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MS-DIAL / Peaks not aligning in MS-Dial without error message
I'm hoping someone might be able to help me solve a problem I'm having with lipidomics data in MS-Dial.
When I process the data to identify the lipids and align the peaks (in negative ion mode), I receive no error messages. However, upon looking at the alignment results, I can see that many of the peaks are not actually aligned (see screenshot), and it seems to be worse the higher the retention time. I have tried increasing the retention time tolerance, but that didn't help. Any advice or suggestions would be much appreciated. I ran this same dataset through positive ion mode and didn't have any issues.
Best,
Christine