Features for target / decoy separation

Oktoberfest creates tab files for target / decoy separation and fdr estimation using Percolator and mokapot. This provides an overview of the features that are used for rescoring with and without peptide property prediction.

Always present

Feature	Description
SpecId	internal spectrum ID
ScanNr	scan number hash
Peptide	peptide sequence
missedCleavages	number of missed cleavages
sequence_length	peptide sequence length
Mass	experimental mass
ExpMass	fixed constant to allow PSMs with different theoretical mass to compete for the same PSM in target-decoy competition
Label	1 indicates target, -1 decoy
Protein	protein description
deltaM_ppm	delta mass in ppm
absDeltaM_ppm	absolute delta mass in ppm
deltaM_da	delta mass in Da
absDeltaM_da	absolute delta mass in Da
Charge2	boolean for charge state 2
Charge3	boolean for charge state 3
KR	number of K or R amino acids in sequence

Features related to Prosit

Feature	Description
spectral_angle	Normalized spectral contrast angle (SA) on all potential y- and b-ions
pred_seen_nonzero	number of observed non-zero ions with non-zero predicted intensity
not_pred_seen	number of observed non-zero ions not predicted
not_pred_seen_b	number of observed non-zero b-ions not predicted
not_pred_seen_y	number of observed non-zero y-ions not predicted
pred_nonZero_fragments	number of ions with non-zero predicted intensity
pred_nonZero_b	number of b-ions with non-zero predicted intensity
pred_nonZero_y	number of y-ions with non-zero predicted intensity
pred_not_seen	number of ions with non-zero predicted intensity not observed
pred_not_seen_b	number of b-ions with non-zero predicted intensity not observed
pred_not_seen_y	number of y-ions with non-zero predicted intensity not observed
pred_seen_nonzero_b	number of observed b-ions with non-zero predicted intensity
pred_seen_nonzero_y	number of observed y-ions with non-zero predicted intensity
pred_seen_zero	number of predicted and observed zero-intensity ions
pred_seen_zero_b	number of predicted and observed zero-intensity b-ions
pred_seen_zero_y	number of predicted and observed zero-intensity y-ions
raw_nonZero_fragments	number of observed ions
raw_nonZero_b	number of observed b-ions
raw_nonZero_y	number of observed y-ions
rel_not_pred_seen	(number of observed ions not predicted) / (number of theoretically observable fragments [length*charge^2])
rel_not_pred_seen_b	(number of observed b-ions not predicted) / (number of theoretically observable fragments [length*charge])
rel_not_pred_seen_y	(number of observed y-ions not predicted) / (number of theoretically observable fragments [length*charge])
rel_pred_nonZero_b	(number of observed b-ions not predicted) / (number of theoretically observable fragments [length*charge])
rel_pred_nonZero_y	(number of observed y-ions not predicted) / (number of theoretically observable fragments [length*charge^2])
rel_pred_not_seen	(number of ions predicted, but not observed) / (number of theoretically observable fragments [length*charge^2])
rel_pred_not_seen_b	(number of b-ions ions predicted, but not observed) / (number of theoretically observable fragments [length*charge])
rel_pred_not_seen_y	(number of y-ions ions predicted, but not observed) / (number of theoretically observable fragments [length*charge])
rel_pred_seen_nonzero	(number of observed ions predicted ) / (number of theoretically observable fragments [length*charge^2])
rel_pred_seen_nonzero_b	(number of observed b-ions predicted) / (number of theoretically observable fragments [length*charge])
rel_pred_seen_nonzero_y	(number of observed y-ions predicted) / (number of theoretically observable fragments [length*charge])
rel_pred_seen_zero	(number of predicted and observed zero-intensity ions) / (number of theoretically observable fragments [length*charge^2])
rel_pred_seen_zero_b	(number of predicted and observed zero-intensity b-ions) / (number of theoretically observable fragments [length*charge])
rel_pred_seen_zero_y	(number of predicted and observed zero-intensity y-ions) / (number of theoretically observable fragments [length*charge])
rel_raw_nonZero_fragments	(number of observed ions) / (number of theoretically observable fragments [length*charge^2])
rel_raw_nonZero_b	(number of observed b-ions) / (number of theoretically observable fragments [length*charge])
rel_raw_nonZero_y	(number of observed y-ions) / (number of theoretically observable fragments [length*charge])
relpred_not_pred_seen2pred_nonZero_fragments	(number of observed non-zero ions not predicted) / (number of ions with non-zero predicted intensity)
relpred_not_pred_seen_b2pred_nonZero_b	(number of observed non-zero b-ions not predicted) / (number of b-ions with non-zero predicted intensity)
relpred_not_pred_seen_y2pred_nonZero_y	(number of observed non-zero y-ions not predicted) / (number of y-ions with non-zero predicted intensity)
relpred_pred_nonZero_b2pred_nonZero_b	(number of b-ions with non-zero predicted intensity) / (number of b-ions with non-zero predicted intensity)
relpred_pred_nonZero_y2pred_nonZero_y	(number of y-ions with non-zero predicted intensity) / (number of y-ions with non-zero predicted intensity)
relpred_pred_not_seen_b2pred_nonZero_b	(number of b-ions with non-zero predicted intensity not observed) / (number of b-ions with non-zero predicted intensity)
relpred_pred_not_seen_y2pred_nonZero_y	(number of y-ions with non-zero predicted intensity not observed) / (number of y-ions with non-zero predicted intensity)
relpred_pred_not_seen2pred_nonZero_fragments	(number of ions with non-zero predicted intensity not observed) / (number of ions with non-zero predicted intensity)
relpred_pred_seen_nonzero_b2pred_nonZero_b	(number of observed b-ions with non-zero predicted intensity) / (number of b-ions with non-zero predicted intensity)
relpred_pred_seen_nonzero_y2pred_nonZero_y	(number of observed y-ions with non-zero predicted intensity) / (number of y-ions with non-zero predicted intensity)
relpred_pred_seen_nonzero2pred_nonZero_fragments	(number of observed non-zero ions with non-zero predicted intensity) / (number of ions with non-zero predicted intensity)
relpred_pred_seen_zero_b2pred_nonZero_b	(number of predicted and observed zero-intensity b-ions) / (number of b-ions with non-zero predicted intensity)
relpred_pred_seen_zero_y2pred_nonZero_y	(number of predicted and observed zero-intensity y-ions) / (number of y-ions with non-zero predicted intensity)
relpred_pred_seen_zero2pred_nonZero_fragments	(number of predicted and observed zero-intensity ions) / (number of ions with non-zero predicted intensity)
abs_rt_diff	absolute difference between retention time and aligned predicted retention time

