This repo is for 'Reproducible untargeted metabolomics data analysis workflow for exhaustive MS/MS annotation'. To access standalone PMDDA workflow, please install rmwf package from GitHub and use rmarkdown::draft("test.Rmd", template = "PMDDA", package = "rmwf") to create a reproducible workflow document for your own studies. Such workflow is also available through xcmsrocker project.
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script.Rmd: the reproducible documents for the paper with all of the details. Some of the files in this repo is generated by this document.
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script.html: generated html document from script.Rmd.
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renv folder: using
renvpackage to create the reproducible data analysis environment for this repo. -
doc folder: host script.html as a webpage.
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data folder: MS1 full scan data for five NIST 1950 and five matrix sample in positive mode.
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datan folder: MS1 full scan data for five NIST 1950 and five matrix sample in negative mode.
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MS2 folder: MS2 data for this study. Due to the size limitation of GitHub, you can download those data via the code in script.Rmd.
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postar folder: selected precursor ion from different workflow for multiple injection in positive mode.
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negtar folder: selected precursor ion from different workflow for multiple injection in negative mode.
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MS2spectra folder: mgf files for future annotion from different workflow.
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para.RData: the optimized parameters for
xcmspeak picking fromIPOpackage positive mode. -
paran.RData: the optimized parameters for
xcmspeak picking fromIPOpackage negative mode. -
srmmzrt.csv: peaks list from MS1 full scan in positive mode.
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srmnmzrt.csv: peaks list from MS1 full scan in negative mode.
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srmxset.rds: xcmsSet object from MS1 full scan in positive mode.
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srmnxset.rds: xcmsSet object from MS1 full scan in negative mode.
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rppmzrt.csv: filtered peaks list based on matrix and rsd% in positive mode.
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rpnmzrt.csv: filtered peaks list based on matrix and rsd% in negative mode.
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posneg.csv: filtered peaks list with connection in positive and negative mode.
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rppanno.csv: molecular networking annotation results from GNPS in positive mode.
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rpnanno.csv: molecular networking annotation results from GNPS in negative mode.
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posneganno.csv: molecular networking annotation results from GNPS for positive and negative mode connection.
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nist1950.csv: known compounds in NIST1950 samples.
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pretar.csv: selected precursor ions from PMDDA in positive mode.
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prentar.csv: selected precursor ions from PMDDA in negative mode.
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cameratar.csv: selected precursor ions from CAMERA in positive mode.
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camerantar.csv: selected precursor ions from CAMERA in negative mode.
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ramclusttar.csv: selected precursor ions from RAMClust in positive mode.
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ramclustntar.csv: selected precursor ions from RAMClust in negative mode.
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rppms1.csv: detected precursor ions from MS2 data in positive mode.
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rpnms2.csv: detected precursor ions from MS2 data in negative mode.
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pmddamzrt.csv: linked MS1 data from PMDDA selected precursor ions MS2 data in positive mode.
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pmddanmzrt.csv: linked MS1 data from PMDDA selected precursor ions MS2 data in negative mode.
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iddamzrt.csv: linked MS1 data from PMDDA selected precursor ions as iterative DDA inclusion list MS2 data in positive mode.
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iddanmzrt.csv: linked MS1 data from PMDDA selected precursor ions as iterative DDA inclusion list MS2 data in negative mode.
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cameramzrt.csv: linked MS1 data from CAMERA selected precursor ions MS2 data in positive mode.
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cameranmzrt.csv: linked MS1 data from CAMERA selected precursor ions MS2 data in negative mode.
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ramclustrmzrt.csv: linked MS1 data from RAMClustR selected precursor ions MS2 data in positive mode.
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ramclustrnmzrt.csv: linked MS1 data from RAMClustR selected precursor ions MS2 data in negative mode.