sda

mass spectrometry contaminants database for PMD check 
getcda()

Perform correlation directed analysis for peaks list. 
getchain()

Get reaction chain for specific mass to charge ratio 
getcluster()

Get PseudoSpectrum as peaks cluster based on pmd analysis. 
getcorcluster()

Get PseudoSpectrum as peaks cluster based on correlation analysis. 
getms2pmd()

read in MSP file as list for ms/ms annotation 
getmspmd()

read in MSP file as list for EIMS annotation 
getpaired()

Filter ions/peaks based on retention time hierarchical clustering, paired mass distances(PMD) and PMD frequency analysis. 
getpmd()

Get pmd for specific reaction 
getposneg()

Link pos mode peak list with neg mode peak list by pmd. 
getrda()

Perform structure/reaction directed analysis for mass only. 
getreact()

Get quantitative paired peaks list for specific reaction/pmd 
getsda()

Perform structure/reaction directed analysis for peaks list. 
getstd()

Find the independent ions for each retention time hierarchical clustering based on PMD relationship within each retention time cluster and isotope and return the index of the std data for each retention time cluster. 
gettarget()

Get multiple injections index for selected retention time 
globalstd()

GlobalStd algorithm with structure/reaction directed analysis 
hmdb

A dataframe containing HMDB with unique accurate mass pmd with three digits frequency larger than 1 and accuracy percentage larger than 0.9. 
keggrall

A dataframe containing reaction related accurate mass pmd and related reaction formula with KEGG ID 
omics

A dataframe containing multiple reaction database ID and their related accurate mass pmd and related reactions 
pcasf()

Compare matrices using PCA similarity factor 
plotcn()

plot PMD KEGG network for certain compounds and output network average distance and degree 
plotpaired()

Plot the mass pairs and high frequency mass distances 
plotrtg()

Plot the retention time group 
plotsda()

Plot the specific structure directed analysis(SDA) groups 
plotstd()

Plot the std mass from GlobalStd algorithm 
plotstdrt()

Plot the std mass from GlobalStd algorithm in certain retention time groups 
plotstdsda()

Plot the std mass from GlobalStd algorithm in structure directed analysis(SDA) groups 
pmdanno()

Perform MS/MS pmd annotation for mgf file 
runPMD()

Shiny application for PMD analysis 
runPMDnet()

Shiny application for PMD network analysis 
sda

A dataset containing common Paired mass distances of substructure, ions replacements, and reaction 
spmeinvivo

A peaks list dataset containing 9 samples from 3 fish with triplicates samples for each fish from LCMS. 