NeighborSeq Class Reference

The Neighbor Peptide functionality is designed to find peptides (neighbors) in a given set of sequences (FASTA file) that are similar to a target peptide (aka relevant peptide) based on mass and spectral characteristics. This provides more power when searching complex samples, when only a subset of the peptides/proteins is of interest. More...

#include <OpenMS/ANALYSIS/ID/NeighborSeq.h>

Collaboration diagram for NeighborSeq:

Classes
struct	NeighborStats
	Statistics of how many neighbors were found per reference peptide. More...

Public Member Functions
	NeighborSeq (std::vector< AASequence > &&digested_relevant_peptides)
MSSpectrum	generateSpectrum (const AASequence &peptide_sequence)
	Generates a theoretical spectrum for a given peptide sequence with b/y ions at charge 1. More...
bool	isNeighborPeptide (const AASequence &neighbor_candidate, const double mass_tolerance_pc, const bool mass_tolerance_pc_ppm, const double min_shared_ion_fraction, const double mz_bin_size)
	Is this peptide a neighbor to one of the relevant peptides? More...
NeighborStats	getNeighborStats () const
	after calling isNeighborPeptide() multiple times, this function returns the statistics of how many neighbors were found per reference peptide More...

Static Public Member Functions
static bool	isNeighborSpectrum (const MSSpectrum &spec1, const MSSpectrum &spec2, const double min_shared_ion_fraction, const double mz_bin_size)
	Compares two spectra to determine if they share a sufficient number of ions. More...
static int	computeSharedIonCount (const MSSpectrum &spec1, const MSSpectrum &spec2, const double &mz_bin_size)
	Compute the number of shared ions between two spectra. More...

Protected Member Functions
std::map< double, std::vector< int > >	createMassLookup_ ()
	Creates a map of masses to positions from the internal relevant peptides. More...
auto	findCandidatePositions_ (const double mono_weight, double mass_tolerance, const bool mass_tolerance_pc_ppm)
	Finds candidate positions based on a given mono-isotopic weight and mass tolerance. More...

Private Attributes
const std::vector< AASequence > &	digested_relevant_peptides_
	digested relevant peptides More...
std::map< double, std::vector< int > >	mass_position_map_
	map of masses to positions in digested_relevant_peptides_ More...
TheoreticalSpectrumGenerator	spec_gen_
	for b/y ions with charge 1 More...
const Residue *	x_residue_
	residue for unknown amino acid More...
std::vector< int >	neighbor_stats_
	how many neighbors per reference peptide searched using isNeighborPeptide()? More...

Detailed Description

The Neighbor Peptide functionality is designed to find peptides (neighbors) in a given set of sequences (FASTA file) that are similar to a target peptide (aka relevant peptide) based on mass and spectral characteristics. This provides more power when searching complex samples, when only a subset of the peptides/proteins is of interest.

The paper on subset neighbor search is www.ncbi.nlm.nih.gov/pmc/articles/PMC8489664/ DOI: 10.1021/acs.jproteome.1c00483

Constructor & Destructor Documentation

NeighborSeq()

NeighborSeq

(

std::vector< AASequence > &&

digested_relevant_peptides

)

Constructor

Parameters

digested_relevant_peptides

A vector of digested relevant peptides

Member Function Documentation

computeSharedIonCount()

static int computeSharedIonCount ( const MSSpectrum &  spec1, const MSSpectrum &  spec2, const double &  mz_bin_size  )

static

Compute the number of shared ions between two spectra.

All peaks are considered. Use generateSpectrum() to generate theoretical spectra with b/y ions.

Parameters

spec1	The first theoretical spectrum.
spec2	The second theoretical spectrum.
mz_bin_size	Bin size for the m/z values, which determines if two peaks are considered to be the same.

Returns

The number of shared ions

createMassLookup_()

std::map<double, std::vector<int> > createMassLookup_ ( )

protected

Creates a map of masses to positions from the internal relevant peptides.

Returns

A map where the key is the mass and the value is a vector of positions.

findCandidatePositions_()

auto findCandidatePositions_ ( const double  mono_weight, double  mass_tolerance, const bool  mass_tolerance_pc_ppm  )

protected

Finds candidate positions based on a given mono-isotopic weight and mass tolerance.

Parameters

mono_weight	The mono-isotopic weight to find candidates for.
mass_tolerance	The allowed tolerance for matching the mass.
mass_tolerance_pc_ppm	Whether the mass tolerance is in ppm.

Returns

A pair of begin/end iterators into mass_position_map_ for the candidate positions

generateSpectrum()

MSSpectrum generateSpectrum

(

const AASequence &

peptide_sequence

)

Generates a theoretical spectrum for a given peptide sequence with b/y ions at charge 1.

Includes all b and y ions with charge 1 (even the prefix ions, e.g. b1), but no internal ions.

Parameters

peptide_sequence

The peptide sequence for which to generate the spectrum.

Returns

The generated theoretical spectrum.

getNeighborStats()

NeighborStats getNeighborStats

(

)

const

after calling isNeighborPeptide() multiple times, this function returns the statistics of how many neighbors were found per reference peptide

isNeighborPeptide()

bool isNeighborPeptide	(	const AASequence &	neighbor_candidate,
		const double	mass_tolerance_pc,
		const bool	mass_tolerance_pc_ppm,
		const double	min_shared_ion_fraction,
		const double	mz_bin_size
	)

Is this peptide a neighbor to one of the relevant peptides?

Also updates the internal statistics, which can be retrieved using getNeighborStats().

Parameters

neighbor_candidate	The peptide sequence (from a neighbor protein) to compare against the internal relevant peptides (see constructor).
mass_tolerance_pc	Maximal precursor mass difference (in Da or ppm; see 'mass_tolerance_pc_ppm') between neighbor and relevant peptide.
mass_tolerance_pc_ppm	Is 'mass_tolerance_pc' in Da or ppm?
min_shared_ion_fraction	The ion tolerance for neighbor peptides.
mz_bin_size	Bin size for spectra m/z comparison (the original study suggests 0.05 Th for high-res and 1.0005079 Th for low-res spectra).

Returns

true if neighbor_candidate is neighbor to one or more relevant peptides, false otherwise.

isNeighborSpectrum()

static bool isNeighborSpectrum ( const MSSpectrum &  spec1, const MSSpectrum &  spec2, const double  min_shared_ion_fraction, const double  mz_bin_size  )

static

Compares two spectra to determine if they share a sufficient number of ions.

All peaks are considered. Use generateSpectrum() to generate theoretical spectra with b/y ions.

Parameters

spec1	The first theoretical spectrum.
spec2	The second theoretical spectrum.
min_shared_ion_fraction	The minimal required proportion of shared ions in [0, 1]
mz_bin_size	Bin size for the m/z values, which determines if two peaks are considered to be the same (typically, 0.05 for high resolution and 1.0005079 for low resolution).

Returns

True if the spectra share a sufficient number of ions, false otherwise.

Member Data Documentation

digested_relevant_peptides_

const std::vector<AASequence>& digested_relevant_peptides_

private

digested relevant peptides

mass_position_map_

std::map<double, std::vector<int> > mass_position_map_

private

map of masses to positions in digested_relevant_peptides_

neighbor_stats_

std::vector<int> neighbor_stats_

private

how many neighbors per reference peptide searched using isNeighborPeptide()?

spec_gen_

TheoreticalSpectrumGenerator spec_gen_

private

for b/y ions with charge 1

x_residue_

const Residue* x_residue_

private

residue for unknown amino acid