Table 2.
Number of features associated with each biological process with FDR of < 5% and a p-value of association < 0.01 for 400,000 shot spectra collected on the RapifleX and SimulTOF100 mass spectrometers using the processing and feature definitions presented in this paper. A comparison is made with the number of associated features obtained with the same 400,000 shot spectra collected on the SimulTOF100 mass spectrometer using an alternative processing and feature definition method [6]. The percentages show the proportion of all analyzed features that show an association with the biological process. Note the substantial increase in the number of associated features identified when the new processing feature definition method is used.
| Biological Process | Associated Features | ||
|---|---|---|---|
| RapifleX | SimulTOF | Ref. [6] | |
| Acute phase response | 655 (43.2%) | 460 (40.6%) | 122 (40.9%) |
| Complement activation | 619 (40.8%) | 383 (33.7%) | 70 (23.5%) |
| Acute inflammatory response | 434 (28.6%) | 317 (27.9%) | 109 (36.6%) |
| IFN γ signaling/response | 266 (17.5%) | 147 (12.9%) | 25 (8.4%) |
| Immune tolerance and suppression | 227 (15.0%) | 189 (16.6%) | 31 (10.4%) |
| Wound healing | 202 (13.3%) | 160 (14.1%) | 100 (33.6%) |
| IFN type 1 signaling/response | 195 (12.9%) | 82 (7.2%) | 33 (11.1%) |
| Type 17 immune response | 73 (4.8%) | 82 (7.2%) | 2 (0.7%) |
| Angiogenesis | 54 (3.6%) | 28 (2.5%) | 2 (0.7%) |
| Response to hypoxia | 42 (2.8%) | 54 (4.7%) | 7 (2.3%) |
| Cellular component morphogenesis | 27 (1.8%) | 6 (0.5%) | 4 (1.3%) |
| Cytokine production involved in immune response | 21 (1.4%) | 31 (2.7%) | 3 (1.0%) |
| Glycolysis | 21 (1.4%) | 36 (3.2%) | 2 (0.7%) |
| Chronic inflammatory response | 19 (1.3%) | 23 (2.0%) | 2 (0.7%) |
| Innate immune response | 18 (1.2%) | 30 (2.6%) | 8 (2.7%) |
| Extracellular matrix organization | 16 (1.1%) | 4 (0.4%) | 0 (0.0%) |
| Behavior | 7 (0.5%) | 2 (0.2%) | 8 (2.7%) |
| Epithelial-mesenchymal transition | 6 (0.4%) | 4 (0.4%) | 0 (0.0%) |
| NK cell mediated immunity | 4 (0.3%) | 11 (1.0%) | N/A * |
| T-cell mediated immunity | 4 (0.3%) | 5 (0.4%) | N/A * |
| Type 2 immune response | 2 (0.1%) | 11 (1.0%) | N/A * |
| B-cell mediated immunity | 2 (0.1%) | 6 (0.5%) | N/A * |
| Type 1 immune response | 1 (0.1%) | 1 (0.1%) | N/A * |
* N/A indicates the number of features associated with the biological process was not published in Ref. [6].