Table 1 Design of factor levels of parameters in evaluation of DISMS2. All 81 different combinations of all parameter values, 72 combinations for design 1, and 9 combinations for design 2
From: DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs
Parameter | Description | Design 1 | Design 2 |
|---|---|---|---|
topn | topn highest peaks, ∞ means no selection | 20, 50, ∞ | 20, 50, ∞ |
bin | binning with binsize bin | 0.01, 0.2 | 0.2 |
ret | size of retention time window | 1000, 3000 | 3000 |
prec | accepted precursor mass shift (ppm) | 10 | 10 |
dist | distances between spectra | d angle(ε=0.05),d cos, | d angle(ε=0.05) |
d PH(δ=0.05;k=50) | |||
cdis | cutoff for distance of spectra | 0.1, 0.3 | 0.4, 0.5, 0.6 |