This PR introduces changes how PyProphet can export the results to legacy and matrix formats:
The parameter max_rs_peakgroup_qvalue is now by default set to 0.05. This means results will only be exported (for both OpenSWATH and IPF modes) if the run-specific MS2 peak group q-value is below 0.05. A benefit here is that the results on matrix and legacy formats are consistent. However, this threshold might be too strict for TRIC and we might want to change this.
If transition-level scoring was conducted, all results will now be exported, even if the transitions were not separately quantified for some. This can be useful for TRIC.
IPF results can alternatively be exported in an "augmented" mode. This is similar to how MaxQuant and other tools report site-localization results. The parameter ipf_max_peptidoform_pep is by default set to 0.4. By default, this excludes ambiguous cases, which is especially important for the matrix report.
This PR introduces changes how PyProphet can export the results to legacy and matrix formats:
max_rs_peakgroup_qvalueis now by default set to0.05. This means results will only be exported (for both OpenSWATH and IPF modes) if the run-specific MS2 peak group q-value is below 0.05. A benefit here is that the results on matrix and legacy formats are consistent. However, this threshold might be too strict for TRIC and we might want to change this.ipf_max_peptidoform_pepis by default set to0.4. By default, this excludes ambiguous cases, which is especially important for the matrix report.