| OpenMS 2.5.0

Classes | Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
PeptideAndProteinQuant Class Reference

Helper class for peptide and protein quantification based on feature data annotated with IDs. More...

`#include <OpenMS/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.h>`

Inheritance diagram for PeptideAndProteinQuant:

## Classes

struct | PeptideData
| Quantitative and associated data for a peptide. More...
struct | ProteinData
| Quantitative and associated data for a protein. More...
struct | Statistics
| Statistics for processing summary. More...

## Public Types

typedef std::map< UInt64, double > | SampleAbundances
| Mapping: sample ID -> abundance. More...
typedef std::map< AASequence, PeptideData > | PeptideQuant
| Mapping: peptide sequence (modified) -> peptide data. More...
typedef std::map< String, ProteinData > | ProteinQuant
| Mapping: protein accession -> protein data. More...

## Public Member Functions

| PeptideAndProteinQuant ()
| Constructor. More...
| ~PeptideAndProteinQuant () override
| Destructor. More...
void | readQuantData (FeatureMap &features, const ExperimentalDesign &ed)
| Read quantitative data from a feature map. More...
void | readQuantData (ConsensusMap &consensus, const ExperimentalDesign &ed)
| Read quantitative data from a consensus map. More...
void | readQuantData (std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const ExperimentalDesign &ed)
| Read quantitative data from identification results (for quantification via spectral counting). More...
void | quantifyPeptides (const std::vector< PeptideIdentification > &peptides=std::vector< PeptideIdentification >())
| Compute peptide abundances. More...
void | quantifyProteins (const ProteinIdentification &proteins=ProteinIdentification())
| Compute protein abundances. More...
const Statistics & | getStatistics ()
| Get summary statistics. More...
const PeptideQuant & | getPeptideResults ()
| Get peptide abundance data. More...
const ProteinQuant & | getProteinResults ()
| Get protein abundance data. 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...

## Static Public Member Functions

static void | annotateQuantificationsToProteins (const ProteinQuant &protein_quants, ProteinIdentification &proteins, const UInt n_samples)
| Annotate protein quant results as meta data to protein ids. More...

## Private Member Functions

PeptideHit | getAnnotation_ (std::vector< PeptideIdentification > &peptides)
| Get the "canonical" annotation (a single peptide hit) of a feature/consensus feature from the associated list of peptide identifications. More...
void | quantifyFeature_ (const FeatureHandle &feature, size_t fraction, size_t sample, const PeptideHit &hit)
| Gather quantitative information from a feature. More...
bool | getBest_ (const std::map< Int, std::map< Int, SampleAbundances >> &peptide_abundances, std::pair< size_t, size_t > &best)
| Determine fraction and charge state of a peptide with the highest number of abundances. More...
template<typename T >
void | orderBest_ (const std::map< T, SampleAbundances > &abundances, std::vector< T > &result)
| Order keys (charges/peptides for peptide/protein quantification) according to how many samples they allow to quantify, breaking ties by total abundance. More...
void | normalizePeptides_ ()
| Normalize peptide abundances across samples by (multiplicative) scaling to equal medians. More...
String | getAccession_ (const std::set< String > &pep_accessions, std::map< String, String > &accession_to_leader)
| Get the "canonical" protein accession from the list of protein accessions of a peptide. More...
void | countPeptides_ (std::vector< PeptideIdentification > &peptides)
| Count the number of identifications (best hits only) of each peptide sequence. More...
void | updateMembers_ () override
| Clear all data when parameters are set. More...

## Private Attributes

Statistics | stats_
| Processing statistics for output in the end. More...
PeptideQuant | pep_quant_
| Peptide quantification data. More...
ProteinQuant | prot_quant_
| Protein quantification data. More...

## Additional Inherited Members

Protected Member Functions inherited from DefaultParamHandler
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

Helper class for peptide and protein quantification based on feature data annotated with IDs.

This class is used by ProteinQuantifier. See there for further documentation.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
top | int | 3 | min: 0 | Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)
average | string | median | median, mean, weighted_mean, sum | Averaging method used to compute protein abundances from peptide abundances
include_all | string | false | true, false | Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)
best_charge_and_fraction | string | false | true, false | Distinguish between fraction and charge states of a peptide. For peptides, abundances will be reported separately for each fraction and charge; for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).
By default, abundances are summed over all charge states.
consensus:normalize | string | false | true, false | Scale peptide abundances so that medians of all samples are equal
consensus:fix_peptides | string | false | true, false | Use the same peptides for protein quantification across all samples. With 'top 0', all peptides that occur in every sample are considered. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,
breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!).

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Member Typedef Documentation

## ◆ PeptideQuant

typedef std::map<AASequence, PeptideData> PeptideQuant

Mapping: peptide sequence (modified) -> peptide data.

## ◆ ProteinQuant

typedef std::map<String, ProteinData> ProteinQuant

Mapping: protein accession -> protein data.

## ◆ SampleAbundances

typedef std::map<UInt64, double> SampleAbundances

Mapping: sample ID -> abundance.

## Constructor & Destructor Documentation

## ◆ PeptideAndProteinQuant()

PeptideAndProteinQuant | ( |  | ) |

Constructor.

## ◆ ~PeptideAndProteinQuant()

~PeptideAndProteinQuant | ( |  | ) |

inline override

Destructor.

## Member Function Documentation

## ◆ annotateQuantificationsToProteins()

static void annotateQuantificationsToProteins | ( | const ProteinQuant & | protein_quants,
|  | ProteinIdentification & | proteins,
|  | const UInt | n_samples
| ) |  |

static

Annotate protein quant results as meta data to protein ids.

Referenced by UTILProteomicsLFQ::main_().

