DecoyGenerator Class Reference

Methods to generate isobaric decoy sequences for DDA target-decoy searches. More...

#include <OpenMS/CHEMISTRY/DecoyGenerator.h>

Collaboration diagram for DecoyGenerator:

Public Member Functions
	DecoyGenerator ()
	~DecoyGenerator ()=default
void	setSeed (UInt64 seed)
AASequence	reverseProtein (const AASequence &protein) const
AASequence	reversePeptides (const AASequence &protein, const String &protease) const
std::vector< AASequence >	shuffle (const AASequence &protein, const String &protease, int decoy_factor=1)
	Generate decoy protein sequences using shuffle algorithm. More...
AASequence	shufflePeptides (const AASequence &aas, const String &protease, const int max_attempts=100)

Static Private Member Functions
static double	SequenceIdentity_ (const String &decoy, const String &target)

Private Attributes
Math::RandomShuffler	shuffler_
std::unordered_map< std::string, std::string >	td_cache_

Detailed Description

Methods to generate isobaric decoy sequences for DDA target-decoy searches.

Constructor & Destructor Documentation

DecoyGenerator()

DecoyGenerator

(

)

~DecoyGenerator()

~DecoyGenerator ( )

default

Member Function Documentation

reversePeptides()

AASequence reversePeptides	(	const AASequence &	protein,
		const String &	protease
	)		const

reverseProtein()

AASequence reverseProtein

(

const AASequence &

protein

)

const

SequenceIdentity_()

static double SequenceIdentity_ ( const String &  decoy, const String &  target  )

staticprivate

setSeed()

void setSeed

(

UInt64

seed

)

shuffle()

std::vector<AASequence> shuffle	(	const AASequence &	protein,
		const String &	protease,
		int	decoy_factor = 1
	)

Generate decoy protein sequences using shuffle algorithm.

Digests the protein using the specified protease and shuffles each resulting peptide to minimize sequence identity with the target. For top-down proteomics, use "no cleavage" as the protease to shuffle the entire protein as a single sequence.

Parameters

protein	The protein sequence to generate decoys from
protease	The enzyme name (e.g., "Trypsin", "Trypsin/P", "no cleavage")
decoy_factor	Number of decoy variants to generate per target peptide (default: 1)

Returns

Vector of shuffled decoy sequences (one entry per decoy variant)

Note

• Peptides <= 2 amino acids are kept unchanged
• Each peptide uses a fresh DecoyGenerator with fixed seed to ensure identical peptides produce identical decoys across different proteins
• Modifications are discarded
• Returns decoy_factor number of complete protein sequences

shufflePeptides()

AASequence shufflePeptides	(	const AASequence &	aas,
		const String &	protease,
		const int	max_attempts = 100
	)

Member Data Documentation

shuffler_

Math::RandomShuffler shuffler_

private

td_cache_

std::unordered_map<std::string, std::string> td_cache_

private