We have a 6430 QQQ instrument with HPLC. We have a very stable LC/MS/MS assay that we've been using the last 10 years. But now when we run a chemical standard in our usual negative mode, the peaks are longer nicely separated; the specified MRMs are instead scattered throughout the entire 8-minute chromatographic run. When we run the same chemical standard in the positive mode, we get very nicely separated peaks at the correct times and with no baseline noise. When we run a full MS2 scan and SIM scan on the same chemical standard in negative mode, we get very nice peaks.
We have excluded any problems on the LC side (even replacing the binary pump). The AutoTune report is fine. We suspect something is wrong with the MRM application but only in negative mode. Our high purity nitrogen gas for the collision cell is full and we replaced the filter.
The only new events that have taken place when we started having issues is: 1) obtained a new Vialsampler, and 2) installed a new electron horn detector multiplier.
Has anyone run into this issue before? We are not sure if the electronics of the QQQ are somehow malfunctioning, therefore falsely detecting our MRM peaks throughout the entire run. Is there a way to check whether the MRM or collision cell are functioning properly?