Features adopted from MS2PIP/MS2Rescore

Feature	Description
pearson_corr	Pearson correlation on all potential y- and b-ions
spearman_corr	Spearman correlation on all potential y- and b-ions
mse	Mean square error
cos	Cosine similarity
std_abs_diff	Standard deviation of the absolute differences
abs_diff_Q3	Quantile 3 of the absolute differences
abs_diff_Q2	Quantile 2 of the absolute differences
abs_diff_Q1	Quantile 1 of the absolute differences
min_abs_diff	Minimum absolute difference
max_abs_diff	Maximum absolute difference
spectral_angle_single_charge	Normalized spectral contrast angle (SA) on singly charged ions
spectral_angle_double_charge	Normalized spectral contrast angle (SA) on doubly charged ions
spectral_angle_triple_charge	Normalized spectral contrast angle (SA) on triply charged ions
spectral_angle_b_ions	Normalized spectral contrast angle (SA) on b-ions
spectral_angle_y_ions	Normalized spectral contrast angle (SA) on y-ions
pearson_corr_single_charge	Pearson correlation on singly charged ions
pearson_corr_double_charge	Pearson correlation on doubly charged ions
pearson_corr_triple_charge	Pearson correlation on triply charged ions
pearson_corr_b_ions	Pearson correlation on b-ions
pearson_corr_y_ions	Pearson correlation on y-ions
spearman_corr_single_charge	Spearman correlation on singly charged ions
spearman_corr_double_charge	Spearman correlation on doubly charged ions
spearman_corr_triple_charge	Spearman correlation on triply charged ions
spearman_corr_b_ions	Spearman correlation on b-ions
spearman_corr_y_ions	Spearman correlation on y-ions