Identification of Low Abundance Proteins in Mouse Plasma
(A) Spectral counts (number of MS2-events acquired per protein) in the experiment performed for early stage pancreatic cancer mouse plasma protein (PanIN) were correlated with protein plasma concentration reported by Rules-Based Medicine (http://www.rulesbasedmedicine.com/case3/Table3.htm). The 21 proteins used for this estimation were: Serpina1b, Adipoq, A2m, Apoa1, Apoc3, Apoh, B2m, C3, Ceacam1, Crp, Fabp1, F7, Ftl1, Fgb, Hp, Icam1, Igf1, Mb, Serbp1, Timp1, Vcam1. As an approximation, we estimated the protein concentration with the correlation (log spectral counts = [0.623 × log protein concentration] + 0.0625).
(B) Taking into consideration the correlation of spectral counts and protein concentration, we observed an inverse relationship between the total number of proteins identified and their abundance (number of MS2/proteins).