title: Can "normal" protein expression ranges be estimated with high-throughput proteomics?
abstract: Although biological science discovery often involves comparing conditions to a normal state, in proteomics little is actually known about normal. Two Human Proteome studies featured in Nature offer new insights into protein expression and an opportunity to assess how high-throughput proteomics measures normal protein ranges. We use data from these studies to estimate technical and biological variability in protein expression and compare them to other expression data sets from normal tissue. Results show that measured protein expression across same-tissue replicates vary by ±4- to 10-fold for most proteins. Coefficients of variation (CV) for protein expression measurements range from 62% to 117% across different tissue experiments; however, adjusting for technical variation reduced this variability by as much as 50%. In addition, the CV could also be reduced by limiting comparisons to proteins with at least 3 or more unique peptide identifications as the CV was on average 33% lower than for proteins with 2 or fewer peptide identifications. We also selected 13 housekeeping proteins and genes that were expressed across all tissues with low variability to determine their utility as a reference set for normalization and comparative purposes. These results present the first step toward estimating normal protein ranges by determining the variability in expression measurements through combining publicly available data. They support an approach that combines standard protocols with replicates of normal tissues to estimate normal protein ranges for large numbers of proteins and tissues. This would be a tremendous resource for normal cellular physiology and comparisons of proteomics studies.
authors: †Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington 98101, United States.|‡CDO Analytics, Seattle Children's Hospital, Seattle, Washington 98101, United States.
authors: Roger
authors: R
authors: Higdon
authors: †Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington 98101, United States.|‡CDO Analytics, Seattle Children's Hospital, Seattle, Washington 98101, United States.|§Departments of Biomedical Informatics and Medical Education and Pediatrics, University of Washington, Seattle, Washington 98195, United States.|∥Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States.
authors: Eugene
authors: E
authors: Kolker
mesh_terms: D057166:High-Throughput Screening Assays; D006801:Humans; D011506:Proteins / Q000378:metabolism*; D040901:Proteomics; D012016:Reference Values; D015203:Reproducibility of Results
chemical_list: D011506:Proteins
keywords: gene expression; normal range; normal tissue; protein expression; proteomics; spectral counts; variability