Package: pmd 0.2.6

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_0.2.6.tar.gz
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pmd_0.2.6.tgz(r-4.4-any)pmd_0.2.6.tgz(r-4.3-any)
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pmd_0.2.6.tgz(r-4.4-emscripten)pmd_0.2.6.tgz(r-4.3-emscripten)
pmd.pdf |pmd.html✨
pmd/json (API)
NEWS

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

Peer review:

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

Datasets:
  • MaConDa - Mass spectrometry contaminants database for PMD check
  • 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
  • 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:

mass-spectrometrymetabolomicsnon-target

6.56 score 9 stars 45 scripts 245 downloads 3 mentions 27 exports 87 dependencies

Last updated 6 months agofrom:ce3d821ea1. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-winOKOct 27 2024
R-4.5-linuxOKOct 27 2024
R-4.4-winNOTEOct 27 2024
R-4.4-macNOTEOct 27 2024
R-4.3-winNOTEOct 27 2024
R-4.3-macNOTEOct 27 2024

Exports:getcdagetchaingetclustergetcorclustergetms2pmdgetmspmdgetpairedgetpmdgetpmddfgetposneggetrdagetreactgetsdagetstdgettargetglobalstdpcasfplotcnplotpairedplotrtgplotsdaplotstdplotstdrtplotstdsdapmdannorunPMDrunPMDnet

Dependencies:animationaskpassbase64encBHBiocParallelbslibcachemclicodetoolscolorspacecpp11crosstalkcurldata.tabledigestdplyrenviGCMSevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphisobandjquerylibjsonlitekernlabknitrlabelinglambda.rlaterlatticelazyevallifecyclemagickmagrittrMASSMatrixmemoisemgcvmimemixtoolsmunsellnlmeopensslpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcppRdisoprlangrmarkdownsassscalessegmentedsnowstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Paired Mass Distance(PMD) analysis for GC/LC-MS based non-targeted analysis

Miao Yu

Rendered fromglobalstd.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2024-04-08
Started: 2018-04-22

Reactomics

Miao Yu

Rendered fromreactomics.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2024-05-30
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 Pseudo-Spectrum as peaks cluster based on pmd analysis.getcluster
Get Pseudo-Spectrum as peaks cluster based on correlation analysis.getcorcluster
read in MSP file as list for ms/ms annotationgetms2pmd
read in MSP file as list for EI-MS annotationgetmspmd
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
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
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.getstd
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
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
Perform MS/MS pmd annotation for mgf filepmdanno
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