|
| | TransitionPQPFile () |
| | Constructor. More...
|
| |
| | ~TransitionPQPFile () override |
| | Destructor. More...
|
| |
| void | convertTargetedExperimentToPQP (const char *filename, OpenMS::TargetedExperiment &targeted_exp) |
| | Write out a targeted experiment (TraML structure) into a PQP file. More...
|
| |
| void | convertPQPToTargetedExperiment (const char *filename, OpenMS::TargetedExperiment &targeted_exp, bool legacy_traml_id=false) |
| | Read in a PQP file and construct a targeted experiment (TraML structure) More...
|
| |
| void | convertPQPToTargetedExperiment (const char *filename, OpenSwath::LightTargetedExperiment &targeted_exp, bool legacy_traml_id=false) |
| | Read in a PQP file and construct a targeted experiment (Light transition structure) More...
|
| |
| | TransitionTSVFile () |
| | Constructor. More...
|
| |
| | ~TransitionTSVFile () override |
| | Destructor. More...
|
| |
| void | convertTargetedExperimentToTSV (const char *filename, OpenMS::TargetedExperiment &targeted_exp) |
| | Write out a targeted experiment (TraML structure) into a tsv file. More...
|
| |
| void | convertTSVToTargetedExperiment (const char *filename, FileTypes::Type filetype, OpenMS::TargetedExperiment &targeted_exp) |
| | Read in a tsv/mrm file and construct a targeted experiment (TraML structure) More...
|
| |
| void | convertTSVToTargetedExperiment (const char *filename, FileTypes::Type filetype, OpenSwath::LightTargetedExperiment &targeted_exp) |
| | Read in a tsv file and construct a targeted experiment (Light transition structure) More...
|
| |
| void | validateTargetedExperiment (const OpenMS::TargetedExperiment &targeted_exp) |
| | Validate a TargetedExperiment (check that all ids are unique) More...
|
| |
| | ProgressLogger () |
| | Constructor. More...
|
| |
| virtual | ~ProgressLogger () |
| | Destructor. More...
|
| |
| | ProgressLogger (const ProgressLogger &other) |
| | Copy constructor. More...
|
| |
| ProgressLogger & | operator= (const ProgressLogger &other) |
| | Assignment Operator. More...
|
| |
| void | setLogType (LogType type) const |
| | Sets the progress log that should be used. The default type is NONE! More...
|
| |
| LogType | getLogType () const |
| | Returns the type of progress log being used. More...
|
| |
| void | setLogger (ProgressLoggerImpl *logger) |
| | Sets the logger to be used for progress logging. More...
|
| |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| | Initializes the progress display. More...
|
| |
| void | setProgress (SignedSize value) const |
| | Sets the current progress. More...
|
| |
| void | endProgress (UInt64 bytes_processed=0) const |
| |
| void | nextProgress () const |
| | increment progress by 1 (according to range begin-end) 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...
|
| |
| DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| | Assignment operator. More...
|
| |
| virtual bool | operator== (const DefaultParamHandler &rhs) const |
| | Equality operator. More...
|
| |
| void | setParameters (const Param ¶m) |
| | 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...
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| |
This class supports reading and writing of PQP files.
The PQP files are SQLite databases consisting of several tables representing the data contained in TraML files. For another file format that stores transitions, see also TransitionTSVFile.
This class can convert TraML and PQP files into each other
The file format has the following tables:
Genes and proteins are described by a primary key as well as a human-readable gene name or protein accession key.
| GENE |
| ID | INT | Primary Key (gene id) |
| GENE_NAME | TEXT | Gene name |
| DECOY | INT (0 or 1) | Whether this is a decoy gene (1: decoy, 0: target) |
|
| PEPTIDE_GENE_MAPPING |
| PEPTIDE_ID | INT | Foreign Key (PEPTIDE.ID) |
| GENE_ID | INT | Foreign Key (GENE.ID) |
|
| PROTEIN |
| ID | INT | Primary Key (protein id) |
| PROTEIN_ACCESSION | TEXT | Protein accession |
| DECOY | INT (0 or 1) | Whether this is a decoy protein (1: decoy, 0: target) |
|
| PEPTIDE_PROTEIN_MAPPING |
| PEPTIDE_ID | INT | Foreign Key (PEPTIDE.ID) |
| PROTEIN_ID | INT | Foreign Key (PROTEIN.ID) |
|
Peptides are physical analytes that are present in the sample and can carry post-translational modifications (PTMs). They are described by their amino-acid sequence and the modifications they carry:
| PEPTIDE |
| ID | INT | Primary Key (peptide id) |
| UNMODIFIED_SEQUENCE | TEXT | Peptide sequence (unmodified) |
| MODIFIED_SEQUENCE | TEXT | Peptide sequence (modified) 1 |
| DECOY | INT (0 or 1) | Whether this is a decoy peptide (1: decoy, 0: target) |
|
| PRECURSOR_PEPTIDE_MAPPING |
| PRECURSOR_ID | INT | Foreign Key (PRECURSOR.ID) |
| PEPTIDE_ID | INT | Foreign Key (PEPTIDE.ID) |
|
