ScoringChart

This chart provides some basic information on scores. Please refer to the Scoring page for more information on scores.

OSW Flag	Score	MS Level	Description	Range	Best Score
use_shape_score	VAR_XCORR_SHAPE	1	Mean of all entries in cross correlation matrix (matrix contains correlations between all pairwise transitions)	(0, 1)	1
	VAR_XCORR_SHAPE_WEIGHTED	2	Intensity weighted mean of all intensities in cross correlation matrix (matrix contains correlations between all pairwise transitions)
use_coelution_score	VAR_XCORR_COELUTION	1	Mean of all delays in cross correlation delay matrix (matrix contains delays between all pairwise transitions)	(0, NUM_RT_POINTS)	0
use_ms1_correlation	VAR_XCORR_SHAPE	1	Mean of all entries in cross correlation matrix (matrix contains contains correlations between all pairwise MS1 isotopes)	(0,1)	1
	VAR_XCORR_COELUTION	1	Mean of all delays in cross correlation delay matrix (matrix contains delays between all pairwise MS1 isotopes)	(0, NUM_RT_POINTS)	0
	VAR_XCORR_SHAPE_CONTRAST	1	Mean of all entries in cross correlation matrix (matrix contains correlations with MS1 isotopes as rows and MS2 transitions as columns)	(0,1)	1
	VAR_XCORR_COELUTION_CONTRAST	1	Mean of all delays in cross correlation delay matrix (matrix contains delays with MS1 isotopes as rows and MS2 transitions as columns)	(0, NUM_RT_POINTS)	0
	VAR_XCORR_SHAPE_COMBINED	1	Mean of all entries in cross correlation matrix (matrix contains correlation between all pairwise feature transitions (MS1 + MS2 level)	(0,1)	1
	VAR_XCORR_COELUTION_COMBINED	1	Mean of all delays in cross correlation matrix (matrix contains correlation between all pairwise feature transitions (MS1 + MS2 level)	(0, NUM_RT_POINTS)	0
use_rt_score	RT_SCORE	2	Absolute difference between the normalized experimental retention time and the library retention time		0
	VAR_NORM_RT_SCORE	2	Divide RT score by rt_normalization_factor	(0,1)	0
use_library_score	VAR_LIBRARY_MANHATTAN	2	Manhattan distance between the library transition intensity vector and the experimental transition intensity vector	(0, inf)	0
	VAR_LIBRARY_DOTPROD	2	Dot product between the library transition intensity vector and the experimental transition intensity vector	(0, 1)	1
	VAR_LIBRARY_SANGLE	2	Acosine of the normalized dot product between the library transition intensity vector and the experimental transition intensity vector	(0,pi/2 (~1.57)	0
	VAR_LIBRARY_RMSD	2	Normalized manhattan distance between the library transition intensity vector and the experimental transition intensity vector	(0,1)	0
use_total_xic_score	TOTAL_XIC	2	Total intensity based on feature finding
use_intensity_score	VAR_INTENSITY_SCORE	2	Intensity of feature / total_XIC	(0,1)	1?
