Hello! I am having an issue with the OrgMassSpecR package. I run my HPLC using a DAD detector. My raw data is exported form chemstation as a csv file. I then upload the csv into Rstudio no problem. Using the DrawChromatogram function, I get a nice chromatogram, and my retention time, peak area, and apex intensity values are given as well. The problem comes with the peak area value given. The peak area is much smaller than a value that would make sense. My peak area value is actually less than my apex intensity value. Is this because I am using a DAD detector rather than an MS? If so, is there a simply way to edit the peak area equation so that it will also work with absorbance values? Any help is greatly appreciated. Thanks for your time. Chris Beaver [[alternative HTML version deleted]]
If you type DrawChromatogram you can see the method used to calculate the peak
area. Looks to me like you could easily hack it if you wanted. The relevant
part about peak areas is this:
for (j in 1:n) {
k <- (j%%n) + 1
x[j] <- peakTime[j] * peakIntensity[k] - peakTime[k] *
peakIntensity[j]
}
peakArea[i] <- abs(sum(x)/2)
which looks pretty standard to me, though I'm not clear right off the top of
my head why they are dividing by 2. You can always contact the maintainer.
Bryan
On Mar 18, 2013, at 1:34 PM, Christopher Beaver <christopher.beaver at
gmail.com> wrote:
> Hello!
>
> I am having an issue with the OrgMassSpecR package. I run my HPLC using a
> DAD detector. My raw data is exported form chemstation as a csv file. I
> then upload the csv into Rstudio no problem. Using the DrawChromatogram
> function, I get a nice chromatogram, and my retention time, peak area, and
> apex intensity values are given as well.
>
> The problem comes with the peak area value given. The peak area is much
> smaller than a value that would make sense. My peak area value is actually
> less than my apex intensity value. Is this because I am using a DAD
> detector rather than an MS? If so, is there a simply way to edit the peak
> area equation so that it will also work with absorbance values?
>
> Any help is greatly appreciated.
>
> Thanks for your time.
>
> Chris Beaver
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Hi Chris,> I am having an issue with the OrgMassSpecR package. I run my HPLC > using a DAD detector.You are on a statistics IDE related mailing list. Have mercy with people from other fields and tell them that you are using a diode array to measure UV/VIS absorption. (And possibly let them know that you expect the absorbance A = lg I_0 - lg I ~ c.)> My raw data is exported form chemstation as a > csv file. I then upload the csv into Rstudio no problem. Using the > DrawChromatogram function, I get a nice chromatogram, and my > retention time, peak area, and apex intensity values are given as > well. > > The problem comes with the peak area value given. The peak area is > much smaller than a value that would make sense.How do you know that (see next comment)?> My peak area value is actually less than my apex intensity value.This is not a good criterion to determine what area value would actually make sense: area and intensity have different units! Possible solution: a glance on the code in DrawChromatogram reveals that really the polygon area is calculated (as the manual specifies). Thus the area will be in counts*s or counts*min, and of course 1 count*min = 60 counts*s. How long does your analyte take to elute? Unless it is > 2 min (if time is in min) or > 2 s (for time scale in s), the numeric value of the area should be < A_max (approximating the peak as triangule). Your apex (max) absorbance should ideally be a bit below 1, so a rough guesstimate for peak area would be 1/2 A_max * ?t which will be quite below 1 if you measure time in minutes. If you detect by mass spec, you get ion counts which are large numbers, so areas are likely to be > 1 (regardless of min or s time scale).> Is this because I am> using a DAD detector rather than an MS? If so, > is there a simply way to edit the peak area equation so that it will > also work with absorbance values?Most probably you just want to get your units right! Hope that helps, Claudia PS: for future questions of this sort, you may want to consider asking on stackoverflow.com (or chemistry.stackexchange.com) where you can post nicely formatted code, calculation results and images with your question. -- Claudia Beleites Spectroscopy/Imaging Institute of Photonic Technology Albert-Einstein-Str. 9 07745 Jena Germany email: claudia.beleites at ipht-jena.de phone: +49 3641 206-133 fax: +49 2641 206-399