NuXLAnnotatedHit Class Reference

#include <OpenMS/ANALYSIS/NUXL/NuXLAnnotatedHit.h>

Collaboration diagram for NuXLAnnotatedHit:

Static Public Member Functions
static bool	hasBetterScore (const NuXLAnnotatedHit &a, const NuXLAnnotatedHit &b)

Public Attributes
StringView	sequence
SignedSize	peptide_mod_index = 0
Size	NA_mod_index = 0
Size	NA_adduct_amb_index = 0
int	isotope_error = 0
char	cross_linked_nucleotide = UNKNOWN_NUCLEOTIDE
float	score = 0
float	mass_error_p = 0
float	total_loss_score = 0
float	immonium_score = 0
float	precursor_score = 0
float	MIC = 0
float	err = 0
float	Morph = 0
float	modds = 0
float	partial_loss_score = 0
float	pl_MIC = 0
float	pl_err = 0.0
float	pl_Morph = 0
float	pl_modds = 0
float	pl_pc_MIC = 0
float	pl_im_MIC = 0
float	total_MIC = 0
float	marker_ions_score = 0
float	ladder_score = 0
float	sequence_score = 0
float	best_localization_score = 0
String	localization_scores = 0
String	best_localization
int	best_localization_position = -1
std::vector< PeptideHit::PeakAnnotation >	fragment_annotations
size_t	tag_unshifted = 0
size_t	tag_shifted = 0
size_t	tag_XLed = 0
double	explained_peak_fraction = 0
double	matched_theo_fraction = 0
double	wTop50 = 0
size_t	n_theoretical_peaks = 0

Static Public Attributes
static constexpr const char	UNKNOWN_NUCLEOTIDE = '?'

Detailed Description

Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space floats need to be initialized to zero as default

Member Function Documentation

hasBetterScore()

static bool hasBetterScore ( const NuXLAnnotatedHit &  a, const NuXLAnnotatedHit &  b  )

inlinestatic

References NuXLAnnotatedHit::score.

Member Data Documentation

best_localization

String best_localization

best_localization_position

int best_localization_position = -1

best_localization_score

float best_localization_score = 0

cross_linked_nucleotide

char cross_linked_nucleotide = UNKNOWN_NUCLEOTIDE

err

float err = 0

explained_peak_fraction

double explained_peak_fraction = 0

fragment_annotations

std::vector<PeptideHit::PeakAnnotation> fragment_annotations

immonium_score

float immonium_score = 0

The matched ion current in immonium (immonium_score) and precursor ions (precursor_score) without any nucleotide shift.

see DOI: 10.1021/pr3007045 A Systematic Investigation into the Nature of Tryptic HCD Spectra imY = EmpiricalFormula("C8H10NO").getMonoWeight(); // 85% imW = EmpiricalFormula("C10H11N2").getMonoWeight(); // 84% imF = EmpiricalFormula("C8H10N").getMonoWeight(); // 84% imL = EmpiricalFormula("C5H12N").getMonoWeight(); // I/L 76% imH = EmpiricalFormula("C5H8N3").getMonoWeight(); // 70% imC = EmpiricalFormula("C2H6NS").getMonoWeight(); // CaC 61% imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); // 2% imP = EmpiricalFormula("C4H8N").getMonoWeight(); //? imQ = 101.0715; // 52% imE = 102.0555; // 37% imM = 104.0534; // 3%

isotope_error

int isotope_error = 0

ladder_score

float ladder_score = 0

Coverage of peptide by prefix or suffix ions (fraction) For example: PEPTIDER 01000100 (two of eight ions observed -> 2/8)
Shifted and non-shifted are combined to determine coverage.

localization_scores

String localization_scores = 0

marker_ions_score

float marker_ions_score = 0

The matched ion current in marker ions (marker_ions_score) is not considered in scoring.

mass_error_p

float mass_error_p = 0

Normalized precursor mass error score. Mass error is assumed normally distributed with:

• mean = 0
• sd = sqrt(precursor_mass_tolerance) => variance = precursor tolerance

matched_theo_fraction

double matched_theo_fraction = 0

MIC

float MIC = 0

The matched ion current (MIC), average fragment error (err), and morpheus score (Morph) are calculated for b-,y-,a-ions without nucleotide shift. Morph is just the number of matched peaks + the fraction of MIC

modds

float modds = 0

The match odds (-log10) of observing this number of b-,a-, and y-ions assuming a uniform distribution of noise peaks.

