This has been a long and frustrating journey — and I thank the two kids who have helped me and a retired professor, and other friends and neighbors who have listened to me complain.  The bottom line….

peak finding programs are great at getting rid of noise, but really poor at detecting subtle bilateral peak symmetry

Its almost like I find them unable to get out of their “ruts”, slopes, thresholds, sliding averages for this, and two peaks before this and what about rounded peaks.  Just doesnt work.

Case in point is the enormous number of times I have plotted the same molecule of SP-D and failed to pick up some really tiny peaks beside the N termini junction of a dodecamer, but managed to find 4 peaks on the downslope of the presumed glycosylation peak. I dont doubt for an instant that adding individual molecules to a site in one, two or three strands of a trimer can result in a bumpy elevation, but if the peak finding algorithms find peaks there, then why not the tiny peak burried right beside the very tall, very wide peak for the N termini.  It is like the curse of position.  I could and should at some point determine whether the direction (before or after) the N term peak the tiny peak at the bottom of that valley is ignored or found.  But then it is at the valley between the two largest grayscale peaks in the molecule, right between the glycosylation peak and the N termini peak.  so it is doomed.  And also, not picked up by novice peak finders.  I know this peak is meaningful but how to get it into the peak detection programs is another story.

Symmetry and subtle peaks are just lost in the numbers.