yufree / pmdda

reproducible repo for PMDDA paper

PMDDA

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.

Description

• 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.

• script.html: generated html document from script.Rmd.

• renv folder: using renv package to create the reproducible data analysis environment for this repo.

• doc folder: host script.html as a webpage.

• data folder: MS1 full scan data for five NIST 1950 and five matrix sample in positive mode.

• datan folder: MS1 full scan data for five NIST 1950 and five matrix sample in negative mode.

• 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.

• postar folder: selected precursor ion from different workflow for multiple injection in positive mode.

• negtar folder: selected precursor ion from different workflow for multiple injection in negative mode.

• MS2spectra folder: mgf files for future annotion from different workflow.

• para.RData: the optimized parameters for xcms peak picking from IPO package positive mode.

• paran.RData: the optimized parameters for xcms peak picking from IPO package negative mode.

• srmmzrt.csv: peaks list from MS1 full scan in positive mode.

• srmnmzrt.csv: peaks list from MS1 full scan in negative mode.

• srmxset.rds: xcmsSet object from MS1 full scan in positive mode.

• srmnxset.rds: xcmsSet object from MS1 full scan in negative mode.

• rppmzrt.csv: filtered peaks list based on matrix and rsd% in positive mode.

• rpnmzrt.csv: filtered peaks list based on matrix and rsd% in negative mode.

• posneg.csv: filtered peaks list with connection in positive and negative mode.

• rppanno.csv: molecular networking annotation results from GNPS in positive mode.

• rpnanno.csv: molecular networking annotation results from GNPS in negative mode.

• posneganno.csv: molecular networking annotation results from GNPS for positive and negative mode connection.

• nist1950.csv: known compounds in NIST1950 samples.

• pretar.csv: selected precursor ions from PMDDA in positive mode.

• prentar.csv: selected precursor ions from PMDDA in negative mode.

• cameratar.csv: selected precursor ions from CAMERA in positive mode.

• camerantar.csv: selected precursor ions from CAMERA in negative mode.

• ramclusttar.csv: selected precursor ions from RAMClust in positive mode.

• ramclustntar.csv: selected precursor ions from RAMClust in negative mode.

• rppms1.csv: detected precursor ions from MS2 data in positive mode.

• rpnms2.csv: detected precursor ions from MS2 data in negative mode.

• pmddamzrt.csv: linked MS1 data from PMDDA selected precursor ions MS2 data in positive mode.

• pmddanmzrt.csv: linked MS1 data from PMDDA selected precursor ions MS2 data in negative mode.

• iddamzrt.csv: linked MS1 data from PMDDA selected precursor ions as iterative DDA inclusion list MS2 data in positive mode.

• iddanmzrt.csv: linked MS1 data from PMDDA selected precursor ions as iterative DDA inclusion list MS2 data in negative mode.

• cameramzrt.csv: linked MS1 data from CAMERA selected precursor ions MS2 data in positive mode.

• cameranmzrt.csv: linked MS1 data from CAMERA selected precursor ions MS2 data in negative mode.

• ramclustrmzrt.csv: linked MS1 data from RAMClustR selected precursor ions MS2 data in positive mode.

• ramclustrnmzrt.csv: linked MS1 data from RAMClustR selected precursor ions MS2 data in negative mode.