Square nm for peak areas: one hexamer of SP-D compared using CorelDRAW and Octave

The very pedestrian calculation of nm sq using a graphics program (which takes a few minutes) versus using Octave autofindpeaks.m is compared.  The values (except for a couple) are pretty close.  If i use the graphics program cut and pasting i can choose my own vertical lines for counting sq nm, but the data from octave are returned in a nice excel file. The problem is that If i disagree with the count and positions of the peaks then that is disconcerting (eg, the peak i colored green in the octave plot (peak 5) has a nm sq that looks totally out of line.  Why would it be 1105 while the peak beside it is only 922. So there is a calculation based on slope and stuff that i dont understand and would like not to use.

In addition, what i have not figured out how to do is to average in a baseline which is a predictable arch, going from CRDs on each end of the plot upwards just slightly to be at its highest under the N termini junction. I can delete grid from that part of the plot in the graphics program quite easily….. but have no clue how to do that in Octave.

I think i am going to step away from the peak area and just count peaks on either side of the N.  (which btw, i am predicting a small peak between the N termini junction and the glycosylation peak (in this case peaks 4 and 7 would be the latter,  peaks 5 and the peak to the right side of N termini junction that i chose to count.

The double peaks of the CRD are so clearly a result of different positions of the intividual trimer CRD, and so easily predictable as a tall peak before the tiny peak in the adjacent presumed (probably not neck) collagen-like domain that I would not give those individual numbers.  Octave wont separate them. Peaks 10 and 11 in Octave should be counted as a single peak.

Purpose: to find reliable ways to use image and signal processing together to suggest structural characteristics for proteins.