How to select appropriate peaks from ClinPro Tools?

Question

I am a researcher of Proteomics. I have several questions while I use ClinPro Tools.

1) Suppose I set peak range from 1000-5000, I got 3 potential candidates with ROC>0.7,
while I set peak range from 1000-10000, I got the same 3 peaks but there are subtle difference in the ROC values of these 3 peaks. I want to ask why would this difference come from normalization process, if it was due to normalization, and why normalization would have influence on this?

Should I also choose potential candidate with ROC values > 0.6 for further ID to avoid potential candidate loss?

2) I have 4 groups A.B.C.D, and A is the study group, B, C, D are all the control. If I want to disease makers of A, which method is better and appropriate:

a) Load A.B.C.D separately, and using ClinPro Tools.
b) Combine B.C.D as a group , and load A and B/C/D, then using ClinPro Tools. Would it be different and why?

Answer 1

There is a study which handles the peaks calculation regarding this software. The calculation and tables are explained and listed as being available. Access the NIH Public Access website to read about it. It's possible that all your questions are answered within document.

Access the study here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516368/