Compounds are generic analytes that are present in the sample (but are not peptides). This is used for small molecules which are described by their molecular formula and the SMILES representation (structural representation):
| COMPOUND |
| ID | INT | Primary Key (compound id) |
| COMPOUND_NAME | TEXT | Compound name (common name of the analyte) |
| SUM_FORMULA | TEXT | Molecular formula of the compound |
| SMILES | TEXT | SMILES representation |
| ADDUCTS | TEXT | List of adducts for the compound |
| DECOY | INT (0 or 1) | Whether this is a decoy compound (1: decoy, 0: target) |
|
| PRECURSOR_COMPOUND_MAPPING |
| PRECURSOR_ID | INT | Foreign Key (PRECURSOR.ID) |
| COMPOUND_ID | INT | Foreign Key (COMPOUND.ID) |
|
Precursors are generated upon ionization from peptides or small molecule analytes (compounds) and are described by their charge state, mass-to-charge ratio, retention time and ion mobility drift time:
| PRECURSOR |
| ID | INT | Primary Key (precursor id) |
| TRAML_ID | TEXT | TraML identifiers (maps to the "id=" attribute in TraML) |
| GROUP_LABEL | TEXT | designates to which peptide label group (as defined in MS:1000893) the peptide belongs to2 |
| PRECURSOR_MZ | REAL | Precursor m/z |
| CHARGE | TEXT | Precursor charge state |
| LIBRARY_INTENSITY | TEXT | Precursor library intensity |
| LIBRARY_RT | TEXT | Library retention time (RT) |
| LIBRARY_DRIFT_TIME | TEXT | Library drift time (ion mobility drift time or collisional cross-section) |
| DECOY | INT (0 or 1) | Whether this is a decoy precursor (1: decoy, 0: target) |
|
| TRANSITION_PRECURSOR_MAPPING |
| TRANSITION_ID | INT | Foreign Key (TRANSITION.ID) |
| PRECURSOR_ID | INT | Foreign Key (PRECURSOR.ID) |
|
Transitions are generated upon fragmentation from precursors and are described by their charge state and (fragment) mass-to-charge ratio. For peptide fragments, an ion type (e.g. y for y-ions) and a ordinal (e.g. 6 for a y6 ion) can be recorded. Note that detecting transitions are used for precursor detection and will indicate whether a given precursor is present or not in the sample. Use detecting transitions for the top N transitions of a precursor to detect a set of transitions in the sample. Identifying transitions will be used to discriminate different peptidoforms of the same precursor (see IPF Workflow for PTM inference).
| TRANSITION |
| ID | INT | Primary Key (transition id) |
| TRAML_ID | TEXT | TraML identifiers (maps to the "id=" attribute in TraML) |
| PRODUCT_MZ | TEXT | Fragment ion m/z |
| CHARGE | TEXT | Fragment ion charge |
| TYPE | CHAR | Fragment ion type (e.g. "b" or "y") |
| ANNOTATION | TEXT | Fragment ion annotation |
| ORDINAL | INT | Fragment ion ordinal |
| DETECTING | INT (0 or 1) | 1: use transition to detect peak group, 0: don't use transition for detection |
| IDENTIFYING | INT (0 or 1) | 1: use transition for peptidoform inference in the IPF Workflow, 0: don't use transition for identification |
| QUANTIFYING | INT (0 or 1) | 1: use transition to quantify peak group, 0: don't use transition for quantification |
| LIBRARY_INTENSITY | REAL | Fragment ion library intensity |
| DECOY | INT (0 or 1) | Whether this is a decoy transition (1: decoy, 0: target) |
|
There is one extra table directly mapping TRANSITION to PEPTIDE which is mainly used for the IPF Workflow for PTM inference. It directly maps transitions to peptidoforms (one identification transition can map to multiple peptidoforms):
|
| TRANSITION_PEPTIDE_MAPPING |
| TRANSITION_ID | INT | Foreign Key (TRANSITION.ID) |
| PEPTIDE_ID | INT | Foreign Key (PEPTIDE.ID) |
|
Another extra table describes the file format version:
| VERSION |
| ID | INT | File Format version |
Remarks:
-
- modifications should be supplied inside the sequence using UniMod identifiers or freetext identifiers that are understood by OpenMS. See also OpenMS::AASequence for more information. For example:
-
PEPT(Phosphorylation)IDE(UniMod:27)A )
-
- peptide label groups designate groups of peptides that are isotopically modified forms of the same peptide species. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label. For example:
-
PEPTIDEAK -> gets label "PEPTIDEAK_gr1"
-
PEPTIDEAK[+8] -> gets label "PEPTIDEAK_gr1"
-
PEPT(Phosphorylation)IDEAK -> gets label "PEPTIDEAK_gr2"
-
PEPT(Phosphorylation)IDEAK[+8] -> gets label "PEPTIDEAK_gr2"
Parameters of this class are:
| Name | Type | Default | Restrictions | Description |
|---|
| retentionTimeInterpretation |
string | iRT |
iRT, seconds, minutes | How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds) |
| override_group_label_check |
string | false |
true, false | Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group). Only turn this off if you know what you are doing. |
| force_invalid_mods |
string | false |
true, false | Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification) |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
1.9.1 
