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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.
1.9.1 