Morph

float Morph = 0

n_theoretical_peaks

size_t n_theoretical_peaks = 0

NA_adduct_amb_index

Size NA_adduct_amb_index = 0

NA_mod_index

Size NA_mod_index = 0

partial_loss_score

float partial_loss_score = 0

The partial loss score is the X!Tandem HyperScore calculated from b-,a-, and y-ions with nucleotide shifts. Matches from b- and a-ions are combined, i.e. a matching a_n-ion is counted as b_n-ion. For a precursor with charge N, all fragment ion charges up to N-1 are considered.

Calculation of HyperScore: yFact = logfactorial_(y_ion_count); bFact = logfactorial_(b_ion_count); hyperScore = log1p(dot_product) + yFact + bFact;

peptide_mod_index

SignedSize peptide_mod_index = 0

pl_err

float pl_err = 0.0

pl_im_MIC

float pl_im_MIC = 0

The matched ion current calculated from immonium ions with nucleotide shifts. Only singly charged immonium ions are considered.

imY = EmpiricalFormula("C8H10NO").getMonoWeight(); imW = EmpiricalFormula("C10H11N2").getMonoWeight(); imF = EmpiricalFormula("C8H10N").getMonoWeight(); imH = EmpiricalFormula("C5H8N3").getMonoWeight(); imC = EmpiricalFormula("C2H6NS").getMonoWeight(); imP = EmpiricalFormula("C4H8N").getMonoWeight(); imL = EmpiricalFormula("C5H12N").getMonoWeight(); imK1 = EmpiricalFormula("C5H13N2").getMonoWeight(); imK2 = EmpiricalFormula("C5H10N1").getMonoWeight(); imK3 = EmpiricalFormula("C6H13N2O").getMonoWeight(); imQ = 101.0715; imE = 102.0555; imM = 104.0534;

pl_MIC

float pl_MIC = 0

The matched ion current (pl_MIC) of ladder ions, average fragment error (pl_err), and morpheus score (pl_Morph) are calculated from b-,y-,a-ions with nucleotide shift. Morph: number of matched peaks + the fraction of MIC

pl_modds

float pl_modds = 0

pl_Morph

float pl_Morph = 0

pl_pc_MIC

float pl_pc_MIC = 0

precursor_score

float precursor_score = 0

score

float score = 0

The main score (score) is a linear combination of (weighted) subscores

For the fast score (ignoring all shifted peaks) we calculate: score = 1.0 * total_loss_score

• 1.0 * total_MIC
• 0.333 * mass_error_p;

For the all-ion score we calculate: peptides: score = -6.486416409280039

• 4.059968526608637 * ah.total_MIC
  
• 0.5842539236790404 * ah.modds
• 0.21721652155697285 * ah.total_loss_score
• 1.9988345415208777 * ah.mass_error_p; XLs: score = -6.648631037190969
• 0.4688059636415974 * ah.Morph
• 4.0386886051238 * ah.MIC
  
• 0.5446999629799386 * ah.modds
• 0.25318342707227187 * ah.total_loss_score
• 0.12472562244230834 * ah.partial_loss_score
• 1.2107674392113372 * ah.mass_error_p
• 2.3319284783288805 * ah.pl_MIC;

Referenced by NuXLAnnotatedHit::hasBetterScore().

sequence

StringView sequence

sequence_score

float sequence_score = 0

Longest sequence covered in peptide by prefix or suffix ions (fraction). Coverage of peptide by prefix or suffix ions (fraction) For example: PEPTIDER 01110001 (three ions form the longest sequence -> 3/8) Shifted and non-shifted are combined to determine coverage.

tag_shifted

size_t tag_shifted = 0

tag_unshifted

size_t tag_unshifted = 0

tag_XLed

size_t tag_XLed = 0

total_loss_score

float total_loss_score = 0

The total loss score is the X!Tandem HyperScore calculated from b-,y-ions without any nucleotide shift.

total_MIC

float total_MIC = 0

The complete TIC fraction of explained peaks (total_MIC) (excludes marker ions) For peptides: total_MIC = MIC + im_MIC + pc_MIC (b-,a-,y-ions, immonium ions, precursor ions) For XLs: total_MIC = MIC + im_MIC + pc_MIC + pl_MIC + pl_pc_MIC + pl_im_MIC + marker_ions_sub_score

UNKNOWN_NUCLEOTIDE

constexpr const char UNKNOWN_NUCLEOTIDE = '?'

staticconstexpr

wTop50

double wTop50 = 0