#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathWorkflow.h>
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| OpenSwathWorkflowBase () |
| Default constructor. More...
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| OpenSwathWorkflowBase (bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop) |
| Constructor. More...
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void | MS1Extraction_ (const OpenSwath::SpectrumAccessPtr &ms1_map, const std::vector< OpenSwath::SwathMap > &swath_maps, std::vector< MSChromatogram > &ms1_chromatograms, const ChromExtractParams &cp, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo_inverse, bool ms1_only=false, int ms1_isotopes=0) |
| Perform MS1 extraction and store result in ms1_chromatograms. More...
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void | prepareExtractionCoordinates_ (std::vector< OpenSwath::ChromatogramPtr > &chrom_list, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, const OpenSwath::LightTargetedExperiment &transition_exp_used, const TransformationDescription &trafo_inverse, const ChromExtractParams &cp, const bool ms1=false, const int ms1_isotopes=-1) const |
| Function to prepare extraction coordinates that also correctly handles RT transformations. More...
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◆ OpenSwathWorkflowBase() [1/2]
Default constructor.
Will not use any ms1 traces and use all threads in the outer loop.
◆ OpenSwathWorkflowBase() [2/2]
OpenSwathWorkflowBase |
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bool |
use_ms1_traces, |
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bool |
use_ms1_ion_mobility, |
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bool |
prm, |
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bool |
pasef, |
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int |
threads_outer_loop |
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) |
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inlineprotected |
Constructor.
- Parameters
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use_ms1_traces | Use MS1 data? |
use_ms1_ion_mobility | Use ion mobility extraction on MS1 traces? |
prm | Is data acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows? |
pasef | Is this diaPASEF data? |
threads_outer_loop | How many threads should be used for the outer loop (-1 will use all threads in the outer loop) |
- Note
- The total number of threads should be divisible by this number (e.g. use 8 in outer loop if you have 24 threads in total and 3 will be used for the inner loop).
◆ MS1Extraction_()
Perform MS1 extraction and store result in ms1_chromatograms.
- Parameters
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ms1_map | Spectrum Access to the MS1 map |
swath_maps | The raw data (swath maps) |
ms1_chromatograms | Output vector for MS1 chromatograms |
cp | Parameter set for the chromatogram extraction |
transition_exp | The set of assays to be extracted and scored |
trafo_inverse | Inverse transformation function |
ms1_only | If true, will only score on MS1 level and ignore MS2 level |
ms1_isotopes | Number of MS1 isotopes to extract (zero means only monoisotopic peak) |
◆ prepareExtractionCoordinates_()
Function to prepare extraction coordinates that also correctly handles RT transformations.
Creates a set of (empty) chromatograms and extraction coordinates with the correct ids, m/z and retention time start/end points to be extracted by the ChromatogramExtractor.
Handles RT extraction windows by calculating the correct transformation for each coordinate.
- Parameters
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chrom_list | Output of chromatograms (will be filled with empty chromatogram ptrs) |
coordinates | Output of extraction coordinates (will be filled with matching extraction coordinates) |
transition_exp_used | The transition experiment used to create the coordinates |
trafo_inverse | Inverse transformation function |
cp | Parameter set for the chromatogram extraction |
ms1 | Whether to perform MS1 (precursor ion) or MS2 (fragment ion) extraction |
ms1_isotopes | Number of MS1 isotopes to extract (zero means only monoisotopic peak)
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◆ ms1_map_
Spectrum Access to the MS1 map (note that this is not threadsafe!)
- Note
- This pointer is not threadsafe, please use the lightClone() function to create a copy for each thread
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This pointer may be NULL if use_ms1_traces_ is set to false
◆ pasef_
Whether data is diaPASEF data.
If set to true, a precursor will only be extracted from a single window that matches both in m/z and whose ion mobility (drift time) center is closest to the library ion mobility of the precursor. This is required if windows overlap in m/z or in ion mobility, as is the case for diaPASEF data.
◆ prm_
Whether data is acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows.
If set to true, a precursor will only be extracted from a single window that matches in m/z and whose m/z center is closest to the library m/z of the precursor. This is required if windows overlap in m/z as is the case for SRM / PRM data where often multiple windows with similar (or overlaping) m/z are used to target different precursors at different RT.
◆ threads_outer_loop_
How many threads should be used for the outer loop.
- Note
- A value of -1 will use all threads in the outer loop
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The total number of threads should be divisible by this number (e.g. use 8 in outer loop if you have 24 threads in total and 3 will be used for the inner loop).
◆ use_ms1_ion_mobility_
bool use_ms1_ion_mobility_ |
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protected |
Whether to use ion mobility extraction on MS1 traces.
◆ use_ms1_traces_
Whether to use the MS1 traces.