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Topic: level 1 identification (best and/or fast practices) (Read 73 times) previous topic - next topic

level 1 identification (best and/or fast practices)


Still trying to figure out how to ask good questions in this informatic space...  :)

Does anyone use nist mspepsearch (batch mode) for level 1 feature identification in a non-targeted workflow? How about COSS? I was initially wanting to use the former, but can't seem to find a good tutorial/example for the command-line.
What do y'all use for this task? I'd like to use something command-line (something linux/dockerized would be even better)! I am also pretty amenable to R. my output features are in individual .msp and .mat files output from RamClustR::do.find.main. As I understand it, this wraps and applies some heuristics to CAMERA for identifying the precursor ion and adduct. Our in-house spectral library is in a single msp file. But I'd like to use a larger reference to see if our in-house spectra will be higher scoring matches to 'knowns' within the same compound, if that makes sense. I have used MS-DIAL's functionality as part of their larger workflow, but don't think there is a way to use that tool just for spectral search apart from peak-detection, deconvolution and alignment.