title: Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins.
abstract: Multiple reaction monitoring (MRM) mass spectrometry has been successfully applied to monitor targeted proteins in biological specimens, raising the possibility that assays could be configured to measure all human proteins. We report the results of a pilot study designed to test the feasibility of a large-scale, international effort for MRM assay generation. We have configured, validated across three laboratories and made publicly available as a resource to the community 645 novel MRM assays representing 319 proteins expressed in human breast cancer. Assays were multiplexed in groups of >150 peptides and deployed to quantify endogenous analytes in a panel of breast cancer-related cell lines. The median assay precision was 5.4%, with high interlaboratory correlation (R(2) > 0.96). Peptide measurements in breast cancer cell lines were able to discriminate among molecular subtypes and identify genome-driven changes in the cancer proteome. These results establish the feasibility of a large-scale effort to develop an MRM assay resource.
authors: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors: Jacob J
authors: JJ
authors: Kennedy
authors: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors: Susan E
authors: SE
authors: Abbatiello
authors: Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, Republic of Korea.
authors: Kyunggon
authors: 0000000230725331
authors: K
authors: Kim
authors: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors: Ping
authors: P
authors: Yan
authors: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors: Jeffrey R
authors: JR
authors: Whiteaker
authors: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors: Chenwei
authors: C
authors: Lin
authors: Center for Theragnosis, Korea Institute of Science and Technology, Seoul, Republic of Korea.
authors: Jun Seok
authors: JS
authors: Kim
authors: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors: Yuzheng
authors: Y
authors: Zhang
authors: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors: Xianlong
authors: X
authors: Wang
authors: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors: Richard G
authors: RG
authors: Ivey
authors: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors: Lei
authors: L
authors: Zhao
authors: Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, Republic of Korea.
authors: Hophil
authors: H
authors: Min
authors: Center for Theragnosis, Korea Institute of Science and Technology, Seoul, Republic of Korea.
authors: Youngju
authors: Y
authors: Lee
authors: Center for Theragnosis, Korea Institute of Science and Technology, Seoul, Republic of Korea.
authors: Myeong-Hee
authors: MH
authors: Yu
authors: Center for Theragnosis, Korea Institute of Science and Technology, Seoul, Republic of Korea.
authors: Eun Gyeong
authors: EG
authors: Yang
authors: Center for Theragnosis, Korea Institute of Science and Technology, Seoul, Republic of Korea.
authors: Cheolju
authors: C
authors: Lee
authors: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors: Pei
authors: P
authors: Wang
authors: Office of Cancer Clinical Proteomics Research, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA.
authors: Henry
authors: H
authors: Rodriguez
authors: Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, Republic of Korea.
authors: Youngsoo
authors: Y
authors: Kim
authors: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors: Steven A
authors: SA
authors: Carr
authors: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors: Amanda G
authors: AG
authors: Paulovich
mesh_terms: D001681:Biological Assay / Q000592:standards*; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism*; D001943:Breast Neoplasms / Q000145:classification / Q000378:metabolism* / Q000401:mortality; D002851:Chromatography, High Pressure Liquid; D015180:Electrophoresis, Gel, Two-Dimensional; D005240:Feasibility Studies; D005260:Female; D006801:Humans; D010865:Pilot Projects; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D015996:Survival Rate; D053719:Tandem Mass Spectrometry / Q000379:methods*; D014407:Tumor Cells, Cultured
chemical_list: D014408:Biomarkers, Tumor; D020543:Proteome