I have shared the parameters setting files screenshot here if that helps. I can save the parameter file only as Parameter.med2 but can not upload that type of file here. It would be great to get suggestions from you.
Thanks for your reply and yes, we used accurate mass setting. Also, once I checked the box "only report the top hit" under identification tab, removes the redundancies of many features but not all. I was planning to filter the ion table in excel for the existing duplicates.
We collected metabolomics data using an Agilent GC coupled to a LECO HRT+ TOFMS. We then exported the data as netCDF, converted to .ABF format, and processed in MS-DIAL 4.70. We used a FAME mix to set the Retention Index to aid in peak identification. We were able to obtain library-matched features, but after checking the alignment table, we found redundancies of features identified. That is, the redundant features have the same retention time, same quant mass and are consecutively repeated 3 to 4 times. Additionally, some features have slight differences in retention times (~0.01 minutes) and quant masses but identified as the same metabolite. Reviewing the XIC's for such features shows these are unlikely to be different molecules but poorly aligned. I've attached a snapshot of the alignment table to illustrate what we're seeing. This is the first time we are using MSDIAL to process a large dataset from this LECO HRT+ instrument (we have used it in the past with single quad GC-MS & extensively with LC-MS data without such issues). We suspect a setting in the identification and/or alignment windows to be the culprit of the redundancies, but would appreciate some guidance and suggestions as to how to solve this issue.
Many thanks in advance. We're happy to share our specific processing settings if that would be helpful.