Closed YUANMENG-1 closed 7 months ago
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Hi YuanMeng-1,
Shuzhao may be able to provide more detail; but, I can address some of the questions posed here.
Currently there are no tools for auto-optimizing the parameters of asari; however, the only parameter we have found that need to be altered are the mass resolution of the instrument and occasionally the minimum peak intensity and its related params. The latter of which, the autoheight function that already exists in asari appears to do a good job. I personally have not compared SLAW with asari.
I don't have those scripts on me right now (at a conference) but when I get back I will ask.
Outputting MGF or other MS2 data formats is something I intend to implement in the future but there is currently another solution that is in the prototype stage that will achieve the same result. We have a pipeline that wraps asari that can also generate MS2 level annotations but instead of outputting the MGF files explicitly, I'm rescanning the mzML files at annotation time to extract the MS2 data and annotate. The annotations generated by the main asari package are MS1 only but are generated using our khipu package that first collects sets of features suspected to belong to the same compound and annotates them as a unit.
Were you able to get the information you needed? If not or you continue to have problems, please re-open this issue.
1.You have compared asari with xcms, mzmine, msdial in upstream processing, but do you have tools like IPO, autotuner, and SLAW for upstream parameter optimization? After parameter optimization, have you also compared mselectivity, SNR, and cselectivity? Additionally, you mentioned SLAW, which is a tool that includes both parameter optimization and upstream processing. Have you compared it with asari?