msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Assess the contribution of the targeted precursor in fragmentation acquired or anticipated isolation windows using a metric called "precursor purity". Also provides simple processing steps (averaging, filtering, blank subtraction, etc) for DI-MS data. Works for both LC-MS(/MS) and DI-MS(/MS) data.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("msPurity")
AuthorThomas N. Lawson, Ralf Weber, Martin Jones, Mark Viant, Warwick Dunn
Bioconductor views MassSpectrometry Metabolomics Software
Date of publicationNone
MaintainerThomas N. Lawson <thomas.nigel.lawson@gmail.com>
LicenseGPL (>= 2)
Version1.0.0

View on Bioconductor

Man pages

assessPuritySingle: Assess the purity of a single LC-MS/MS or DI-MS/MS file

averageSpectra-purityD-method: Using purityD object, calculates to average mz, intensity and...

averageSpectraSingle: Calculates to average mz, intensity and signal-to-noise of...

dimsPredictPurity-purityD-method: Using purityD object, assess anticipated purity from a DI-MS...

dimsPredictPuritySingle: Predict the precursor purity from a DI-MS dataset

filterp-purityD-method: Filter out peaks based on intensity and RSD criteria

frag4feature-purityA-method: Assign precursor purity scored fragmentation spectra to XCMS...

Getfiles: Get files for DI-MS processing

getP-purityD-method: Get peaklist for a purityD object

groupPeaksEx: Group peaklists from a list of dataframes

groupPeaks-purityD-method: Using purityD object, group multiple peaklists by similar mz...

initialize-purityD-method: Constructor for S4 class to represent a DI-MS purityD

purityA: Assess the purity of multiple LC-MS/MS or DI-MS/MS files...

purityD-class: An S4 class to represent a DI-MS purityD

purityX: Assessing anticipated purity of XCMS features from an LC-MS...

show-purityA-method: Show method for purityA class

show-purityD-method: Show method for purityD

show-purityX-method: Show method for purityX

subtractMZ: Subtract MZ values based on ppm tolerance and noise ratio

subtract-purityD-method: Using Subtract MZ values based on ppm tolerance and noise...

validate-purityA-method: Validate precursor purity predictions using LC-MS and...

writeOut-purityD-method: Using purityD object, save peaks as text files

Functions

assessPuritySingle Man page
averageSpectra Man page
averageSpectra,purityD-method Man page
averageSpectraSingle Man page
dimsPredictPurity Man page
dimsPredictPurity,purityD-method Man page
dimsPredictPuritySingle Man page
filterp Man page
filterp,purityD-method Man page
frag4feature Man page
frag4feature,purityA-method Man page
Getfiles Man page
getP Man page
getP,purityD-method Man page
groupPeaks Man page
groupPeaksEx Man page
groupPeaks,purityD-method Man page
initialize,purityD-method Man page
purityA Man page
purityD Man page
purityD-class Man page
purityX Man page
show,purityA-method Man page
show,purityD-method Man page
show,purityX-method Man page
subtract Man page
subtractMZ Man page
subtract,purityD-method Man page
validate Man page
validate,purityA-method Man page
writeOut Man page
writeOut,purityD-method Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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