Fig. 3
From: Cardiovascular proteomics in the era of big data: experimental and computational advances
Common label-free quantification in proteomics studies. Two common label-free quantification approaches in use are based on spectral count (top) and ion intensity (bottom). Top: spectral counting methods leverage the fact that in stochastic shotgun profiling, the frequency of a protein being sampled by the instrument scales with its relative abundance in the sample. The numbers of spectra matched to an identical protein in healthy (green) versus diseased (red) samples can therefore be compared if appropriate normalization and bioinformatics workflows are implemented. Bottom: ion intensity methods integrate the total signal intensity of peptide ion signals in the mass spectrometer to infer protein quantity. Software is now available to automatically identify and quantify peptide ion signals from mass spectra