Data
Variablea Levelb 1 2 3 4 5 6 7 8 9 10
Ion Type b 50.4 50.3 49.9 50.2 50.3 50.2 50.3 50.6 50.3 50.4
Mass loss None 55.0 54.8 55.0 54.9 54.8 54.4 54.6 54.0 54.5 55.0
Proton Mobile 53.5 53.1 54.2 52.7 55.7 51.3 53.2 53.0 55.3 53.5
Protein N 777 776 776 776 776 776 776 776 776 777
Peptide N 6087 5840 5248 5783 6380 6852 5881 7431 6056 6087
Fragment N 634K 609K 514K 592K 656K 723K 601K 782K 621K 634K
Charge 2 1 45.0 45.0 46.5 44.6 45.4 44.2 45.5 45.3 45.1 45.0
Basic 2 1 28.4 28.2 29.0 28.8 27.7 28.3 28.2 29.4 28.8 28.4
Proline 0 0 41.2 43.2 45.3 42.4 42.2 45.1 42.0 46.1 43.8 41.2
Arginine 0 0 48.2 46.5 47.8 50.0 49.0 49.1 48.8 48.2 46.8 48.2
Lysine 1 1 38.1 37.5 38.7 40.2 39.4 41.4 39.6 39.9 37.7 38.1
Histidine 0 0 62.0 63.2 62.9 64.2 67.3 63.9 64.2 64.4 66.5 62.0
aFragment ion Type: b-series; Neutral Mass Loss: none; Protein, Peptide and Fragment Ion N: number of proteins, peptide ions and fragment ions, respectively; Charge 2 1: charge state in the peptide ion of +2 and resulting in fragment ion of +1; Basic 2 1: two or more basic residues (H, R, and K) in the peptide ion and one basic residue in the fragment ion proline 0 0: no proline in the peptide ion and no proline in the fragment ion; arginine 0 0: no arginine in the peptide ion and no arginine in the fragment ion; Lysine 1 1: one lysine in the peptide ion and one lysine in the fragment ion; histidine 0 0: no histidine in the peptide ion and no histidine in the fragment ion.
bLevels of the factor. First and second positions in the level denote the level of the indicator in the peptide ion and in the fragment ion, respectively.
Table 1: Percentage of fragment ions for the most representative level of selected factors that influence fragment ion abundance across the ten data sets analyzed (complete description is in Supplementary Tables 1 and 2).