Table 2. Selected proteins identified using the PROP analysis that were preferentially identified before H2O2 oxidation treatment of cells.
| Protein | H2O2 † | Untreated† | ||||||||||||
| gi | Description | pValue‡ | 1 | 2 | 3 | 4 | 5 | 6 | 1 | 2 | 3 | 4 | 5 | 6 |
| 48255889 | glucosidase 2 subunit beta isoform 1 | 5.55E−119 | 9 (17) | 9 (18) | 7 (12) | 8 (18) | 8 (19) | 8 (19) | 13 (29) | 12 (27) | 13 (29) | 11 (25) | 13 (29) | 11 (23) |
| 42794771 | thioredoxin domain-containing protein 5 iso1 | 1.73E−049 | 2 (3) | 3 (3) | 1 (1) | 2 (2) | 1 (1) | 1 (1) | 5 (7) | 7 (8) | 6 (7) | 6 (8) | 6 (8) | 5 (7) |
| 10835143 | complement decay-accelerating factor isofo1 | 6.62E−045 | 1 (1) | 2 (3) | 1 (1) | 1 (1) | 2 (2) | 1 (1) | 6 (11) | 6 (8) | 6 (9) | 4 (9) | 3 (5) | 4 (7) |
| 4505591 | peroxiredoxin-1 | 2.81E−018 | 1 (1) | 1 (1) | X | 1 (1) | 1 (1) | X | 1 (1) | 2 (2) | 2 (2) | 1 (1) | 1 (2) | 2 (2) |
| 5453549 | peroxiredoxin-4 | 1.20E−007 | 2 (2) | X | 1 (1) | 1 (1) | X | X | 1 (2) | 2 (3) | 2 (2) | 2 (3) | 1 (1) | 2 (2) |
| 4758638 | peroxiredoxin-6 | 0.00E+000 | X | X | X | X | 1 (1) | X | 2 (2) | 3 (4) | 2 (2) | 2 (2) | 2 (3) | 1 (1) |
| 10835165 | CD59 glycoprotein preproprotein | 1.45E−018 | 1 (1) | 1 (1) | X | 1 (1) | X | X | 3 (3) | X | 1 (1) | 2 (2) | X | X |
| 10716563 | calnexin precursor | 0.00E+000 | X | X | X | X | 1 (1) | X | 3 (4) | 2 (2) | 2 (3) | 2 (2) | 3 (3) | 2 (2) |
| 38202257 | neutral alpha-glucosidase AB isoform 2 | 0.00E+000 | X | X | X | X | X | 1 (1) | 4 (5) | 3 (3) | 1 (1) | 2 (2) | 2 (2) | 1 (1) |
| 304376266 | putative serine protease 56 | 0.00E+000 | X | X | X | X | X | X | 4 (5) | 4 (4) | 5 (7) | 5 (9) | 3 (3) | 7 (8) |
| 38372919 | basigin isoform 1 precursor | 3.47E−036 | 1 (1) | X | X | X | X | X | 3 (4) | 3 (4) | 2 (3) | 2 (3) | 2 (2) | 3 (4) |
| 4758412 | polypeptide N-acetylgalactosaminyltransferase 2 | 1.16E−021 | X | X | X | X | X | X | 2 (2) | X | 1 (1) | 1 (1) | 2 (2) | 2 (3) |
| 40317626 | thrombospondin-1 precursor | 2.07E−021 | X | X | X | X | X | X | X | 2 (2) | X | 1 (1) | 1 (1) | 1 (1) |
| 24797067 | HLA class I histocompatibility antigen, A-1 alpha | 2.82E−007 | 1 (1) | X | X | X | X | X | 1 (1) | 1 (1) | 1 (2) | 1 (2) | 1 (1) | 1 (2) |
| 17986001 | major histocompatibility complex, class I, B precur | 1.54E−006 | X | X | X | X | X | X | 1 (2) | 1 (2) | 1 (2) | 1 (1) | 1 (2) | 1 (1) |
| 29725609 | epidermal growth factor receptor isoform a precur | 5.25E−006 | X | X | X | X | X | X | 1 (1) | 1 (2) | 1 (1) | 1 (1) | X | 1 (2) |
| 31542331 | protein CYR61 precursor | 2.10E−017 | X | X | X | X | X | X | 1 (1) | 1 (2) | 1 (1) | 1 (2) | 1 (1) | 2 (3) |
| 116734717 | alkaline phosphatase tissue-nonspec isozyme iso1 | 2.58E−012 | X | X | X | X | X | X | 1 (1) | 1 (1) | X | X | X | 1 (1) |
| 4503143 | cathepsin D preproprotein | 1.04E−024 | X | 1 (1) | 1(1) | X | 1 (1) | X | 1 (1) | 3 (3) | 2 (3) | 1 (1) | X | X |
| 22538442 | cathepsin Z preproprotein | 3.78E−014 | X | X | X | X | X | X | X | X | X | 1 (1) | 1 (1) | X |
| 5031863 | galectin-3-binding protein | 5.66E−004 | X | X | X | X | X | X | X | X | X | X | 1 (1) | X |
| 17149842 | peptidyl-prolyl cis-trans isomerase FKBP2 precur | 2.48E−022 | X | X | X | X | X | 1 (1) | 2 (2) | 1 (1) | 1 (1) | X | 1 (1) | 1 (1) |
| 167614504 | laminin subunit beta-1 precursor | 1.29E−016 | X | X | X | X | X | X | X | 2 (2) | 1 (1) | X | X | 1 (1) |
| 54607120 | lactotransferrin isoform 1 precursor | 9.38E−011 | X | X | X | X | X | 1 (1) | 1 (1) | 2 (2) | 1 (1) | 2 (2) | 1 (1) | 1 (1) |
Leading number indicates the number of unique peptides for a particular protein that were observed while the number in parentheses indicates the total number of scans that were observed for that protein. All of the scans tabulated passed a 3% FDR filter cutoff. An “X” indicates that no scans were observed that passed the FDR filter. The replicate analysis of 6 independent biological samples for both the control and H2O2 treated cells are shown. Data referred to in the text combine the replicate analyses.
The pValue represents the product of the best (i.e. smallest) eValue score observed for each unique peptide sequence for the given protein. This provides a relative measure of the overall confidence that the protein was in the sample (i.e. a true positive), with 0.00E+000 representing the highest confidence.