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RMassBank Compound Mix Workflow

Usage

Prescreening

1. Generate prescreening data frames,

   presc.do(list.files(path="~/ECI_SCRATCH/20190627_HEROBER",patt=".*.mzML",full.names=T),
            mode="pH",fn_cmpd_l="./cutlist.csv",proc=F,dest=".")
       

   This is to be carried out inside the directory containing the mzML files. For sequential execution, leave out the proc argument.

2. Plot,

   require(rmbmix)
   presc.plot(list.files(".",patt="2.*POS",include.dirs=T),mode="pH",cex=0.7,rt_digits=2,m_digits=4,pal="Dark2",out="prescreen.pdf")
       

   The only argument is a sequence of absolute paths to directories containing the prescreen data. The resulting plot file is going to be placed into the current working directory.

Record generation

The entire sequentual procedure,

pos<-rmbmix::sw.do(list.files(patt=".*pos.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="pH")
pos_pmb<-rmbmix::mb.prep(pos)
pos_mb<-rmbmix::mb.do(pos_pmb)

neg<-rmbmix::sw.do(list.files(patt=".*neg.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="mH")
neg_pmb<-rmbmix::mb.prep(neg)
neg_mb<-rmbmix::mb.do(neg_pmb)
  

The entire parallel procedure,

pos<-rmbmix::sw.do(list.files(patt=".*pos.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="pH",proc=4)
pos_pmb<-rmbmix::mb.prep(pos)
pos_mb<-rmbmix::mb.do(pos_pmb,proc=4)

neg<-rmbmix::sw.do(list.files(patt=".*neg.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="mH",proc=4)
neg_pmb<-rmbmix::mb.prep(neg)
neg_mb<-rmbmix::mb.do(neg_pmb,proc=4)

The fn_cmpd_list argument is the compound list, from Chemistry Dashboard, or in a RMassBank format. The first argument to sw.do is the list of mzML files containing spectral data to be processed using the spectral workflow. Each mzML file should have an associated YAML file with RMassBank settings describing it. The settings file does not need to be complete, it can only contain the settings which are different from the settings template.

Once the spectral workflow is complete, first run the MassBank preparation procedure using mb.prep function. Then, finalise the MassBank record workflow by using the mb.do function.

The resulting record files and info lists are under “<data-dir>/info/XX” paths, where data-dir is the mzML filename without the mzML suffix.