## ◆ countPeptides_()

void countPeptides_ | ( | std::vector< PeptideIdentification > & | peptides | ) |

private

Count the number of identifications (best hits only) of each peptide sequence.

The peptide hits in `peptides` are sorted by score in the process.

## ◆ getAccession_()

String getAccession_ | ( | const std::set< String > & | pep_accessions,
|  | std::map< String, String > & | accession_to_leader
| ) |  |

private

Get the "canonical" protein accession from the list of protein accessions of a peptide.

Parameters

  pep_accessions | Protein accessions of a peptide
  accession_to_leader | Captures information about indistinguishable proteins (maps accession to accession of group leader)

If there is no information about indistinguishable proteins (from protXML) available, a canonical accession exists only for proteotypic peptides - it's the single accession for the respective peptide.

Otherwise, a peptide has a canonical accession if it maps only to proteins of one indistinguishable group. In this case, the canonical accession is that of the group leader.

If there is no canonical accession, the empty string is returned.

## ◆ getAnnotation_()

PeptideHit getAnnotation_ | ( | std::vector< PeptideIdentification > & | peptides | ) |

private

Get the "canonical" annotation (a single peptide hit) of a feature/consensus feature from the associated list of peptide identifications.

Only the best-scoring peptide hit of each ID in `peptides` is taken into account. The hits of each ID must already be sorted! If there's more than one ID and the best hits are not identical by sequence, or if there's no peptide ID, an empty peptide hit (for "ambiguous/no annotation") is returned. Protein accessions from identical peptide hits are accumulated.

## ◆ getBest_()

bool getBest_ | ( | const std::map< Int, std::map< Int, SampleAbundances >> & | peptide_abundances,
|  | std::pair< size_t, size_t > & | best
| ) |  |

inline private

Determine fraction and charge state of a peptide with the highest number of abundances.

Parameters

  peptide_abundances | Const input map fraction -> charge -> SampleAbundances
  best | Will additionally return the best fraction and charge state

Returns
  true if at least one abundance was found, false otherwise

## ◆ getPeptideResults()

const PeptideQuant& getPeptideResults | ( |  | ) |

Get peptide abundance data.

## ◆ getProteinResults()

const ProteinQuant& getProteinResults | ( |  | ) |

Get protein abundance data.

Referenced by UTILProteomicsLFQ::main_().

## ◆ getStatistics()

const Statistics& getStatistics | ( |  | ) |

Get summary statistics.

## ◆ normalizePeptides_()

void normalizePeptides_ | ( |  | ) |

private

Normalize peptide abundances across samples by (multiplicative) scaling to equal medians.

## ◆ orderBest_()

void orderBest_ | ( | const std::map< T, SampleAbundances > & | abundances,
|  | std::vector< T > & | result
| ) |  |

inline private

Order keys (charges/peptides for peptide/protein quantification) according to how many samples they allow to quantify, breaking ties by total abundance.

The keys of `abundances` are stored ordered in `result`, best first.

## ◆ quantifyFeature_()

void quantifyFeature_ | ( | const FeatureHandle & | feature,
|  | size_t | fraction,
|  | size_t | sample,
|  | const PeptideHit & | hit
| ) |  |

private

Gather quantitative information from a feature.

Store quantitative information from `feature` in member `pep_quant_`, based on the peptide annotation in `hit`. `fraction`, use 0 for first fraction (or if no fractionation was performed) `sample`, use 0 for first sample, 1 for second, ... If `hit` is empty ("ambiguous/no annotation"), nothing is stored.

## ◆ quantifyPeptides()

void quantifyPeptides | ( | const std::vector< PeptideIdentification > & | peptides = `std::vector< PeptideIdentification >()` | ) |

Compute peptide abundances.

Based on quantitative data for individual charge states (in member `pep_quant_`), overall abundances for peptides are computed (and stored again in `pep_quant_`).

Quantitative data must first be read via readQuantData().

Optional (peptide-level) protein inference information (e.g. from Fido or ProteinProphet) can be supplied via `peptides`. In that case, peptide-to-protein associations - the basis for protein-level quantification - will also be read from `peptides!`

Referenced by UTILProteomicsLFQ::main_().

## ◆ quantifyProteins()

void quantifyProteins | ( | const ProteinIdentification & | proteins = `ProteinIdentification()` | ) |

Compute protein abundances.

Peptide abundances must be computed first with quantifyPeptides(). Optional protein inference information (e.g. from Fido or ProteinProphet) can be supplied via `proteins`.

Referenced by UTILProteomicsLFQ::main_().

## ◆ readQuantData() [1/3]

void readQuantData | ( | FeatureMap & | features,
|  | const ExperimentalDesign & | ed
| ) |  |

Read quantitative data from a feature map.

Parameters should be set before using this method, as setting parameters will clear all results.

Referenced by UTILProteomicsLFQ::main_().

## ◆ readQuantData() [2/3]

void readQuantData | ( | ConsensusMap & | consensus,
|  | const ExperimentalDesign & | ed
| ) |  |

Read quantitative data from a consensus map.

Parameters should be set before using this method, as setting parameters will clear all results.

## ◆ readQuantData() [3/3]

void readQuantData | ( | std::vector< ProteinIdentification > & | proteins,
|  | std::vector< PeptideIdentification > & | peptides,
|  | const ExperimentalDesign & | ed
| ) |  |

Read quantitative data from identification results (for quantification via spectral counting).

Parameters should be set before using this method, as setting parameters will clear all results.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override private virtual

Clear all data when parameters are set.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ pep_quant_

PeptideQuant pep_quant_

private

Peptide quantification data.

## ◆ prot_quant_

ProteinQuant prot_quant_

private

Protein quantification data.

## ◆ stats_

Statistics stats_

private

Processing statistics for output in the end.