OpenMS  2.8.0
Classes | Public Member Functions | Public Attributes | List of all members
MzTabPSMSectionRow Struct Reference

PSM - PSM section (Table based) More...

#include <OpenMS/FORMAT/MzTab.h>

Collaboration diagram for MzTabPSMSectionRow:
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Classes

struct  RowCompare
 Comparison operator for sorting rows. More...
 

Public Member Functions

void addPepEvidenceToRows (const std::vector< PeptideEvidence > &peptide_evidences)
 Gets peptide_evidences with data from internal structures adds their info to an MzTabPSMSectionRow (pre- or unfilled) More...
 

Public Attributes

MzTabString sequence
 The peptide’s sequence. More...
 
MzTabInteger PSM_ID
 A unique ID of a PSM line. More...
 
MzTabString accession
 List of potential parent protein accessions as in the fasta DB. More...
 
MzTabBoolean unique
 0=false, 1=true, null else: Peptide is unique for the protein. More...
 
MzTabString database
 Name of the sequence database. More...
 
MzTabString database_version
 Version (and optionally # of entries). More...
 
MzTabParameterList search_engine
 Search engine(s) that identified the peptide. More...
 
std::map< Size, MzTabDoublesearch_engine_score
 Search engine(s) score(s) for the peptide. More...
 
MzTabInteger reliability
 (1-3) 0=null Identification reliability for the peptide. More...
 
MzTabModificationList modifications
 Modifications identified in the peptide. More...
 
MzTabDoubleList retention_time
 Time points in seconds. Semantics may vary. More...
 
MzTabInteger charge
 The charge of the experimental precursor ion. More...
 
MzTabDouble exp_mass_to_charge
 The observed m/z ratio of the experimental precursor ion (either directly from the raw data or corrected). More...
 
MzTabDouble calc_mass_to_charge
 The calculated m/z ratio of the experimental precursor ion. More...
 
MzTabString uri
 Location of the PSM’s source entry. More...
 
MzTabSpectraRef spectra_ref
 Spectrum for this PSM. More...
 
MzTabString pre
 (List of) Amino acid in parent protein(s) before the start of the current PSM More...
 
MzTabString post
 (List of) Amino acid in parent protein(s) after the start of the current PSM More...
 
MzTabString start
 (List of) Start positions in parent protein(s) More...
 
MzTabString end
 (List of) Start positions in parent protein(s) More...
 
std::vector< MzTabOptionalColumnEntryopt_
 Optional columns must start with “opt_”. More...
 

Detailed Description

PSM - PSM section (Table based)

Member Function Documentation

◆ addPepEvidenceToRows()

void addPepEvidenceToRows ( const std::vector< PeptideEvidence > &  peptide_evidences)

Gets peptide_evidences with data from internal structures adds their info to an MzTabPSMSectionRow (pre- or unfilled)

Parameters
peptide_evidencesVector of PeptideEvidence holding internal data.

Member Data Documentation

◆ accession

MzTabString accession

List of potential parent protein accessions as in the fasta DB.

Referenced by MzTabPSMSectionRow::RowCompare::operator()().

◆ calc_mass_to_charge

MzTabDouble calc_mass_to_charge

The calculated m/z ratio of the experimental precursor ion.

◆ charge

MzTabInteger charge

The charge of the experimental precursor ion.

◆ database

MzTabString database

Name of the sequence database.

◆ database_version

MzTabString database_version

Version (and optionally # of entries).

◆ end

(List of) Start positions in parent protein(s)

◆ exp_mass_to_charge

MzTabDouble exp_mass_to_charge

The observed m/z ratio of the experimental precursor ion (either directly from the raw data or corrected).

◆ modifications

MzTabModificationList modifications

Modifications identified in the peptide.

◆ opt_

std::vector<MzTabOptionalColumnEntry> opt_

Optional columns must start with “opt_”.

◆ post

(List of) Amino acid in parent protein(s) after the start of the current PSM

◆ pre

(List of) Amino acid in parent protein(s) before the start of the current PSM

◆ PSM_ID

MzTabInteger PSM_ID

A unique ID of a PSM line.

◆ reliability

MzTabInteger reliability

(1-3) 0=null Identification reliability for the peptide.

◆ retention_time

MzTabDoubleList retention_time

Time points in seconds. Semantics may vary.

◆ search_engine

MzTabParameterList search_engine

Search engine(s) that identified the peptide.

◆ search_engine_score

std::map<Size, MzTabDouble> search_engine_score

Search engine(s) score(s) for the peptide.

◆ sequence

MzTabString sequence

The peptide’s sequence.

Referenced by MzTabPSMSectionRow::RowCompare::operator()().

◆ spectra_ref

MzTabSpectraRef spectra_ref

Spectrum for this PSM.

Referenced by MzTabPSMSectionRow::RowCompare::operator()().

◆ start

MzTabString start

(List of) Start positions in parent protein(s)

◆ unique

MzTabBoolean unique

0=false, 1=true, null else: Peptide is unique for the protein.

◆ uri

Location of the PSM’s source entry.