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.