Missing Peaks Issue when Batch-Processing in Empower 3

edited July 2020 in Informatics

I am seeing a strange issue when I am batch-processing samples in Empower 3. I am using an ApexTrack processing method (let's call it X). When I run a sample set and process it using a method set (i.e. run samples, process using X, and generate a PDF report automatically), I see the integration of peaks as expected (for example, let's say for an SEC chromatogram, you see a small aggregate peak and the main species peak running as expected, with 1% aggregate peak and 99% main peak). However, there are also a few other 'peaks' that show up in the integration in the Review window. The 'Int Type' column for these rows says 'Missing'. They are at random retention times, but none of these peaks are part of the integrated chromatogram and add nothing to the peak area. The PDF report just includes these missing peak retention times as lines on the table. I get the same behavior if I batch process samples after a run in the project window (i.e. right-click-->Process).

However, when I integrate any of these samples individually using the exact same processing method X, these 'missing' peak entries disappear from the table and the integration is still the same as before (1% aggregate peak and 99% main peak). I contacted the Waters phone support and the suggested approach was that perhaps if the sample set was getting interrupted, this may be causing this type of glitch, but running a fresh sample set without interruption does not resolve the issue.

Screenshot is an example.

Does anyone have thoughts on what may be causing this behavior and how to address it?
Lines 4-6 (missing peaks), which also appear in the report.
These lines disappear when processing chromatogram individually


  • Hello
    I do not see your attachment.  If you take the Result set into Review do you see these "missing peaks" or is it only in the PDF of the report?  What do you have in the component table of the processing method?  
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