All functions 


mass spectrometry contaminants database for PMD check 

Perform correlation directed analysis for peaks list. 

Get reaction chain for specific mass to charge ratio 

Get PseudoSpectrum as peaks cluster based on pmd analysis. 

Get PseudoSpectrum as peaks cluster based on correlation analysis. 

read in MSP file as list for ms/ms annotation 

read in MSP file as list for EIMS annotation 

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

Get pmd for specific reaction 

Link pos mode peak list with neg mode peak list by pmd. 

Perform structure/reaction directed analysis for mass only. 

Get quantitative paired peaks list for specific reaction/pmd 

Perform structure/reaction directed analysis for peaks list. 

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. 

Get multiple injections index for selected retention time 

GlobalStd algorithm with structure/reaction directed analysis 

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

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

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

Compare matrices using PCA similarity factor 

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

Plot the mass pairs and high frequency mass distances 

Plot the retention time group 

Plot the specific structure directed analysis(SDA) groups 

Plot the std mass from GlobalStd algorithm 

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

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

Perform MS/MS pmd annotation for mgf file 

Shiny application for PMD analysis 

Shiny application for PMD network analysis 

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

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