EnzymaticDigestion Class Reference [Chemistry]

Class for the enzymatic digestion of proteins. More...

#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>

List of all members.

Classes
struct	BindingSite
struct	CleavageModel
Public Types
enum	Enzyme { TRYPSIN, SIZE_OF_ENZYMES }
	Possible enzymes for the digestion (adapt NamesOfEnzymes & getEnzymeByName() & nextCleavageSite_() if you add more enzymes here). More...
Public Member Functions
	EnzymaticDigestion ()
	Default constructor.
SignedSize	getMissedCleavages () const
	Returns the number of missed cleavages for the digestion.
void	setMissedCleavages (SignedSize missed_cleavages)
	Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when log model is used.
Enzyme	getEnzyme () const
	Returns the enzyme for the digestion.
void	setEnzyme (Enzyme enzyme)
	Sets the enzyme for the digestion (default is TRYPSIN).
Enzyme	getEnzymeByName (const String &name)
void	digest (const AASequence &protein, std::vector< AASequence > &output)
	Performs the enzymatic digestion of a protein.
Size	peptideCount (const AASequence &protein)
	Returns the number of peptides a digestion of protein would yield.
bool	isLogModelEnabled () const
	use trained model when digesting?
void	setLogModelEnabled (bool enabled)
	enables/disabled the trained model
DoubleReal	getLogThreshold () const
	Returns the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data).
void	setLogThreshold (DoubleReal threshold)
Static Public Attributes
static const std::string	NamesOfEnzymes [SIZE_OF_ENZYMES]
	Names of the Enzymes.
Protected Member Functions
void	nextCleavageSite_ (const AASequence &sequence, AASequence::ConstIterator &iterator)
	moves the iterator it after the next cleavage site of the sequence
Protected Attributes
SignedSize	missed_cleavages_
	Number of missed cleavages.
Enzyme	enzyme_
	Used enzyme.
bool	use_log_model_
	use the log model or naive digestion (with missed cleavages)
DoubleReal	log_model_threshold_
	Threshold to decide if position is cleaved or missed (only for the model).
Map< BindingSite, CleavageModel >	model_data_
	Holds the cleavage model.

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Detailed Description

Class for the enzymatic digestion of proteins.

Digestion can be performed using simple regular expressions, e.g. [KR] | [^P] for trypsin. Also missed cleavages can be modelled, i.e. adjacent peptides are not cleaved due to enzyme malfunction/access restrictions. If n missed cleavages are given, all possible resulting peptides (cleaved and uncleaved) with up to n missed cleavages are returned. Thus no random selection of just n specific missed cleavage sites is performed.

An alternative model is also available, where the protein is cleaved only at positions where a cleavage model trained on real data, exceeds a certain threshold. The model is published in Siepen et al. (2007), "Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.", doi: 10.1021/pr060507u The model is only available for trypsin and ignores the missed cleavage setting. You should however use setLogThreshold() to adjust FP vs FN rates. A higher threshold increases the number of cleavages predicted.

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Member Enumeration Documentation

enum Enzyme

Possible enzymes for the digestion (adapt NamesOfEnzymes & getEnzymeByName() & nextCleavageSite_() if you add more enzymes here).

Enumerator:

TRYPSIN
SIZE_OF_ENZYMES

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Constructor & Destructor Documentation

EnzymaticDigestion

(

)

Default constructor.

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Member Function Documentation

void digest	(	const AASequence &	protein,
		std::vector< AASequence > &	output
	)

Performs the enzymatic digestion of a protein.

Enzyme getEnzyme

(

)

const

Returns the enzyme for the digestion.

Enzyme getEnzymeByName

(

const String &

name

)

convert enzyme string name to enum returns SIZE_OF_ENZYMES if name is not valid

DoubleReal getLogThreshold

(

)

const

Returns the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data).

SignedSize getMissedCleavages

(

)

const

Returns the number of missed cleavages for the digestion.

bool isLogModelEnabled

(

)

const

use trained model when digesting?

void nextCleavageSite_	(	const AASequence &	sequence,
		AASequence::ConstIterator &	iterator
	)			[protected]

moves the iterator it after the next cleavage site of the sequence

Size peptideCount

(

const AASequence &

protein

)

Returns the number of peptides a digestion of protein would yield.

void setEnzyme

(

Enzyme

enzyme

)

Sets the enzyme for the digestion (default is TRYPSIN).

void setLogModelEnabled

(

bool

enabled

)

enables/disabled the trained model

void setLogThreshold

(

DoubleReal

threshold

)

Sets the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data) Default is 0.25

void setMissedCleavages

(

SignedSize

missed_cleavages

)

Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when log model is used.

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Member Data Documentation

Enzyme enzyme_ [protected]

Used enzyme.

DoubleReal log_model_threshold_ [protected]

Threshold to decide if position is cleaved or missed (only for the model).

SignedSize missed_cleavages_ [protected]

Number of missed cleavages.

Map<BindingSite, CleavageModel> model_data_ [protected]

Holds the cleavage model.

const std::string NamesOfEnzymes[SIZE_OF_ENZYMES] [static]

Names of the Enzymes.

bool use_log_model_ [protected]

use the log model or naive digestion (with missed cleavages)