Batmode ignores Retention Length

[Annika W]

Dear MQL team,

I'm trying to set up the MQL run using the Batmode - targeting. 

Thusfar I'm having problems setting it up both for the Targeted MS2 and SIM scan set ups. It ignores the retention length I assigned my peptides, and starts measuring when I start my run, and then seems to go through my targeting list, ignoring the retention length, from top to bottom. 

Could it be that the Batmode only works with RealtimeCorrection enabled? That wouldn't be a problem for the final application, but I wanted to test different MQL set ups (1. SIM + TargetLabeled, 2. TargetedMs2 with a targeting list that includes the heavy and light masses sequentially) all with Batmode enabled. I wanted to run every method a couple of minutes without HPLC, to check if the scans are what I expect them to be, and to double check if I need to adjust the IT etc. But unfortunately the targeting behaves unexpectedly. Would love some support! 

I'm looking at my raw.files using the Thermo Scientific FreeStyle. Measuring on HF-X, using MQL version 1.0.

With kind regards,