Table 1. Analysis of the protein lists and comparison to mRNA signal intensities on Affymetrix GeneChips.
| Profile element | Short list | Long list | Membrane sample* | Total list | Protein-coding genes expressed on Affymetrix arrays† |
|---|---|---|---|---|---|
| Proteins | 404 | 986 | 287 | 1,147 | — |
| Corresponding mRNA detected | 401 | 964 | 275 | 1,113 | 2,826 |
| Mean mRNA signal (arithmetic) | 7,990 | 5,670 | 8,080 | 5,330 | 2,850 |
| Mean mRNA signal (geometric) | 3,830 | 2,450 | 2,940 | 2,270 | 1,020 |
| Mean number of tryptic peptides detected | 8.0‡ | 4.2 | 2.4 | 4.0§ | — |
| Mean number of tryptic peptides predicted | 21.0 | 16.1 | 16.5 | 15.9 | 13.4 |
| Membrane proteins (low estimate to high estimate) | 7-15 | 22-56 | 94-138 | 99-160 | 317-592 |
| Proteins of unknown function¶ | 14 | 163 | 49 | 199 | 803 |
If we consider only the membrane proteins in the sample, which was prepared without washing, the values are as follows (low estimate to high estimate): proteins, 94-138; corresponding mRNA detected, 87-130; mean mRNA signal (arithmetic), 6,530-5,840; mean mRNA signal (geometric), 2,240-2,130; mean number of tryptic peptides detected, 2.8-2.7; mean number of tryptic peptides predicted, 15.1-15.9; proteins of unknown function, 3-17. If we consider the proteins identified only in the membrane sample, the values are as follows: proteins, 161; corresponding mRNA detected, 149; mean mRNA signal (arithmetic), 3,240; mean mRNA signal (geometric), 1,410; mean number of tryptic peptides detected, 2.0; mean number of tryptic peptides predicted, 15.0; membrane proteins, 77-104; proteins of unknown function, 36.
E. coli has a total of 4,291 protein-coding genes. Values for these were as follows: mean mRNA signal (arithmetic), 1,950; mean mRNA signal (geometric), 460; mean number of tryptic peptides predicted, 13.1; membrane proteins, 532-1,017; proteins of unknown function, 1,409.
With the criteria employed for the total list (see Materials and Methods), this value was 7.8.
Only one tryptic peptide was detected for 381 of the proteins.
This is the same as open reading frames (19). The overlap between these and membrane proteins is as follows: short list, 0-0; long list, 1-4; membrane sample, 3-17; total list, 3-18; all expressed protein-coding genes, 11-134.