Table 1. Selected proteins identified using the PROP analysis on six replicate cell cultures treated or not with H2O2 that were preferentially identified after H2O2 oxidation treatment of cells.
| Protein | H2O2 † | Untreated† | ||||||||||||
| gi | Description | pValue‡ | 1 | 2 | 3 | 4 | 5 | 6 | 1 | 2 | 3 | 4 | 5 | 6 |
| 50592994 | thioredoxin | 3.89E−046 | 4 (35) | 5 (46) | 5 (30) | 5 (31) | 4 (23) | 4 (23) | 1 (2) | 2 (4) | 2 (5) | 1 (1) | 1 (2) | 1 (1) |
| 4503483 | elongation factor 2 | 1.42E−102 | 6 (9) | 9 (13) | 4 (7) | 7 (13) | 8 (14) | 5 (9) | 1 (1) | 1 (1) | 1 (1) | X | X | 1 (1) |
| 4503481 | elongation factor 1-gamma | 9.40E−016 | 2 (2) | 1 (1) | 1 (1) | 1 (1) | 2 (2) | X | X | X | X | X | X | X |
| 15082258 | chromobox protein homolog 3 | 0.00E+000 | 2 (2) | 3 (5) | 1 (1) | 2 (3) | 1 (1) | 2 (3) | X | X | X | X | X | X |
| 4503545 | eukaryotic translation initiation factor 5A-1 iso B | 0.00E+000 | 8 (28) | 8 (23) | 12 (26) | 10 (21) | 8 (27) | 10 (24) | X | X | X | X | X | X |
| 4758516 | hepatoma-derived growth factor isoform a | 0.00E+000 | 8 (15) | 9 (16) | 7 (17) | 6 (12) | 6 (14) | 8 (11) | X | X | X | X | X | X |
| 10835063 | nucleophosmin isoform 1 | 0.00E+000 | 10 (43) | 9 (43) | 9 (40) | 10 (31) | 9 (35) | 9 (36) | X | X | X | X | X | X |
| 23308579 | prostaglandin E synthase 3 | 9.68E−023 | 2 (2) | 2 (2) | 2 (3) | 1 (2) | X | 1 (1) | X | X | X | X | X | X |
| 5031635 | cofilin-1 | 1.75E−134 | 9 (16) | 7 (11) | 6 (9) | 8 (12) | 8 (16) | 6 (13) | X | X | X | X | X | X |
| 10863927 | peptidyl-prolyl cis-trans isomerase A | 3.39E−087 | 6 (18) | 8 (23) | 8 (16) | 7 (21) | 6 (20) | 8 (27) | X | 1 (1) | X | X | X | X |
| 4504425 | high mobility group protein B1 | 4.40E−058 | 4 (5) | 5 (8) | 4 (5) | 3 (6) | 3 (4) | 2 (3) | X | X | X | X | X | X |
| 4506901 | serine/arginine-rich splicing factor 3 | 9.06E−047 | 3 (4) | 5 (6) | 4 (6) | 4 (7) | 4 (8) | 4 (5) | X | X | X | X | X | X |
| 17986258 | myosin light polypeptide 6 isoform 1 | 9.95E−039 | 3 (14) | 4 (13) | 3 (9) | 3 (13) | 3 (12) | 3 (10) | X | X | X | X | X | X |
| 4505303 | myosin light chain 6B | 2.40E−016 | 2 (2) | 2 (4) | 1 (1) | 2 (4) | 2 (4) | 2 (4) | X | X | X | X | X | X |
| 4557777 | myosin light chain 3 | 1.40E−013 | 1 (1) | 1 (2) | X | 1 (1) | 1 (1) | 1 (2) | X | X | X | X | X | X |
| 222352151 | poly(rC)-binding protein 1 | 1.98E−036 | 1 (1) | 2 (2) | 1 (1) | 1 (1) | 4 (5) | 1 (1) | X | X | X | X | X | X |
| 23308577 | D-3-phosphoglycerate dehydrogenase | 2.82E−025 | X | 2 (2) | 2 (3) | 1 (1) | 2 (2) | 1 (1) | X | X | X | X | X | X |
| 4505409 | nucleoside diphosphate kinase B isoform a | 1.62E−016 | 1 (1) | 1 (2) | 2 (2) | 2 (3) | 1 (1) | 1 (2) | X | X | X | X | X | X |
| 4504981 | galectin-1 | 5.82E−019 | 3 (7) | 4 (7) | 3 (7) | 2 (5) | 3 (4) | 3 (8) | X | X | X | X | X | X |
| 50053795 | eukaryotic translation initiation factor 4B | 2.84E−018 | 1 (1) | 1 (2) | 1 (3) | 1 (2) | 1 (2) | 1 (1) | X | X | X | X | X | X |
| 154355000 | far upstream element-binding protein 2 | 4.85E−014 | 3 (4) | 2 (3) | 2 (3) | 1 (2) | 3 (3) | 2 (3) | X | X | X | X | X | X |
| 72534660 | serine/arginine-rich splicing factor 7 isoform 1 | 5.18E−011 | 1 (1) | 2 (2) | 1 (1) | 2 (2) | 2 (2) | X | X | X | X | X | X | X |
| 14277700 | 40S ribosomal protein S12 | 1.29E−010 | 1 (2) | 1 (1) | 1 (2) | 1 (1) | X | 1 (1) | X | X | X | X | X | X |
| 4757714 | phosphotyrosine protein phosphatase isoform c | 5.75E−010 | 1 (1) | 1 (3) | X | 1 (1) | 1 (1) | 1 (2) | X | X | X | X | X | X |
| 4759098 | transformer-2 protein homolog beta | 2.51E−008 | 1 (2) | 2 (5) | 1 (1) | 2 (4) | X | X | X | X | X | X | X | X |
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; in other words, a protein indicated as 3(13) had three unique peptides identified a total of 13 times. 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.