Are your mass specs trying to tell you something? For my stuff, my current favorite is RawBeans but that's for -omics and I can't imagine it's current iterations would translate well to your high throughput validated targeted assays.
SMACK is an open toolkit that thinks through all the hard stuff that is pretty convenient to not know about when you're out there throwing around words like "translational" about your work. This group is on the ground applying new mass spec assays to patient samples and has to think about these things, and it's beyond cool that they'd make these tools open-source. You can drop $250k on setup plus $40k/year on LIMS systems that don't have trend monitoring capabilities nearly this advanced.
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