Chromatography Forum

Hello,

I am currently working with a very basic piece of equipment that dumps all data into a Microsoft Excel file with time and emission plotted in two columns. I currently have to sift through the numbers the old fashioned way and was wondering if there is any free/cheap software that can plot the numbers from an excel file and identify the peaks.

Any help is greatly appreciated.

You can plot the chromatogram directly in Excel - choose a scatterplot with lines between the points, but no symbols at the points.

I'm not sure what you mean by identifying the peaks - do you want their areas integrated ?, or a name label printed next to them ?

Peter

Well, i tried graphing in excel but the resolution capabilities are very limited. I stretched the graph out 400 or so cells and the peaks were easily visible but i still had to go through and find them all by scrolling through and manually identifying the peaks. This was also too much for my computer to handle. It was VERY slow. All i need is to identify the time at which the peaks in emission occur. There are 30-40 peaks in each data set and numerous data sets per week.

If you have 30 peaks in each chromatogram, then 1,000 points doesn't give you a lot of working room. Of course, Excel accommodates up to 65k rows, so at 10 Hz, you have enough room for 100+ minutes' worth of chromatography.

It's quite possible to program a "peak picker" in Excel, but you will have to teach yourself a lot about Excel in the process (you are essentially "reinventing the wheel") and the resulting processing *will* be very slow because of the huge overhead involved with such a general-purpose program. I suppose a lot depends on whether you have more time or money!

As to specifics:

Depending on how fast you were acquiring data, you might want to smooth the signal a bit by calculating a running average over some number of data points (you would have to play with your data to find out what works best). A simple "peak picker" would be to look for the first derivative (essentially the difference between successive measurements) to drop down below zero. You could then in essence query the data for those transition points.

It's not going to be as good as a purpose-made data system, but . . .

If the data is not too noisy you might simply be able to subtract each signal value from the preceding value, and then set up a conditional format on whether the difference is positive or negative - in effect a crude way of doing the first derivative as Tom suggested. There are all sorts of reasons why this might not work, but it might be worth a shot.

Peter

....
any free/cheap software that can plot the numbers from an excel file and identify the peaks....

Any help is greatly appreciated.

With R this is easily done (www.R-project.org).
You could setup a function that picks every datafile in a map, process the file and write out the desired results and plots.
Although a steep learning curve, I think it's worth to give it a try.

Ace

Ranimick,

There is no way to get the signal out as a voltage?? Because if there is, there are faster alternatives and they can be very inexpensive. There is an integrator (can be had used for $50), there are data systems as little as $350 and others for as little as $1500.

I use Excel for presentation because I can make the signal nice and fat (and, therefore, visible across the room) but with the number of peaks you are dealing with, you will have your work cut out for you. Still, I appreciate the question because it applies to work I am currently doing.....

Best regards.

I have the same problem. Peakfinder from systat is roughly 600 bucks, and seems to work (ymmv)
The suggestion to use R is not , imho, very helpful - if i knew enough to use R I wouldn't be asking the question in the first place
Igor pro (wavemetrics) may also work.
In any event, I don't think using excel to simply find retention times and peak areas and so forth is a good idea, unless the data is really clean, as (afaik) it actually takes some math to do the baseline correction right.

In any event, I don't think using excel to simply find retention times and peak areas and so forth is a good idea, unless the data is really clean, as (afaik) it actually takes some math to do the baseline correction right.

You're right, but the original post didn't mention areas, merely flagging the peaks, which is a much simpler process -- but still a *lot* of work.

I am having a voltage output in the excel, but I am more concerned about how to get the area underneath the peak. Is there anyone that may know about this? Any suggestions on how to integrate so that I can get an area underneath the peaks?

I actually posted another one in this thread, which contains more information about what I am trying to do.

Thanks a lot!
Have a good night!

Emma :)

Hi,
I think everyone has looked at doing something similar, I am assuming your not in a ISO 17025 Lab, otherwise getting any spreadsheet accepted is going to be a trial.

some links for what you may be interested in.

http://www.duncanwil.co.uk/areacurv.html

http://www.cem.msu.edu/~cem333/POTTITR.html

http://www.jce.divched.org/JCEDLib/WebW ... index.html

http://terpconnect.umd.edu/~toh/spectrum/SPECTRUM.html

viewtopic.php?p=53932&sid=ebeab4028245b ... 9c77a1fd5c
using
viewtopic.php?p=64219&sid=51c8935fc42ee ... 9dda747660

Also, once AMDIS 2.68 , gets fixed and released, it is written to have better algorithm for quantitation, after making a .cdf file with 'R', or maybe learn to use 'R', though i haven't used it myself.

Alex