Table 1.
The number of protein spots resolved in replicate gels of the same biological sample.
| Sample No (Treatment group) | No. of Replicates | Total Proteins resolved (occurring in at least one replicate) (%) | Number resolved in all replicates (%) | Number resolved in all but one replicate (%) | Number resolved in all but two (%) | Number resolved in just one (%) |
| 6 (GSE) | 3 | 4064 (100) | 309 (8) | 563 (14) | 3192 (78) | - |
| 7 (GSE) | 4 | 546 (100) | 169 (31) | 130 (26) | 97 (18) | 150 (27) |
| 8 (GSE) | 4 | 954 (100) | 186 (19) | 120 (12) | 105 (11) | 543 (57) |
| 9 (GSE) | 2 | 904 (100) | 342 (39) | 562 (62) | - | - |
| 10 (GSE) | 2 | 396 (100) | 229 (58) | 167 (42) | - | - |
| 22 (CONT) | 4 | 924 (100) | 234 (25) | 89 (10) | 109 (12) | 492 (53) |
| 23 (CONT) | 4 | 950 (100) | 161 (17) | 151 (16) | 102 (11) | 536 (59) |
| 24 (CONT) | 2 | 879 (100) | 312 (35) | 567 (65) | - | - |
| 25 (CONT) | 3 | 957 (100) | 272 (28) | 117 (12) | 568 (59) | |
| 26 (CONT) | 2 | 432 (100) | 183 (42) | 249 (58) | - | - |
The variability in the resolution of protein spots in technical replicates in a 2D gel experiments is one of the causes of the large number of missing spot intensities. The variability in the table above demonstrates the need for technical replicates as a quality control measure to identify spots that are most 'reliable' and common and therefore most useful to generalize to a larger population.