Issue 621: Change default centroiding value to summed intensity from trapezoidal area

issues
Status:resolved
Assigned To:Brendan MacLean
Type:Todo
Area:Skyline
Priority:2
Milestone:4.3
Opened:2018-12-27 by Brendan MacLean
Changed:2019-04-25 by matt.chambers42
Resolved:2019-04-25 by matt.chambers42
Resolution:Fixed
Closed:
2018-12-27 Brendan MacLean
Title»Change default centroiding value to summed intensity from trapezoidal area
Assigned ToGuest»Brendan MacLean
Notify»david.cox
Type»Todo
Area»Skyline
Priority»2
Milestone»4.3
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.

2019-01-16 matt.chambers42
Assigned ToBrendan MacLean»matt.chambers42@gmail.com

2019-04-25 matt.chambers42
resolve as Fixed
Statusopen»resolved
Assigned Tomatt.chambers42@gmail.com»Brendan MacLean
Fixed in PR #514