| OpenMS 2.5.0

Classes | Public Member Functions | Private Member Functions | Private Attributes | List of all members
MultiplexDeltaMassesGenerator Class Reference

generates complete list of all possible mass shifts due to isotopic labelling More...

`#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexDeltaMassesGenerator.h>`

Inheritance diagram for MultiplexDeltaMassesGenerator:

## Classes

struct | Label
| complete label information More...

## Public Member Functions

| MultiplexDeltaMassesGenerator ()
| constructor More...
| MultiplexDeltaMassesGenerator (String labels, int missed_cleavages, std::map< String, double > label_mass_shift)
| constructor More...
void | generateKnockoutDeltaMasses ()
| generate all mass shifts that can occur due to the absence of one or multiple peptides (e.g. for a triplet experiment generate the doublets and singlets that might be present) More...
void | printSamplesLabelsList (std::ostream &stream) const
| write the list of labels for each of the sample More...
void | printDeltaMassesList (std::ostream &stream) const
| write the list of all mass patterns More...
std::vector< MultiplexDeltaMasses > | getDeltaMassesList ()
| returns the list of mass shift patterns More...
const std::vector< MultiplexDeltaMasses > & | getDeltaMassesList () const
| returns the list of mass shift patterns More...
std::vector< std::vector< String > > | getSamplesLabelsList ()
| returns the list of samples with their corresponding labels More...
const std::vector< std::vector< String > > & | getSamplesLabelsList () const
| returns the list of samples with their corresponding labels More...
String | getLabelShort (String label)
| returns the short label string More...
String | getLabelLong (String label)
| returns the long label string More...
MultiplexDeltaMasses::LabelSet | extractLabelSet (AASequence sequence)
| extract the label set from the 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...

## Private Member Functions

void | fillLabelMasterList_ ()
| fill label master list More...

## Private Attributes

String | labels_
| isotopic labels More...
std::vector< String > | labels_list_
| flat list of all occurring isotopic labels More...
std::vector< std::vector< String > > | samples_labels_
| list of samples with their corresponding labels More...
int | missed_cleavages_
| maximum number of missed cleavages More...
std::vector< MultiplexDeltaMasses > | delta_masses_list_
| list of all possible mass shift patterns More...
std::vector< Label > | label_master_list_
| master list of all labels More...
std::map< String, double > | label_delta_mass_
| mapping from single label to delta mass e.g. "Arg10" -> 10.0082686 More...
std::map< String, String > | label_short_long_
| mapping from a short label (as in the user params) to a long label (as in PSI-MS name) e.g. "Arg10" -> "Label:13C(6)15N(4)" More...
std::map< String, String > | label_long_short_
| mapping from a long label (as in PSI-MS name) to a short label (as in the user params) e.g. "Label:13C(6)15N(4)" -> "Arg10" More...

## Additional Inherited Members

Protected Member Functions inherited from DefaultParamHandler
virtual void | updateMembers_ ()
| This method is used to update extra member variables at the end of the setParameters() method. More...
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...
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...

## Detailed Description

generates complete list of all possible mass shifts due to isotopic labelling

Isotopic labelling results in the shift of peptide masses.

For example in a Lys8/Arg10 SILAC labelled sample, some peptides (the ones with one Arg in their sequence) will show a relative mass shift between light and heavy partners of 10 Da. This class constructs the complete list of all possible mass shifts that arise from isotopic labelling.

## Constructor & Destructor Documentation

## ◆ MultiplexDeltaMassesGenerator() [1/2]

MultiplexDeltaMassesGenerator | ( |  | ) |

constructor

## ◆ MultiplexDeltaMassesGenerator() [2/2]

MultiplexDeltaMassesGenerator | ( | String | labels,
|  | int | missed_cleavages,
|  | std::map< String, double > | label_mass_shift
| ) |  |

constructor

Parameters

  labels | string describing the labels used in each sample. [...] specifies the labels for a single sample. For example For example, [][Lys8,Arg10] describes a standard SILAC experiment. In the "light" sample, none of the amino acids are labelled []. In the "heavy" sample, lysines and arginines are isotopically labelled [Lys8,Arg10].
  missed_cleavages | maximum number of missed cleavages due to incomplete digestion
  label_mass_shift | name of labels (e.g. Lys8) and their corresponding mass shifts (e.g. 8.0141988132)

## Member Function Documentation

## ◆ extractLabelSet()

MultiplexDeltaMasses::LabelSet extractLabelSet | ( | AASequence | sequence | ) |

extract the label set from the sequence

Parameters

  sequence | amino acid sequence

For example, the sequence VLSEEEIDDNFK(Label:13C(6)15N(2))AQR(Label:13C(6)15N(4)) contains a set of two labels, Lys8 and Arg10.

