Table 1 Attributes used in machine learning algorithms.
From: Improved machine learning method for analysis of gas phase chemistry of peptides
Set A: 27 Attributes derived from sequence | |
|---|---|
AacidN1, AacidN2, AacidN3, AacidN4, AacidN5 | First 5 amino acids on N-terminus. |
AacidC1, AacidC2 | Last 2 amino acids on C-terminus. |
HydnN1, HydnN2,..., HydnC2 | Hydrophobicity for each of the above seven amino acids. |
BasicityN1, BasicityN2,..., BasicityC2 | Basicity for each of the above seven amino acids. |
Ave_basicity | Average peptide basicity. |
NumRs | Number of arginine residues in peptide. |
mobileH | Number of basic residues subtracted from peptide charge (indicates existence of mobile proton). |
NumHKR_RN2 | Number of basic residues to the left of N2 bond. |
NumHKR_LN2 | Number of basic residues to the right of N2 bond. |
OMW | Observed Molecular Weight. |
Set B: 5 Attributes derived from MAE feature recognition function | |
OYMinusB | The balance between y and b ions. |
NumIon | Total number of ions. |
P_intensity | Intensity of the parent ion. |
Osum | (sum of intensity of observed major ions)/(sum of intensity of all ions in the MS/MS output). |
Tsum | (sum of intensity of theoretical major ions)/(sum of intensity of all ions) |
Set C: 6 Attributes based on scores generated by database search/sequence validation programs and from our sequence validation methods | |
Mowse | Mascot's score |
Xcorr | Sequest's score |
SumScore | Summary score; A combination of Sequest's XCorr and Mascot's Mowse score. |
PIC | Proportion of the total ion current score for each MS/MS spectrum which accounts for fragment ion assignments. |
SIM | Evaluates chemical plausibility based on relative fragment ion intensities when comparing observed MS/MS spectrum to theoretical spectrum. |
InterScore | The percentage of observed fragments accounted for by multiple fragmentation events. |