While designing algorithms for C/N isotope labeling analysis, I noticed that findChromPeaks using CentWavePredIsoParam (and the underlying centWaveWithPredIsoROIs algorithm) is somewhat insensitive to certain Nitrogen isotope labeled peaks.
Upon inspecting the source code, I discovered that the algorithm seems to only consider Carbon isotopes ( isotopeDistance <- 1.0033548378 in do_define_isotopes) for predicted isotope ROIs. However, this specific limitation does not appear to be explicitly mentioned in the current documentation.
To improve the usability of the package for stable isotope labeling experiments, I would like to propose two points:
-
Documentation Update
Could you please update the documentation (e.g., the help page for ?CentWavePredIsoParam or related functions) to clearly state that the current implementation is strictly optimized for Carbon isotopes? This would save researchers a lot of time when troubleshooting missing N/O labeled peaks.
-
Feature Enhancement (Optional Parameters for N, O isotopes)
If feasible, it would be extremely helpful to expose an optional parameter (e.g., isotope_mz_diff or a dedicated list of target isotopes) to allow the algorithm to search for other common labels like 15N or 18O. Specifically, adding support for 3rd or 4th rounds of ROI searching targeting these specific mass differences would make findChromPeaks much more robust for multi-isotope tracing studies.
While designing algorithms for C/N isotope labeling analysis, I noticed that
findChromPeaksusingCentWavePredIsoParam(and the underlyingcentWaveWithPredIsoROIsalgorithm) is somewhat insensitive to certain Nitrogen isotope labeled peaks.Upon inspecting the source code, I discovered that the algorithm seems to only consider Carbon isotopes (
isotopeDistance <- 1.0033548378indo_define_isotopes) for predicted isotope ROIs. However, this specific limitation does not appear to be explicitly mentioned in the current documentation.To improve the usability of the package for stable isotope labeling experiments, I would like to propose two points:
Documentation Update
Could you please update the documentation (e.g., the help page for ?
CentWavePredIsoParamor related functions) to clearly state that the current implementation is strictly optimized for Carbon isotopes? This would save researchers a lot of time when troubleshooting missing N/O labeled peaks.Feature Enhancement (Optional Parameters for N, O isotopes)
If feasible, it would be extremely helpful to expose an optional parameter (e.g., isotope_mz_diff or a dedicated list of target isotopes) to allow the algorithm to search for other common labels like 15N or 18O. Specifically, adding support for 3rd or 4th rounds of ROI searching targeting these specific mass differences would make
findChromPeaksmuch more robust for multi-isotope tracing studies.