Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis
Perform correlation directed analysis for peaks list.
Get reaction chain for specific mass to charge ratio
Get Pseudo-Spectrum as peaks cluster based on pmd analysis.
Get Pseudo-Spectrum as peaks cluster based on correlation analysis.
read in MSP file as list for ms/ms annotation
read in MSP file as list for EI-MS annotation
Filter ions/peaks based on retention time hierarchical clustering, pai...
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 cluster...
Get multiple injections index for selected retention time
GlobalStd algorithm with structure/reaction directed analysis
Compare matrices using PCA similarity factor
plot PMD KEGG network for certain compounds and output network average...
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 g...
Plot the std mass from GlobalStd algorithm in structure directed analy...
Perform MS/MS pmd annotation for mgf file
Shiny application for PMD analysis
Shiny application for PMD network analysis
Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> and PMD based reactomics analysis proposed in Yu and Petrick (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.