|Title||»||Change default centroiding value to summed intensity from trapezoidal area|
|Assigned To||Guest||»||Brendan MacLean|
We need to change the default centroiding mode for SCIEX WIFF file summed intensity from the trapezoidal area mode we currently use. David Cox has requested this repeatedly. The trapezoidal area yields very small numbers because the units end up being ions / per second / Thompson, which is meaningless.
As long as we have an option in msconvert to use the old value, I think we are safe. From a Skyline perspective, we don't really recommend people use centroid mode for directly importing WIFF files, because it is so slow. If you ever decide to re-import a WIFF file in centroid mode, you pay twice for the centroiding calculation. Instead, I have always converted WIFF files to mzML (or mz5, but more recently mostly mzML because of how poorly mz5 behaves under multi-threaded access when the file is on a spinning drive).
So, I don't think we need an option inside Skyline for the current behavior. If anyone notices and complains, we can just recommend they convert their WIFF files to mzML with the backward compatibility argument to msconvert.