Package: pmd 0.3.0

Miao YU

pmd: Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics 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.

Authors:Miao YU [aut, cre]

pmd_0.3.0.tar.gz
pmd_0.3.0.zip(r-4.7)pmd_0.3.0.zip(r-4.6)pmd_0.3.0.zip(r-4.5)
pmd_0.3.0.tgz(r-4.6-any)pmd_0.3.0.tgz(r-4.5-any)
pmd_0.3.0.tar.gz(r-4.7-any)pmd_0.3.0.tar.gz(r-4.6-any)
pmd_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pmd/json (API)

# Install 'pmd' in R:
install.packages('pmd', repos = c('https://yufree.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yufree/pmd/issues

Pkgdown/docs site:https://yufree.github.io

Datasets:
  • 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
  • MaConDa - Mass spectrometry contaminants database for PMD check
  • omics - A dataframe containing multiple reaction database ID and their related accurate mass pmd and related reactions
  • 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.

On CRAN:

Conda:

mass-spectrometrymetabolomicsnon-target

6.26 score 12 stars 51 scripts 262 downloads 3 mentions 31 exports 24 dependencies

Last updated from:055816392e. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK156
source / vignettesOK215
linux-release-x86_64OK147
macos-release-arm64OK101
macos-oldrel-arm64OK94
windows-develOK123
windows-releaseOK126
windows-oldrelOK109
wasm-releaseOK106

Exports:getcdagetchaingetchainseqgetcorpseudospectrumgethomologgetms2pmdgetmspmdgetnsegetpairedgetpmdgetpmddfgetposneggetpseudospectrumgetrdagetreactgetsdagetsimgetstdgettargetglobalstdparse_pmd_patternpcasfplotcnplotpairedplotrtgplotsdaplotstdplotstdrtplotstdsdarunPMDrunPMDnet

Dependencies:BHBiocParallelclicodetoolscpp11data.tableenviGCMSformatRfutile.loggerfutile.optionsglueigraphlambda.rlatticelifecyclemagrittrMatrixpkgconfigRColorBrewerRcppRdisoprlangsnowvctrs

Paired Mass Distance(PMD) analysis for GC/LC-MS based non-targeted analysis
Introduction of Paired Mass Distance analysis | PMD from the same compound | PMD from different compounds | Data format | GlobalStd algorithm | STEP1: Retention time hierarchical clustering | STEP2: Relationship among adducts, neutral loss, isotopologues and common fragments ions | STEP3: Screen the independent peaks | Extra filter with correlation coefficient cutoff | Validation by principal components analysis(PCA) | Comparison with other pseudo spectra extraction method | Benchmark different datasets by Normalized Spectral Entropy (Sample Consistency Metric) | Structure/Reaction directed analysis | Structure/reaction directed analysis for peaks/compounds only data | Wrap function for GlobalStd algorithm | Use independent peaks for MS/MS validation (PMDDA) | Shiny application | Conclusion
Rendered fromglobalstd.Rmdusingknitr::rmarkdown

Last update: 2026-04-22
Started: 2018-04-22

Reactomics
PMD network analysis | Shiny application | Tracing specific reaction paths and homologous series | Source appointment | Biomarker reaction | Reactomics analysis for MS only data | PMD Reaction Database
Rendered fromreactomics.Rmdusingknitr::rmarkdown

Last update: 2026-04-22
Started: 2020-08-12

Readme and manuals

Help Manual

Help pageTopics
Perform correlation directed analysis for peaks list.getcda
Get reaction chain for specific mass to charge ratiogetchain
Get reaction pathway chains matching an ordered PMD pattern with quantifiersgetchainseq
Get Pseudo-Spectrum as peaks cluster based on correlation analysis.getcorpseudospectrum
Find homologous series by a repeating PMD unitgethomolog
read in MSP file as list for ms/ms annotationgetms2pmd
read in MSP file as list for EI-MS annotationgetmspmd
Calculate Normalized Spectral Entropy (NSE)getnse
Filter ions/peaks based on retention time hierarchical clustering, paired mass distances(PMD) and PMD frequency analysis.getpaired
Get pmd for specific reactiongetpmd
Get pmd details for specific reaction after the removal of isotopouge.getpmddf
Link pos mode peak list with neg mode peak list by pmd.getposneg
Get Pseudo-Spectrum as peaks cluster based on correlation analysis.getpseudospectrum
Perform structure/reaction directed analysis for mass only.getrda
Get quantitative paired peaks list for specific reaction/pmdgetreact
Perform structure/reaction directed analysis for peaks list.getsda
Evaluate the similarity of two matrices or dataframesgetsim
Identify standard ions through retention time clustering and PMD relationshipsgetstd
Get multiple injections index for selected retention timegettarget
GlobalStd algorithm with structure/reaction directed analysisglobalstd
A dataframe containing HMDB with unique accurate mass pmd with three digits frequency larger than 1 and accuracy percentage larger than 0.9.hmdb
A dataframe containing reaction related accurate mass pmd and related reaction formula with KEGG IDkeggrall
mass spectrometry contaminants database for PMD checkMaConDa
A dataframe containing multiple reaction database ID and their related accurate mass pmd and related reactionsomics
Parse a PMD pattern string into a list of step specsparse_pmd_pattern
Compare matrices using PCA similarity factorpcasf
plot PMD KEGG network for certain compounds and output network average distance and degreeplotcn
Plot the mass pairs and high frequency mass distancesplotpaired
Plot the retention time groupplotrtg
Plot the specific structure directed analysis(SDA) groupsplotsda
Plot the std mass from GlobalStd algorithmplotstd
Plot the std mass from GlobalStd algorithm in certain retention time groupsplotstdrt
Plot the std mass from GlobalStd algorithm in structure directed analysis(SDA) groupsplotstdsda
Shiny application for PMD analysisrunPMD
Shiny application for PMD network analysisrunPMDnet
A dataset containing common Paired mass distances of substructure, ions replacements, and reactionsda
A peaks list dataset containing 9 samples from 3 fish with triplicates samples for each fish from LC-MS.spmeinvivo