[R] OrgMassSpecR peak area issue

[Claudia Beleites]

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 * Δt 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