Table 1 Features used in the machine learning formulation
From: An improved machine learning protocol for the identification of correct Sequest search results
Group | Name | Meaning | Origin |
|---|---|---|---|
SEQUEST | XCorr | Rank score from the SEQUEST search. | SEQUEST |
deltaMH | Difference between mass of parent ion and identified peptide mass. | SEQUEST | |
deltCn | Difference between XCorr of the highest ranked peptide and the peptide in question | SEQUEST | |
SP score | Preliminary score of peptide in search procedure | SEQUEST | |
SP rank | Initial rank of peptide based on SP-score | SEQUEST | |
Ion fraction | Percentage of ions in the mass spectra that could be correlated with the spectrum | SEQUEST | |
Published | Number of tryptic | Number of tryptic cleavage sites in the peptide targets (NTT) | Calculated |
Peptide lenght | Residue count of the peptide | Calculated | |
Summed Intesity | Sum of peak intensities in the spectra | Calculated | |
Mobil proton factor (MPF) | Measure of the proton mobility in peptide | Calculated | |
C-terminal Residue | Amino acid residue at c-terminal (Arg = 1, Lys = 2, Other = 3) | Calculated | |
Mass-window peptides | # of DB peptides within prespecified mass-window of the parent ion | Calculated | |
Proline count | # of Pro residues in the peptide | Calculated | |
Arginine count | # of Arg residues in the peptide | Calculated | |
Novel | Intensity Mean | The mean of the peak intensities | Calculated |
Intensity Std. | Std. of the peak intensities | Calculated | |
Intensity bins | The distribution of intensities in 20%-bins | Calculated | |
Protein Hit Count (PHC) | Probability score of observing × number of peptides from parent protein | Calculated | |
Potential Coverage Ratio | The potential sequence coverage | Calculated | |
PTM percentage | The percentage of possible PTMs found in a peptide | Calculated |