## ◆ fillLabelMasterList_()

void fillLabelMasterList_ | ( |  | ) |

private

fill label master list

## ◆ generateKnockoutDeltaMasses()

void generateKnockoutDeltaMasses | ( |  | ) |

generate all mass shifts that can occur due to the absence of one or multiple peptides (e.g. for a triplet experiment generate the doublets and singlets that might be present)

## ◆ getDeltaMassesList() [1/2]

std::vector<MultiplexDeltaMasses> getDeltaMassesList | ( |  | ) |

returns the list of mass shift patterns

Parameters

  stream | output stream

## ◆ getDeltaMassesList() [2/2]

const std::vector<MultiplexDeltaMasses>& getDeltaMassesList | ( |  | ) | const

returns the list of mass shift patterns

## ◆ getLabelLong()

String getLabelLong | ( | String | label | ) |

returns the long label string

Parameters

  label | short label, as it appears in the "labels" parameter, e.g. "Arg10"

## ◆ getLabelShort()

String getLabelShort | ( | String | label | ) |

returns the short label string

Parameters

  label | long label, UniMod name as it appears in peptide sequences, e.g. "Label:13C(6)15N(4)"

## ◆ getSamplesLabelsList() [1/2]

std::vector<std::vector<String> > getSamplesLabelsList | ( |  | ) |

returns the list of samples with their corresponding labels

For example in a standard SILAC experiment: sample 1: no_label sample 2: Lys8 Arg10

## ◆ getSamplesLabelsList() [2/2]

const std::vector<std::vector<String> >& getSamplesLabelsList | ( |  | ) | const

returns the list of samples with their corresponding labels

For example in a standard SILAC experiment: sample 1: no_label sample 2: Lys8 Arg10

## ◆ printDeltaMassesList()

void printDeltaMassesList | ( | std::ostream & | stream | ) | const

write the list of all mass patterns

For example in a standard SILAC experiment allowing for one missed cleavage, five mass shift patterns are possible. mass shift 1: 0 (no_label) 8.0142 (Lys8) mass shift 2: 0 (no_label) 10.0083 (Arg10) mass shift 3: 0 (no_label) 16.0284 (Lys8,Lys8) mass shift 4: 0 (no_label) 18.0225 (Arg10,Lys8) mass shift 5: 0 (no_label) 20.0165 (Arg10,Arg10)

Parameters

  stream | output stream

## ◆ printSamplesLabelsList()

void printSamplesLabelsList | ( | std::ostream & | stream | ) | const

write the list of labels for each of the sample

For example in a standard SILAC experiment, sample 1 (light) is unlabelled and sample 2 (heavy) contains Lys8 and Arg 10 labels. sample 1: no_label sample 2: Lys8 Arg10

## Member Data Documentation

## ◆ delta_masses_list_

std::vector<MultiplexDeltaMasses> delta_masses_list_

private

list of all possible mass shift patterns

## ◆ label_delta_mass_

std::map<String, double> label_delta_mass_

private

mapping from single label to delta mass e.g. "Arg10" -> 10.0082686

## ◆ label_long_short_

std::map<String, String> label_long_short_

private

mapping from a long label (as in PSI-MS name) to a short label (as in the user params) e.g. "Label:13C(6)15N(4)" -> "Arg10"

## ◆ label_master_list_

std::vector<Label> label_master_list_

private

master list of all labels

## ◆ label_short_long_

std::map<String, String> label_short_long_

private

mapping from a short label (as in the user params) to a long label (as in PSI-MS name) e.g. "Arg10" -> "Label:13C(6)15N(4)"

## ◆ labels_

String labels_

private

isotopic labels

## ◆ labels_list_

std::vector<String> labels_list_

private

flat list of all occurring isotopic labels

## ◆ missed_cleavages_

int missed_cleavages_

private

maximum number of missed cleavages

## ◆ samples_labels_

std::vector<std::vector<String> > samples_labels_

private

list of samples with their corresponding labels