| Name | Type | Default | Restrictions | Description |
|---|
| local_rt_range |
float | 10.0 |
| RT range where to look for coeluting mass traces |
| local_im_range |
float | 0.02 |
| IM range where to look for coeluting mass traces |
| local_mz_range |
float | 6.5 |
| MZ range where to look for isotopic mass traces |
| charge_lower_bound |
int | 1 |
| Lowest charge state to consider |
| charge_upper_bound |
int | 3 |
| Highest charge state to consider |
| chrom_fwhm |
float | 5.0 |
| Expected chromatographic peak width (in seconds). |
| report_summed_ints |
string | false |
false, true | Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone. |
| enable_RT_filtering |
string | true |
false, true | Require sufficient overlap in RT while assembling mass traces. Disable for direct injection data.. |
| isotope_rt_overlap_reference |
string | longer |
longer, shorter | Reference trace the RT overlap is measured against when scoring two co-eluting mass traces (only used if 'enable_RT_filtering' is enabled): 'longer' measures the overlap against the longer trace (default, historic behavior); 'shorter' measures it against the shorter trace and additionally requires the apex of the longer trace to fall within the RT range of the shorter trace. Since low-intensity isotope traces are usually much shorter than the monoisotopic trace, 'shorter' better groups them (see issue @#4483). |
| min_isotope_rt_overlap |
float | 0.7 |
min: 0.0 max: 1.0 | Minimum fraction of the reference trace (see 'isotope_rt_overlap_reference') in RT (within FWHM) that must overlap the other trace so the two are scored as isotopes. Only used if 'enable_RT_filtering' is enabled. |
| isotope_filtering_model |
string | metabolites (5% RMS) |
metabolites (2% RMS), metabolites (5% RMS), peptides, none | Remove/score candidate assemblies based on isotope intensities. SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device. |
| mz_scoring_13C |
string | false |
false, true | Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!). Disable for general metabolites (as described in Kenar et al. 2014, MCP.). |
| use_smoothed_intensities |
string | true |
false, true | Use LOWESS intensities instead of raw intensities. |
| report_smoothed_intensities |
string | true |
false, true | Report smoothed intensities (only if use_smoothed_intensities is true). |
| report_convex_hulls |
string | false |
false, true | Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably). |
| report_chromatograms |
string | false |
false, true | Adds Chromatogram for each reported feature (Output in mzml). |
| remove_single_traces |
string | false |
false, true | Remove unassembled traces (single traces). |
| mz_scoring_by_elements |
string | false |
false, true | Use the m/z range of the assumed elements to detect isotope peaks. A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C' |
| elements |
string | CHNOPS |
| Elements assumes to be present in the sample (this influences isotope detection). |
1.9.8 