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Collecting data is one thing, however sometimes one needs to plot or analyse data at a later date when access to the original software may no longer be feasible or possible.

Open Source software is at times a good alternative to commercial products. In this case, please list open source and/or free software for gas chromatography. (Having said that, the databases for mass spectrometry are not open as far as I am aware, though suggestions are also welcome.)

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One software that I have come across and used is OpenChrom https://www.openchrom.net/

At least for basic tasks it performs well as far as I can tell.

For those seeking pretty chromatograms, OpenChrom can be used in conjunction with R. Open a plot in OpenChrom, export it to a csv file and then plot the data using R.

A script for plotting two overlapped chromatograms in R is below:

filename = "Dodecane-Neat"
filename2 = "Dodecane-Stressed"
PlotTitle = "Dodecane Neat Chromatogram - Pre and Post Test"

infilename = paste0("./",paste(filename,"csv",sep="."))
infilename2 = paste0("./",paste(filename2,"csv",sep="."))
outfilename = paste(filename,"pdf",sep="-rect.")

## Read Data -> File is called 14mielczarek11.csv
undiluted <- read.table(infilename, sep=";", header=TRUE, nrows=10000)
undiluted2 <- read.table(infilename2, sep=";", header=TRUE, nrows=10000)
## Work out Total Peak (want the Chromatogram, not the mass spec)
undiluted$peaks <- rowSums( undiluted[,3:404] )
undiluted2$peaks <- rowSums( undiluted2[,3:404] )

GCxx <- c(undiluted$RT.milliseconds./1000/60, rev(undiluted$RT.milliseconds./1000/60))
GCyy <- c(rep(0, nrow(undiluted)), rev(undiluted$peaks)/max(undiluted$peaks))
GCxx2 <- c(undiluted2$RT.milliseconds./1000/60, rev(undiluted2$RT.milliseconds./1000/60))
GCyy2 <- c(rep(0, nrow(undiluted2)), rev(undiluted2$peaks)/max(undiluted2$peaks))

library(survival)
library(Hmisc)

# A4 is 8.27 × 11.7 
pdf(outfilename, height=5, width=8)
par(mar=c(5,5,3,2))

plot("",
tck=-0.02,lab=c(10,10,4),las=1,
xaxs="i",xlab="Time (min)",
xlim=c(0,15),
yaxs="i",ylab="Detector Count Fraction",
ylim=c(0,0.15)
)

polygon(GCxx2+0.017, GCyy2, col= rgb(0,0,1,0.5), border=NA) #Blue - Shift the blue ever so slightly to properly overlap
polygon(GCxx, GCyy, col= rgb(1,1,1,1), border=NA) # White (so we don't get violet)
polygon(GCxx, GCyy, col= rgb(1,0,0,0.6), border=NA) # Red

lines(undiluted2$RT.milliseconds./1000/60+0.017,undiluted2$peaks/max(undiluted2$peaks),
type="l",col=4,lwd="0.05",lty=1) #Blue
lines(undiluted$RT.milliseconds./1000/60,undiluted$peaks/max(undiluted$peaks),
type="l",col=2,lwd="0.05",lty=1) # Red

title(PlotTitle)
minor.tick(nx=5, ny=5, tick.ratio=0.3)

dev.off()

And the results:

Dodecane pre and post test - magnified view of the "interesting region".

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  • $\begingroup$ R is a great suggestion, though I hardly believe this code will be useful to anyone else the way it is. With this amount of detail for limits, data transformation and such, it's probably better to plot the bare chromatogram x/y values with lines and let people do the adjustments themselves. $\endgroup$ – Molx Jul 26 '15 at 21:14
  • $\begingroup$ @Molx Yes, people who want to plot their own would need to adjust the limits of course - I would have thought that is obvious? Maybe one could write an automatic function - however if this is possible I wouldn't know how to do this. $\endgroup$ – DetlevCM Jul 27 '15 at 9:06

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