All functions

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 Pseudo-Spectrum as peaks cluster based on pmd analysis.

getcorcluster()

Get Pseudo-Spectrum 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 EI-MS 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

getpmddf()

Get pmd details for specific reaction after the removal of isotopouge.

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 LC-MS.