waters_connect processing issue with imported MassLynx data - WKB255965

SYMPTOMS

• After importing MassLynx data into UNIFI and opening the resulting sample set, peaks are clearly seen in the Investigate view
• After processing the data in UNIFI, there are no component peaks identified in the analysis from the sample set
• The processing log for this analysis shows the following message for each sample: "There is no PLG processing required"

ENVIRONMENT

• UNIFI/waters_connect
• Imported MassLynx data

CAUSE

The MassLynx MSe data was acquired in centroid mode. The peak detection in UNIFI uses continuum MSe. The low energy and high energy thresholds in UNIFI's 3D detection are actually peak volume settings, not peak height, and, because centered peaks have zero volume, they cannot be detected by UNIFI 3D peak detection processing. Because it sees no 3D peaks that it can work with, the software gives the "No PLG processing required" message.

FIX or WORKAROUND

The only way to resolve this is to reacquire the data using a MassLynx method for Continuum MSe with lock mass acquired but not applied, and then import that data into waters_connect/UNIFI for processing.

ADDITIONAL INFORMATION