Qualitative and quantitative analysis of contaminants are the core of the Environmental Science. GC/LC-MS might be one of the most popular instruments for such analytical methods. Previous works such as xcms
were developed for GC-MS data. However, such packages have limited functions for environmental analysis. In this package. I added functions for various GC/LC-MS data analysis purposes used in environmental analysis. Such feature could not only reveal certain problems, but also help the user find out the unknown patterns in the dataset of GC/LC-MS.
GC/LC is used for separation and MS is used for detection in a GC/LC-MS system. The collected data are intensities of certain mass at different retention time. When we perform analysis on certain column in full scan mode, the counts of different mass were collected in each scan. The dwell time for each scan might only last for 500ms or less. Then the next scan begins with a different retention time. Here we could use a matrix to stand for those data. Each column stands for each mass and row stands for the retention time of that scan. Such matrix could be treated as time series data. In this package, we treat such data as matrix
type.
For high-resolution MS, building such matrix is tricky. We might need to bin the RAW data to make alignment for different scans into a matrix. Such works could be done by xcms
.
When you perform a selected ions monitor(SIM) mode analysis, only few mass data were collected and each mass would have counts and retention time as a time series data. In this package, we treat such data as data.frame
type.
You could use getmd
to import the mass spectrum data as supported by xcms
and get the profile of GC-MS data matrix. mzstep
is the bin step for mass:
data <- enviGCMS:::getmd('data/data1.CDF', mzstep = 0.1)
You could also subset the data by the mass(m/z 100-1000) or retention time range(40-100s) in getmd
function:
data <- enviGCMS:::getmd(data,mzrange=c(100,1000),rtrange=c(40,100))
You could also combined the mass full-scan data with the same range of retention time by cbmd
:
data <- cbmd(data1,data2,data3)
You could plot the Total Ion Chromatogram(TIC) for certain RT and mass range.
plottic(data,rt=c(3.1,25),ms=c(100,1000))
You could also plot the mass spectrum for certain RT range. You could use the returned MSP files for NIST search:
plotrtms(data,rt=c(3.1,25),ms=c(100,1000))
The Extracted Ion Chromatogram(EIC) is also support by enviGCMS
and the returned data could be analyzed for molecular isotopes:
plotmsrt(data,ms=500,rt=c(3.1,25))
You could use plotms
or plotmz
to show the heatmap or scatter plot for LC/GC-MS data, which is very useful for exploratory data analysis.
plotms(data) plotmz(data)
You could change the retention time into the temperature if it is a constant speed of temperature rising process. But you need show the temperature range.
plott(data,temp = c(100,320))
enviGCMS
supplied many functions for decreasing the noise during the analysis process. findline
could be used for find line of the boundary regression model for noise. comparems
could be used to make a point-to-point data subtraction of two full-scan mass spectrum data. plotgroup
could be used convert the data matrix into a 0-1 heatmap according to threshold. plotsub
could be used to show the self background subtraction of full-scan data. plotsms
shows the RSD of the intensity of full scan data. plothist
could be used to find the data distribution of the histogram of the intensities of full scan data.
Some functions could be used to calculate the molecular isotope ratio. EIC data could be import into GetIntergration
and return the information of found peaks. Getisotoplogues
could be used to calculate the molecular isotope ratio of certain molecular. Some shortcut function such as batch
and qbatch
could be used to calculate molecular isotope ratio for multiple and single molecular in EIC data.
enviGCMS
supply function to perform Quantitative analysis for short-chain chlorinated paraffins(SCCPs) with Q-tof data. Use getsccp
to make Quantitative analysis for SCCPs.
If you want a graphical user interface for SCCPs analysis, a shiny application is developed in this package. You could use runsccp()
to power on the application in a browser.
In environmental non-target analysis, when multiple samples are collected, problem will raise from the heterogeneity among samples. For example, retention time would shift due to the column. In those cases, xcms
package could be used to get a peaks list across samples within certain retention time and m/z. enviGCMS
package has some wrapped function to get the peaks list. Besides, some specific functions such as group comparison, batch correction and visualization are also included.
xcms
packagegetdata
could be used to get the xcmsSet
object in one step with optimized methods
getdata2
could be used to get the XCMSnExp
object in one step with optimized methods
getmzrt
could get a list as mzrt
object with peaks list, mz, retention time and class of samples from xcmsSet
/XCMSnExp
object. You could also save related xcmsSet
and xcmsEIC
object for further analysis. It also support to output the file for metaboanalyst, xMSannotator, Mummichog pathway analysis and paired mass distance(PMD) analysis.
getmzrtcsv
could read in the csv files and return a list for peaks list as mzrt
object
getimputation
could impute NA in the peaks list.
getfilter
could filter the data based on row and column index.
getdoe
could filter the data based on rsd and intensity and generate group mean, standard deviation, and group rsd.
getpower
could compute the power for known peaks list or the sample numbers for each peak
getoverlappeak
could get the overlap peaks by mass and retention time range for two different list objects
plotmr
could plot the scatter plot for peaks list with threshold
plotmrc
could plot the differences as scatter plot for peaks list with threshold between two group of data
plotrsd
could plot the rsd influences of data in different groups
gifmr
could plot scatter plot for peaks list and output gif file for multiple groups
plotpca
could plot pca score plot
plothm
could plot heatmap
plotden
could plot density of multiple samples
plotrla
could plot Relative Log Abundance (RLA) plots
plotridges
could plot Relative Log Abundance Ridge (RLAR) plots
In general, enviGCMS
could be used to explore single data or peaks list from GC/LC-MS and extract certain patterns in the data with various purposes.
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