title: A targeted proteomics-based pipeline for verification of biomarkers in plasma.
abstract: High-throughput technologies can now identify hundreds of candidate protein biomarkers for any disease with relative ease. However, because there are no assays for the majority of proteins and de novo immunoassay development is prohibitively expensive, few candidate biomarkers are tested in clinical studies. We tested whether the analytical performance of a biomarker identification pipeline based on targeted mass spectrometry would be sufficient for data-dependent prioritization of candidate biomarkers, de novo development of assays and multiplexed biomarker verification. We used a data-dependent triage process to prioritize a subset of putative plasma biomarkers from >1,000 candidates previously identified using a mouse model of breast cancer. Eighty-eight novel quantitative assays based on selected reaction monitoring mass spectrometry were developed, multiplexed and evaluated in 80 plasma samples. Thirty-six proteins were verified as being elevated in the plasma of tumor-bearing animals. The analytical performance of this pipeline suggests that it should support the use of an analogous approach with human samples.
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Whiteaker
authors.forename: Chenwei
authors.initials: C
authors.lastname: Lin
authors.forename: Jacob
authors.initials: J
authors.lastname: Kennedy
authors.forename: Liming
authors.initials: L
authors.lastname: Hou
authors.forename: Mary
authors.initials: M
authors.lastname: Trute
authors.forename: Izabela
authors.initials: I
authors.lastname: Sokal
authors.forename: Ping
authors.initials: P
authors.lastname: Yan
authors.forename: Regine M
authors.initials: RM
authors.lastname: Schoenherr
authors.forename: Lei
authors.initials: L
authors.lastname: Zhao
authors.forename: Uliana J
authors.initials: UJ
authors.lastname: Voytovich
authors.forename: Karen S
authors.initials: KS
authors.lastname: Kelly-Spratt
authors.forename: Alexei
authors.initials: A
authors.lastname: Krasnoselsky
authors.forename: Philip R
authors.initials: PR
authors.lastname: Gafken
authors.forename: Jason M
authors.initials: JM
authors.lastname: Hogan
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Jones
authors.forename: Pei
authors.initials: P
authors.lastname: Wang
authors.forename: Lynn
authors.initials: L
authors.lastname: Amon
authors.forename: Lewis A
authors.initials: LA
authors.lastname: Chodosh
authors.forename: Peter S
authors.initials: PS
authors.lastname: Nelson
authors.forename: Martin W
authors.initials: MW
authors.lastname: McIntosh
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Kemp
authors.forename: Amanda G
authors.initials: AG
authors.lastname: Paulovich
mesh_terms: D000818:Animals; D014408:Biomarkers, Tumor / Q000097:blood*; D001774:Blood Chemical Analysis / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D051379:Mice; D009363:Neoplasm Proteins / Q000097:blood*; D009374:Neoplasms, Experimental / Q000097:blood*; D010449:Peptide Mapping / Q000379:methods*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D020543:Proteome