use_nr_peaks_score	NR_PEAKS	2	Number of transitions in peak group
use_sn_score	VAR_LOG_SN_SCORE	2	log(S/N) score	(0, inf)	inf
use_mi_score	VAR_MI_SCORE	2	Mean of all entries in mutual information (MI) matrix (matrix contains pairwise MI scores between all pairwise transitions)
	VAR_MI_WEIGHTED_SCORE	2	Intensity weighted mean of all entries in mutual information (MI) matrix (matrix contains pairwise MI scores between all pairwise transitions)
use_total_mi_score	TOTAL_MI	2	TODO
	VAR_MI_RATIO_SCORE	2	VAR_MI_SCORE / TOTAL_MI
use_ms1_mi	VAR_MI_SCORE	1	Mean of all entries in mutual information (MI) matrix (matrix contains pairwise MI scores between all MS1 isotopes)
	VAR_MI_CONTRAST_SCORE	1	Mean of all entries in mutual information (MI) matrix (matrix contains MI scores with MS1 isotopes as rows and MS2 transitions as columns)
	VAR_MI_COMBINED_SCORE	1	Mean of all delays in mutual information (MI) matrix (matrix contains correlation between all pairwise feature transitions (MS1 + MS2 level)
use_ion_mobility_scores	VAR_IM_DELTA_SCORE	2	Absolute difference between experimental and library ion mobility	(0, RANGE_IM)	0
	VAR_IM_XCORR_SHAPE	2	Mean of all entries in cross correlation matrix (matrix contains correlations between all pairwise transitions)	(0, 1)	1
	VAR_IM_XCORR_COELUTION	2	Mean of all delays in cross correlation delay matrix (matrix contains delays between all pairwise transitions)	(0, RANGE_IM)	0
use_ion_mobility_scores enable_ms1	VAR_IM_MS1_DELTA_SCORE	1	MS1 level difference between library and experimental ion mobility	(0, RANGE_IM)	0
	VAR_IM_XCORR_SHAPE_CONTRAST	1	Mean of all entries in cross correlation matrix (matrix contains correlations with MS1 isotopes as rows and MS2 transitions as columns)	(0,1)	1
	VAR_IM_XCORR_COELUTION_CONTRAST	1	Mean of all delays in cross correlation delay matrix (matrix contains delays with MS1 isotopes as rows and MS2 transitions as columns)	(0, RANGE_IM)	0
use_ms1_fullscan	VAR_MS1_PPM_DIFF	1	Difference in PPM between library and experimental m/z	(0, inf)	0
	VAR_MS1_ISOTOPE_CORRELATION	1	Pearson correlation of each transition level feature's isotopic envelope and its theoretical isotopic envelope (compare intensities)?? (MS1 Level)	(0,1)	1
	VAR_MS1_ISOTOPE_OVERLAP	1	Number of isotopes found to the left of the transition (suggesting transition is not the monoisotopic peak) ??	(0, 1)??	1
use_dia_scores	VAR_MASSDEV_SCORE	2	Absolute difference in ppm between experimental and expected signal	(0, MAX(MS1_EXTRACTION))
	VAR_MASSDEV_SCORE_WEIGHTED	2	TODO
use_dia_scores use_ionseries_scores	VAR_BSERIES_SCORE	2	Number of B ions matched	(0, NUM_LIB_B_IONS)	NUM_LIB_B_IONS
	VAR_YSERIES_SCORE	2	Number of Y ions matched	(0, NUM_LIB_Y_IONS)	(0, NUM_LIB_Y_IONS)
use_dia_scores use_ms2_isotope_scores	VAR_MANHATTAN_SCORE	2	Manhattan distance between experimental and theoretical normalized intensity arrays of all isotopes of each MS2 transition in a single spectrum	(0, inf)?	0?
	VAR_DOTPROD_SCORE	2	Dot product between experimental and theoretical normalized intensity arrays of all isotopes of each MS2 transition in a single spectrum	(0, 1)?	1?
	VAR_ISOTOPE_CORRELATION_SCORE	2	Pearson correlation of each transition level feature's isotopic envelope and its theoretical isotopic envelope (compare intensities)	(0, 1)	1
	VAR_ISOTOPE_OVERLAP_SCORE	2	Number of isotopes found to the left of the transition (suggesting transition is not the monoisotopic peak)	(0, 1)??	0
use_sonar_scores	VAR_SONAR_LAG	2	TODO
	VAR_SONAR_SHAPE	2	TODO
	VAR_SONAR_LOG_SN	2	TODO
	VAR_SONAR_LOG_DIFF	2	TODO
	VAR_SONAR_LOG_TREND	2	TODO
	VAR_SONAR_RSQ	2	TODO
use_uis_scores