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Other / Peak alignment with large dataset (over 2500 samples and growing)
Dear all,

I am trying to process over 2500 files from a UPLC-QTOF-MS dataset. The goal is to eventually increase this number to 10,000 and beyond. Currently I am using MZmine 2. I am fortunate to have access to a big server (80 core, 350+ GB RAM). However, it seems that the peak alignment step is not optimized for this number of samples. See my other post for more details about this issue:

Any ideas on a more efficient peak alignment method? As far as I can tell, the raw data are already pretty well aligned; the UPLC seems to be fairly consistent. My main objective right now is to get all the samples/peaks into a single matrix.

I am actively trying different approaches, but it all takes time. I am hoping that someone else who has trod this ground before can offer advice to help save time and effort.

Many thanks!