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OpenMS
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#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>#include <OpenMS/KERNEL/FeatureMap.h>#include <OpenMS/KERNEL/MSExperiment.h>#include <map>#include <vector>Go to the source code of this file.
Classes | |
| class | Biosaur2Algorithm |
| Implementation of the Biosaur2 feature detection workflow for LC-MS1 data. More... | |
| struct | Biosaur2Algorithm::Hill |
| Representation of a single hill (continuous m/z trace across adjacent scans). More... | |
| struct | Biosaur2Algorithm::IsotopeCandidate |
| Candidate isotope peak that can be associated with a monoisotopic hill. More... | |
| struct | Biosaur2Algorithm::PeptideFeature |
| Aggregated properties of a detected peptide feature. More... | |
| struct | Biosaur2Algorithm::FastHillEntry |
| Lightweight index entry for fast m/z-based hill lookup. More... | |
| struct | Biosaur2Algorithm::PatternCandidate |
| Internal representation of a candidate isotope pattern. More... | |
Namespaces | |
| OpenMS | |
| Main OpenMS namespace. | |
| struct OpenMS::Biosaur2Algorithm::Hill |
Representation of a single hill (continuous m/z trace across adjacent scans).
A hill represents a contiguous series of peaks at similar m/z values across multiple consecutive scans. Hills are the fundamental building blocks for feature detection. Each hill stores the raw peak data (indices, m/z, intensity, RT) along with optional ion mobility information for PASEF/TIMS data. Summary statistics (intensity-weighted mean m/z, apex RT/intensity, etc.) are precomputed for efficient downstream processing.
| Class Members | ||
|---|---|---|
| double | drift_time_median | Median drift time (-1 if not available) |
| vector< double > | drift_times | Drift time values (TIMS data), empty if not available. |
| Size | hill_idx | Unique identifier for this hill. |
| vector< double > | intensities | Intensity values of peaks in this hill. |
| double | intensity_apex | Maximum intensity value in the hill. |
| double | intensity_sum | Sum of all intensities in the hill. |
| vector< double > | ion_mobilities | Ion mobility values, empty if not available. |
| double | ion_mobility_median | Intensity-weighted mean ion mobility (median fallback; -1 if not available) |
| Size | length | Number of points/peaks in this hill. |
| vector< double > | mz_values | m/z values of peaks in this hill |
| double | mz_weighted_mean | Intensity-weighted mean m/z (hill center) |
| vector< Size > | peak_indices | Indices of peaks within each spectrum. |
| double | rt_apex | Retention time at maximum intensity. |
| double | rt_end | Retention time of last peak. |
| double | rt_start | Retention time of first peak. |
| vector< double > | rt_values | Retention time values corresponding to each peak. |
| vector< Size > | scan_indices | Indices of spectra containing peaks of this hill. |
| struct OpenMS::Biosaur2Algorithm::IsotopeCandidate |
Candidate isotope peak that can be associated with a monoisotopic hill.
During isotope pattern detection, candidate hills are evaluated for their suitability as isotope peaks of a monoisotopic hill. This structure stores the association along with quality metrics that quantify how well the candidate matches the expected isotope pattern in terms of mass accuracy and intensity correlation.
| Class Members | ||
|---|---|---|
| double | cos_corr | Cosine correlation between monoisotopic and isotope intensity traces. |
| Size | hill_idx | Index of the hill that represents this isotope peak. |
| Size | isotope_number | Ordinal isotope number (0=monoisotopic, 1=first isotope, etc.) |
| double | mass_diff_ppm | Mass difference to expected isotope position in ppm. |
| struct OpenMS::Biosaur2Algorithm::PeptideFeature |
Aggregated properties of a detected peptide feature.
A peptide feature represents a complete isotope pattern detected across multiple scans. It aggregates information from the monoisotopic hill and its associated isotope hills, providing comprehensive characterization including m/z, retention time, charge state, and intensity metrics. For ion mobility data, drift time and ion mobility values are also included.
| Class Members | ||
|---|---|---|
| int | charge | Detected charge state. |
| double | drift_time | Median drift time (-1 if not available) |
| double | intensity_apex | Maximum intensity across the feature. |
| double | intensity_sum | Sum of intensities (based on iuse parameter) |
| double | ion_mobility | Intensity-weighted mean ion mobility (median fallback; -1 if not available) |
| vector< IsotopeCandidate > | isotopes | List of associated isotope peaks. |
| double | mass_calib | Calibrated neutral mass of the feature in Da (neutral_mass = mz * charge ± charge * proton_mass; + for negative mode, − for positive mode) |
| Size | mono_hill_idx | Index of the monoisotopic hill. |
| double | mz | Monoisotopic m/z value. |
| Size | n_isotopes | Number of detected isotope peaks. |
| Size | n_scans | Number of scans contributing to the monoisotopic hill. |
| double | rt_apex | Retention time at maximum intensity. |
| double | rt_end | Retention time of last detection. |
| double | rt_start | Retention time of first detection. |
| struct OpenMS::Biosaur2Algorithm::FastHillEntry |
Lightweight index entry for fast m/z-based hill lookup.
Stores the hill index in the main Hill vector together with the first and last scan index for quick RT overlap checks when assembling isotope patterns.
| Class Members | ||
|---|---|---|
| Size | first_scan | |
| Size | hill_index | |
| Size | last_scan | |
| struct OpenMS::Biosaur2Algorithm::PatternCandidate |
Internal representation of a candidate isotope pattern.
Encapsulates a monoisotopic hill together with a set of isotope candidates, the associated charge state and quality metrics used during pattern refinement.
| Class Members | ||
|---|---|---|
| int | charge | Charge state of the pattern. |
| double | cos_cor_isotopes | Cosine correlation in isotope-intensity space. |
| vector< IsotopeCandidate > | isotopes | Associated isotope candidates. |
| Size | mono_index | Index of the monoisotopic hill in the hills vector. |
| double | mono_mz | Monoisotopic m/z. |
| Size | n_scans | Number of scans contributing to the monoisotopic hill. |
1.9.1