Table 1.
Summary of peptide-level and protein-level results for each experiment, with MS/MS data alone and with MS/MS data combined with AMT data. All peptide counts are with PeptideProphet or AMT probability ≥ 0.9. All protein counts are of protein groups with ProteinProphet probability ≥ 0.9. Fraction-level numbers are averages over all fractions in each experiment. Counts of unique and quantified proteins per fraction are counts of protein groups with any high-quality peptide evidence (with isotopic ratios, for quantified summary) for the group in the fraction.
| Experiment (Number of Fractions) |
Analysis Approach |
Experiment-Level Summary | Fraction-Level Summary | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Unique Peptides |
Quant. Peptides |
Unique Proteins |
Quant. Proteins |
Unique Peptides |
Quant. Peptides |
Unique Proteins |
Quant. Proteins |
||
| 1 (96) |
MS/MS | 6128 | 1726 | 841 | 392 | 722.7 | 255.2 | 145.9 | 77.5 |
| +AMT (% Increase) |
7357 ( 20.1%) |
1922 (11.4%) |
1038 (23.4%) |
428 (9.2%) |
1165.3 (61.2%) |
343.9 (34.8%) |
213.9 (46.6%) |
97.3 (25.5%) |
|
| 2 (96) |
MS/MS | 7230 | 1408 | 1103 | 329 | 742.4 | 209.3 | 160.0 | 60.9 |
| +AMT (% Increase) |
8204 (13.5%) |
1603 (13.8%) |
1227 (11.2%) |
354 (7.6%) |
1045.5 (40.8%) |
253.3 (21.0%) |
218.5 (36.6%) |
71.7 (17.7%) |
|
| 3 (88) |
MS/MS | 5843 | 1401 | 710 | 270 | 760.6 | 214.9 | 142.3 | 65.9 |
| +AMT (% increase) |
7069 (21.0%) |
1632 (16.5%) |
875 (23.2%) |
314 (16.2%) |
1069.6 (40.6%) |
270.7 (26.0%) |
191.5 (34.6%) |
77.1 (17.0%) |
|
| 4 (94) |
MS/MS | 7400 | 1774 | 1044 | 346 | 996.6 | 298.3 | 177.4 | 83.4 |
| + AMT (% increase) |
8815 (19.1%) |
2003 (12.9%) |
1335 (27.9%) |
403 (16.5%) |
1112.9 (11.7%) |
419.9 (40.8%) |
268.1 (51.1%) |
108.9 (30.6%) |
|
|
Mean
(93.5) |
MS/MS | 6650.3 | 1577.3 | 924.5 | 334.3 | 805.6 | 244.4 | 156.4 | 69.2 |
|
+ AMT
(% increase) |
7861.3
(18.2%) |
1790.0
(13.5%) |
1118.8
(21.0%) |
374.5
(12.0%) |
1098.3
(36.3%) |
322.0
(31.7%) |
223.0
(42.6%) |
88.8
(28.3%) |
|