LC-MS/MS raw spectral data processing got stuck at database searching

MetaboAnalyst
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1

I’m running the tutorial example for processing LC-MS/MS raw spectral data with MetaboAnalystR. I’m using the exact example provided at LC-MS/MS Raw Spectral Data Processing. I only changed database directory and adjusted core numbers to make sure it runs on my machine.

The script runs fine but was stuck at PerformDBSearchingBatch. It showed “==== Database searching against MS2ID_Bio_v09102023.sqlite started ====…” but never passed that. Both CPU and RAM were busy. The longest time I ran was 2 days, but nothing changed. Is it supposed to take this long?

My computer has Core i7-12700H and 32G RAM with Windows 11 and R 4.2.2. I hope you can help me diagnose the issue. Thanks!

2

Never mind. I benchmarked with a much smaller database. The program ran just fine. I guess I need to run it on an HTC.

3

Hello. I am new to this, and I had the same problem as described, and coincidentally my computer has similar specs. For anyone who has successfully run the PerformDBSearchingBatch step, how long did it take and what kind of computer system did you use. Any insights would be appreciated. Thanks!