Table 1.
Number of Peptides and Proteins Identified, Quantitated, and Differentially Expressed from the SILAC MS/MS Analysis
| Cell fraction | Peptides identified | Proteins identified | Peptides used for quantitation | Proteins used for quantitation | Peptides used for quantitation (P < 0.05)∗ | Proteins used for quantitation (P < 0.05)∗ | Proteins down-regulated at least 20% | Proteins up-regulated at least 20% |
|---|---|---|---|---|---|---|---|---|
| Cytosol | 6489 | 842 | 6025 | 797 | 2384 | 223 | 36 | 31 |
| Nucleus | 5210 | 818 | 3217 | 564 | 1607 | 218 | 58 | 16 |
| Membrane | 3983 | 609 | 2478 | 430 | 960 | 124 | 9 | 11 |
| Cytoskeleton | 3497 | 423 | 3228 | 397 | 2085 | 196 | 22 | 63 |
| Total | 19,179 | 2692 | 14,948 | 2188 | 7036 | 761 | 125 | 121 |
MS/MS, tandem mass spectrometry; SILAC, stable isotope labeling of amino acids in cell culture.
∗
Differentially regulated proteins were selected only from proteins with significant quantitative precision (P ≤ 0.05). P values were calculated using peptide ratios using t-test.