MzTabPSMSectionRow Struct Reference

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

#include <OpenMS/FORMAT/MzTab.h>

Collaboration diagram for MzTabPSMSectionRow:

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, MzTabDouble >	search_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< MzTabOptionalColumnEntry >	opt_
	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_evidences

Vector 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

MzTabString 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

MzTabString post

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

pre

MzTabString 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

MzTabString uri

Location of the PSM’s source entry.