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