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Identification of Low Abundance Proteins in Mouse Plasma

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posted on 2008-06-10, 00:00 authored by Vitor M Faca, Kenneth S Song, Hong Wang, Qing Zhang, Alexei L Krasnoselsky, Lisa F Newcomb, Ruben R Plentz, Sushma Gurumurthy, Mark S Redston, Sharon J Pitteri, Sandra R Pereira-Faca, Renee C Ireton, Hiroyuki Katayama, Veronika Glukhova, Douglas Phanstiel, Dean E Brenner, Michelle A Anderson, David Misek, Nathalie Scholler, Nicole D Urban, Matt J Barnett, Cim Edelstein, Gary E Goodman, Mark D Thornquist, Martin W McIntosh, Ronald A DePinho, Nabeel Bardeesy, Samir M Hanash

(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).