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.
I’ve installed Msfinder on a linux machine and would like to replicate the results I am getting from windows.
The command: `/usr/local/bin/MsfinderConsole_v350_linux/MsfinderConsoleApp` Produces the expected console help screen with options for mssearch, mspredict, annotate and generate. However, the command: `/usr/local/bin/MsfinderConsole_v350_linux/MsfinderConsoleApp mssearch -i .\mat\ -o .\ -m .\batchparam-2021_3_16_16_2_52.txt` Produces the error message: “error message: the first word must be 'generate' or 'annotate'”
I am new to XCMS Online, but so far nothing seems to be working as expected.
We uploaded 82 .raw files and all appear to be taking up space in our account ranging from 1.5-3 MB. However, only the first 7 are active. Are the rest still uploading (20+ days later) or did they fail a test of some sort?
I then attempted to duplicate the dataset in order to separate control and treatment groups. The status says copying but it still shows 0 files in the cloned dataset after a few hours. How long should this take?
In attempt to resolve some of these issues, I clicked on FAQ under help, resulting in xcmsonline1.scripps.edu refused to connect (chrome) or The server at xcmsonline1.scripps.edu is taking too long to respond (firefox).