| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
MRMDecoy Class Reference

This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object. More...

`#include <OpenMS/ANALYSIS/OPENSWATH/MRMDecoy.h>`

Inheritance diagram for MRMDecoy:

## Public Types

typedef std::vector< size_t > | IndexType
typedef std::vector< OpenMS::TargetedExperiment::Protein > | ProteinVectorType
typedef std::vector< OpenMS::TargetedExperiment::Peptide > | PeptideVectorType
typedef std::vector< OpenMS::ReactionMonitoringTransition > | TransitionVectorType
typedef std::map< String, std::vector< const ReactionMonitoringTransition * > > | PeptideTransitionMapType
Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...

## Public Member Functions

| MRMDecoy ()
void | generateDecoys (const OpenMS::TargetedExperiment &exp, OpenMS::TargetedExperiment &dec, const String &method, const double aim_decoy_fraction, const bool switchKR, const String &decoy_tag, const int max_attempts, const double identity_threshold, const double precursor_mz_shift, const double product_mz_shift, const double product_mz_threshold, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, const bool enable_specific_losses, const bool enable_unspecific_losses, const int round_decPow=-4) const
| Generate decoys from a TargetedExperiment. More...
float | AASequenceIdentity (const String &sequence, const String &decoy) const
| Compute relative identity (relative number of matches of amino acids at the same position) between two sequences. More...
OpenMS::TargetedExperiment::Peptide | shufflePeptide (OpenMS::TargetedExperiment::Peptide peptide, const double identity_threshold, int seed=-1, const int max_attempts=100) const
| Shuffle a peptide (with its modifications) sequence. More...
Public Member Functions inherited from DefaultParamHandler
| DefaultParamHandler (const String &name)
| Constructor with name that is displayed in error messages. More...
| DefaultParamHandler (const DefaultParamHandler &rhs)
| Copy constructor. More...
virtual | ~DefaultParamHandler ()
| Destructor. More...
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs)
| Assignment operator. More...
virtual bool | operator== (const DefaultParamHandler &rhs) const
| Equality operator. More...
void | setParameters (const Param &param)
| Sets the parameters. More...
const Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () const
| Non-mutable access to the name. More...
void | setName (const String &name)
| Mutable access to the name. More...
const std::vector< String > & | getSubsections () const
| Non-mutable access to the registered subsections. More...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (const ProgressLogger &other)
| Assignment Operator. More...
void | setLogType (LogType type) const
| Sets the progress log that should be used. The default type is NONE! More...
LogType | getLogType () const
| Returns the type of progress log being used. More...
void | startProgress (SignedSize begin, SignedSize end, const String &label) const
| Initializes the progress display. More...
void | setProgress (SignedSize value) const
| Sets the current progress. More...
void | endProgress () const
| Ends the progress display. More...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Static Public Member Functions

static OpenMS::TargetedExperiment::Peptide | reversePeptide (const OpenMS::TargetedExperiment::Peptide &peptide, const bool keepN, const bool keepC, const String &const_pattern=String())
| Reverse a peptide sequence (with its modifications) More...
static IndexType | findFixedResidues (const std::string &sequence, bool keepN, bool keepC, const OpenMS::String &keep_const_pattern)
| Find all residues in a sequence that should not be reversed / shuffled. More...

## Protected Member Functions

bool | hasCNterminalMods_ (const OpenMS::TargetedExperiment::Peptide &peptide, bool checkCterminalAA) const
| Check if a peptide has C or N terminal modifications. More...
IndexType | findFixedResidues_ (const std::string &sequence) const
| Find all K, R, P sites in a sequence to be set as fixed. More...
IndexType | findFixedAndTermResidues_ (const std::string &sequence) const
| Find all K, R, P and C-/N-terminal sites in a sequence to be set as fixed. More...
OpenMS::TargetedExperiment::Peptide | pseudoreversePeptide_ (const OpenMS::TargetedExperiment::Peptide &peptide) const
| Pseudo-reverse a peptide sequence (with its modifications) More...
OpenMS::TargetedExperiment::Peptide | reversePeptide_ (const OpenMS::TargetedExperiment::Peptide &peptide) const
| Reverse a peptide sequence (with its modifications) More...
void | updateMembers_ () override
| Synchronize members with param class. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

String | keep_const_pattern_
bool | keepN_
bool | keepC_
Protected Attributes inherited from DefaultParamHandler
Param | param_
| Container for current parameters. More...
Param | defaults_
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String > | subsections_
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String | error_name_
| Name that is displayed in error messages during the parameter checking. More...
bool | check_defaults_
| If this member is set to false no checking if parameters in done;. More...
bool | warn_empty_defaults_
| If this member is set to false no warning is emitted when defaults are empty;. More...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_

## Additional Inherited Members

Static Protected Member Functions inherited from ProgressLogger
static String | logTypeToFactoryName_ (LogType type)
| Return the name of the factory product used for this log type. More...
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object.

There are multiple methods to create the decoy transitions, the simplest ones are reverse and pseudo-reverse which reverse the sequence either completely or leaving the last (tryptic) AA untouched respectively.

Another decoy generation method is "shuffle" which uses an algorithm similar to the one described in Lam, Henry, et al. (2010). "Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics". Journal of Proteome Research 9, 605-610. It shuffles the amino acid sequence and shuffles the fragment ion intensities accordingly, however for this to work the fragment ions need to be matched to annotated before.

