Subset-neighbor peptide search: find peptides from a wider pool (typically a FASTA digest) that are spectral neighbors of a smaller "relevant" peptide set, useful when only part of a complex sample is of interest. More...

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

Collaboration diagram for NeighborSeq:

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

Public Member Functions
	NeighborSeq (std::vector< AASequence > &&digested_relevant_peptides)
	Construct from a vector of "relevant" digested peptides.

MSSpectrum	generateSpectrum (const AASequence &peptide_sequence)
	Generates a theoretical spectrum for a given peptide sequence with b/y ions at charge 1.

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)
	Whether `neighbor_candidate` is a spectral neighbor of any of the relevant peptides.

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

Static Public Member Functions
static bool	isNeighborSpectrum (const MSSpectrum &spec1, const MSSpectrum &spec2, const double min_shared_ion_fraction, const double mz_bin_size)
	Whether two spectra share enough peaks (in `mz_bin_size` m/z bins) to be considered neighbors.

static int	computeSharedIonCount (const MSSpectrum &spec1, const MSSpectrum &spec2, const double &mz_bin_size)
	Compute the number of shared ions between two spectra.

Protected Member Functions
std::map< double, std::vector< int > >	createMassLookup_ ()
	Creates a map of masses to positions from the internal relevant peptides.

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.

Private Attributes
const std::vector< AASequence > &	digested_relevant_peptides_
	digested relevant peptides

std::map< double, std::vector< int > >	mass_position_map_
	map of masses to positions in digested_relevant_peptides_

TheoreticalSpectrumGenerator	spec_gen_
	for b/y ions with charge 1

const Residue *	x_residue_
	residue for unknown amino acid

std::vector< int >	neighbor_stats_
	how many neighbors per reference peptide searched using isNeighborPeptide()?

Detailed Description

Subset-neighbor peptide search: find peptides from a wider pool (typically a FASTA digest) that are spectral neighbors of a smaller "relevant" peptide set, useful when only part of a complex sample is of interest.

Two peptides are considered neighbors when their precursor masses are within tolerance and their theoretical b/y fragment spectra share enough peaks. The class is constructed once with the relevant peptides, then queried with isNeighborPeptide for each candidate. After the queries are done, getNeighborStats summarises how many relevant peptides had zero, one, or multiple neighbors.

Background: Cormen et al., J. Proteome Research 2021, 10.1021/acs.jproteome.1c00483 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8489664/).

Constructor & Destructor Documentation

◆ NeighborSeq()

NeighborSeq ( std::vector< AASequence > && digested_relevant_peptides )

Construct from a vector of "relevant" digested peptides.

Builds an internal mass index (relevant peptides containing the unknown-amino-acid residue 'X' are skipped and a count is logged via OPENMS_LOG_WARN) and configures the internal theoretical-spectrum generator for charge-1 b/y ions including the b1 prefix ion.

Note: The class stores a const-reference to the moved-in vector via its internal member (not a copy). The vector passed to the constructor must therefore outlive every call on this instance.

Parameters

[in] digested_relevant_peptides Digested peptides to use as the "relevant" reference set.

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

[in]	spec1	The first theoretical spectrum.
[in]	spec2	The second theoretical spectrum.
[in]	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

[in]	mono_weight	The mono-isotopic weight to find candidates for.
[in]	mass_tolerance	The allowed tolerance for matching the mass.
[in]	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

[in] 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
	)

Whether neighbor_candidate is a spectral neighbor of any of the relevant peptides.

Looks up the relevant peptides whose precursor mass is within mass_tolerance_pc of neighbor_candidate's mono-isotopic mass, generates b/y spectra for each candidate match plus neighbor_candidate, and compares them with isNeighborSpectrum. Returns true as soon as any relevant peptide qualifies, but continues iterating so that the internal per-relevant-peptide neighbor counters are updated for every match. Call getNeighborStats once all candidates have been queried.

Parameters

[in]	neighbor_candidate	Candidate peptide (typically from a digested FASTA).
[in]	mass_tolerance_pc	Maximum precursor mass difference between `neighbor_candidate` and a relevant peptide, expressed in Da or ppm per `mass_tolerance_pc_ppm`.
[in]	mass_tolerance_pc_ppm	`true` to interpret `mass_tolerance_pc` as ppm (converted internally via `Math::ppmToMass`); `false` to interpret it as Da.
[in]	min_shared_ion_fraction	Threshold passed straight to isNeighborSpectrum.
[in]	mz_bin_size	m/z bin size passed straight to isNeighborSpectrum (typical values: `0.05` Th for high-res, `1.0005079` Th for low-res).

Returns: true when at least one relevant peptide is a neighbor.

◆ isNeighborSpectrum()

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

static

Whether two spectra share enough peaks (in mz_bin_size m/z bins) to be considered neighbors.

Computes the Dice-style fraction 2 * shared_peaks / (spec1.size() + spec2.size()) and returns true when it is strictly greater than min_shared_ion_fraction. All peaks of both spectra are considered.

Parameters

[in]	spec1	First theoretical spectrum.
[in]	spec2	Second theoretical spectrum.
[in]	min_shared_ion_fraction	Minimum required Dice-style shared-peak fraction (in [0, `1`]).
[in]	mz_bin_size	Bin size for m/z comparison (typical values: `0.05` Th for high-resolution data, `1.0005079` Th for low-resolution data).

Returns: true when the shared fraction is strictly greater than min_shared_ion_fraction.

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

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ NeighborSeq()

Member Function Documentation

◆ computeSharedIonCount()

◆ createMassLookup_()

◆ findCandidatePositions_()

◆ generateSpectrum()

◆ getNeighborStats()

◆ isNeighborPeptide()

◆ isNeighborSpectrum()

Member Data Documentation

◆ digested_relevant_peptides_

◆ mass_position_map_

◆ neighbor_stats_

◆ spec_gen_

◆ x_residue_