Table 1 Features used to represent PSMs in TIDD model
From: TIDD: tool-independent and data-dependent machine learning for peptide identification
Index | Name | Description |
|---|---|---|
1 | XCorr | cross correlation between theoretical and experimental spectra |
2 | delta XCorr | difference of XCorr score between rank 1 and 2 (If there’s rank 2 hit) |
3 | charge | vector: 1 to 6 (consider as 6 when the charge is above 6) |
4 | pepLen | the length of stripped peptide sequence |
5 | tryptic | vector: 0 c-term tryptic; 1 n-term tryptic; 2 fully-tryptic |
6 | #missed cleavage | the number of missed cleavages in the peptide sequence |
7 | precursorM | observed mass of spectra |
8 | massDiff | the mass difference between calculated and observed mass |
9 | -absolutMassDiff | the absolute value of the difference between calculated and observed mass |
10 | calPepM | calculated mass of the matched peptide |
11–13 | sum_intensity_all/y/b | logarithm value of sum of intensity of spectra (TIC) / sum of intensity of matched y ions (or b ions) |
14–15 | frac_intensity_y/b | the fraction of sum_intensity_y (sum_intensity_b) among sum_intensity_all |
16–18 | max_intensity_all/y/b | logarithm value of maximum intensity of spectra (base peak intensity) / maximum intensity of matched y ions (or b ions) |
19–20 | seq_cover y/b | sequence coverage of y ions (or b ions) |
21–22 | num_consecutive_y/b | the number of consecutive y ions (or b ions) |
23–24 | mean/sd _fragMassErr | mean (or standard deviation) values of mass difference distribution between fragment ions and theoretical ions |
25 | #AnnoPeaks | the number of annotated peaks |