First, the algorithm goes through all peptides and applies the decoy method to the target peptide sequence (pseudo-reverse, reverse or shuffle) in order to produce the decoy sequence. Then, for each peptide, the fragment ions in the target library are matched to their most likely origin (e.g. the ions are annotated with their ion series (a,b,y) and the fragment number and optionally a neutral loss (10 different neutral losses are currently implemented)). For each fragment ion from the target peptide, an equivalent ion is created for the decoy peptide with the same intensity (e.g. if the target peptide sequence has a b5 ion with a normalized intensity of 200, an equivalent b5 ion for the decoy sequence is created and assigned the intensity 200). Optionally, the m/z values are corrected to reflect the theoretical value rather than the experimental value in the library.

## Member Typedef Documentation

## ◆ IndexType

typedef std::vector<size_t> IndexType

## ◆ PeptideTransitionMapType

typedef std::map<String, std::vector<const ReactionMonitoringTransition*> > PeptideTransitionMapType

## ◆ PeptideVectorType

typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType

## ◆ ProteinVectorType

typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType

## ◆ TransitionVectorType

typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType

## Constructor & Destructor Documentation

## ◆ MRMDecoy()

MRMDecoy | ( |  | ) |

## Member Function Documentation

## ◆ AASequenceIdentity()

float AASequenceIdentity | ( | const String & | sequence,
|  | const String & | decoy
| ) |  | const

Compute relative identity (relative number of matches of amino acids at the same position) between two sequences.

## ◆ findFixedAndTermResidues_()

IndexType findFixedAndTermResidues_ | ( | const std::string & | sequence | ) | const

protected

Find all K, R, P and C-/N-terminal sites in a sequence to be set as fixed.

This method was adapted from the SpectraST decoy generator

## ◆ findFixedResidues()

static IndexType findFixedResidues | ( | const std::string & | sequence,
|  | bool | keepN,
|  | bool | keepC,
|  | const OpenMS::String & | keep_const_pattern
| ) |  |

static

Find all residues in a sequence that should not be reversed / shuffled.

Parameters

  sequence | The amino acid sequence
  keepN | Whether to keep N terminus constant
  keepC | Whether to keep C terminus constant
  keep_const_pattern | A string containing the AA to not change (e.g. 'KRP')

## ◆ findFixedResidues_()

IndexType findFixedResidues_ | ( | const std::string & | sequence | ) | const

protected

Find all K, R, P sites in a sequence to be set as fixed.

This method was adapted from the SpectraST decoy generator

## ◆ generateDecoys()

void generateDecoys | ( | const OpenMS::TargetedExperiment & | exp,
|  | OpenMS::TargetedExperiment & | dec,
|  | const String & | method,
|  | const double | aim_decoy_fraction,
|  | const bool | switchKR,
|  | const String & | decoy_tag,
|  | const int | max_attempts,
|  | const double | identity_threshold,
|  | const double | precursor_mz_shift,
|  | const double | product_mz_shift,
|  | const double | product_mz_threshold,
|  | const std::vector< String > & | fragment_types,
|  | const std::vector< size_t > & | fragment_charges,
|  | const bool | enable_specific_losses,
|  | const bool | enable_unspecific_losses,
|  | const int | round_decPow = `-4`
| ) |  | const

Generate decoys from a TargetedExperiment.

Will generate decoy peptides for each target peptide provided in exp and write them into the decoy experiment.

Valid methods: shuffle, reverse, pseudo-reverse

If theoretical is true, the target transitions will be returned but their masses will be adjusted to match the theoretical value of the fragment ion that is the most likely explanation for the product.

mz_threshold is used for the matching of theoretical ion series to the observed one

To generate decoys with different precursor mass, use the "switchKR" flag which switches terminal K/R (switches K to R and R to K). This generates different precursor m/z and ensures that the y ion series has a different mass. For a description of the procedure, see (supplemental material)

Bruderer et al. Mol Cell Proteomics. 2017. 10.1074/mcp.RA117.000314.

## ◆ hasCNterminalMods_()

bool hasCNterminalMods_ | ( | const OpenMS::TargetedExperiment::Peptide & | peptide,
|  | bool | checkCterminalAA
| ) |  | const

protected

Check if a peptide has C or N terminal modifications.

## ◆ pseudoreversePeptide_()

OpenMS::TargetedExperiment::Peptide pseudoreversePeptide_ | ( | const OpenMS::TargetedExperiment::Peptide & | peptide | ) | const

protected

Pseudo-reverse a peptide sequence (with its modifications)

Note
  Pseudo reverses a peptide sequence, leaving the C terminus (the last AA constant)

## ◆ reversePeptide()

static OpenMS::TargetedExperiment::Peptide reversePeptide | ( | const OpenMS::TargetedExperiment::Peptide & | peptide,
|  | const bool | keepN,
|  | const bool | keepC,
|  | const String & | const_pattern = `String()`
| ) |  |

static

Reverse a peptide sequence (with its modifications)

Parameters

  peptide | The peptide sequence and modifications
  keepN | Whether to keep N terminus in place
  keepC | Whether to keep C terminus in place
  const_pattern | A list of AA to leave in place

## ◆ reversePeptide_()

OpenMS::TargetedExperiment::Peptide reversePeptide_ | ( | const OpenMS::TargetedExperiment::Peptide & | peptide | ) | const

protected

Reverse a peptide sequence (with its modifications)

Note
  Does not keep N / C terminus in place.

## ◆ shufflePeptide()

OpenMS::TargetedExperiment::Peptide shufflePeptide | ( | OpenMS::TargetedExperiment::Peptide | peptide,
|  | const double | identity_threshold,
|  | int | seed = `-1`,
|  | const int | max_attempts = `100`
| ) |  | const

Shuffle a peptide (with its modifications) sequence.

This function will shuffle the given peptide sequences and its modifications such that the resulting relative sequence identity is below identity_threshold.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ keep_const_pattern_

String keep_const_pattern_

protected

## ◆ keepC_

bool keepC_

protected

## ◆ keepN_

bool keepN_

protected