Class to write out an OpenSwath TSV output (mProphet input).
The output is organized as a set of rows where each row describes a single peak in a chromatogram with a start and end retention time. Per chromatogram multiple rows can be reported if more than one potential peak was found. See also OpenSwathOSWWriter for another output format.
The class can take a FeatureMap and create a set of string from it suitable for output to tsv using the prepareLine() function. These lines can also be directly written to a file using writeLines().
The output format written by this class is a TSV file (tab-separated plain text file) with the following columns:
| transition_group_id | string | designates the transition group [e.g. peptide/molecule] to which this transition belongs |
| peptide_group_label | string | designates to which peptide label group (as defined in MS:1000893) the peptide belongs to2 |
| run_id | integer | LC-MS/MS run (currently always 0) |
| filename | string | filename of the raw LC-MS/MS file |
| RT | float | peak group retention time (apex) |
| id | string | unique peak group identifier |
| Sequence | string | Peptide sequence |
| MC | int | Number of missed cleavages |
| FullPeptideName | string | Full peptide sequence including modifications 1 |
| Charge | string | Peptide (analyte) precursor charge |
| m/z | string | Peptide (analyte) precursor m/z |
| Intensity | float | Peptide (analyte) intensity (sum over all fragment ion intensities) |
| ProteinName | string | Protein Identifier |
| GeneName | string | Gene identifier |
| decoy | string | Whether peak group was found in a decoy chromatogram (0 = false) |
| assay_rt | string | The retention time at which the peptide (analyte) was expected to elute based on the retention time calibration |
| delta_rt | string | The difference in retention between expected retention time (assay_rt) and peak group retention time (RT) |
| leftWidth | float | Retention time start of the peak (left width) in seconds |
| main_var_xx_swath_prelim_score | float | Preliminary separation for pyProphet initialization |
| norm_RT | string | The position of the peak group in the normalized retention time space (e.g. fx(RT) where fx describes the transformation fx) |
| nr_peaks | int | The number of transitions used |
| peak_apices_sum | float | The sum of the peak apices intensities |
| potentialOutlier | string | Potential outlier transition |
| initialPeakQuality | float | Initial peak quality score (if computing peak quality was enabled) |
| rightWidth | string | Retention time end of the peak (left width) in seconds |
| rt_score | string | sequence |
| sn_ratio | float | Signal-to-Noise ratio |
| total_xic | float | Total XIC |
| var_... | float | A variable used for the post-processing and scoring |
| aggr_prec_Peak_Area | float-list | MS1 Precursor peak area (for each isotope) |
| aggr_prec_Peak_Apex | float-list | MS1 Precursor peak apex (for each isotope) |
| aggr_prec_Annotation | string-list | MS1 Precursor annotation (for each isotope) |
| aggr_Peak_Area | float-list | Fragment ion peak area (for each transition) |
| aggr_Peak_Apex | float-list | Fragment ion peak apex (for each transition) |
| aggr_Fragment_Annotation | string-list | Fragment ion annotation (for each transition) |
| masserror_ppm | string | Fragment-level mass error for each transition (see aggr_Fragment_Annotation for order) |
| rt_fwhm | string | Fragment-level FWHM (full width half maximum) for each individual transition (see aggr_Fragment_Annotation for order) |
Remarks:
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1. 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:
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PEPT(Phosphorylation)IDE(UniMod:27)A )
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2. 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:
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PEPTIDEAK -> gets label "PEPTIDEAK_gr1"
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PEPTIDEAK[+8] -> gets label "PEPTIDEAK_gr1"
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PEPT(Phosphorylation)IDEAK -> gets label "PEPTIDEAK_gr2"
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PEPT(Phosphorylation)IDEAK[+8] -> gets label "PEPTIDEAK_gr2"
1.9.1 
