down-Regulated Proteins | |||||
| NP_001618 | activated leukocyte cell adhesion molecule | Y | 0.07 ± 0.03 | 0 | 15 |
| NP_001760 | CD9 antigen | Y | 0.31 ± 0.02 | 1 | 4 |
| NP_004422 | ephrin receptor EphA2 | Y | 0.36 ± 0.06 | 0 | 9 |
| NP_001005862 | erbB-2 isoform b | Y | 0.29 ± 0.07 | 0 | 3 |
| NP_003536 | H4 histone family, member J | R | 0.45 ± 0.26 | 19 | 20 |
| NP_001019770 | histone 2, H2bf | R | 0.38 ± 0.19 | 1 | 9 |
| NP_055148 | immunoglobulin superfamily, member 4D isoform 1 | Y | 0.47 ± 0.11 | 3 | 4 |
| NP_005388 | podocalyxin-like precursor isoform 2 | Y | <0.05 | 0 | 2 |
| NP_543006 | signal-regulatory protein beta 2 isoform 2 | Y | 0.29 ± 0.07 | 1 | 2 |
| NP_003371 | vimentin | R | 0.43 ± 0.03 | 1 | 4 |
a
GO database annotations, Y, cell surface/membrane protein; R, membrane-associated protein based on previous publications (see Supporting Information for details).
b
Hits: total number of peptides (including same peptides with multiple identification and different m/z) identified with SEQUEST search based on LC-MS/MS data acquired in data-dependent scan mode. Although no peptides were identified for some of the listed proteins from LC-MS/MS data acquired in the data-dependent scan mode, biotinylated peptide(s) was (were) identified from LC-MS/MS results obtained in the SIM mode.
c
H, heavy.
d
L, light.