title: Head-to-head comparison of serum fractionation techniques.
abstract: Multiple approaches for simplifying the serum proteome have been described. These techniques are generally developed across different laboratories, samples, mass spectrometry platforms, and analysis tools. Hence, comparing the available schemes is impossible from the existing literature because of confounding variables. We describe a head-to-head comparison of several serum fractionation schemes, including N-linked glycopeptide enrichment, cysteinyl-peptide enrichment, magnetic bead separation (C3, C8, and WCX), size fractionation, protein A/G depletion, and immunoaffinity column depletion of abundant serum proteins. Each technique was compared to results obtained from unfractionated human serum. The results show immunoaffinity subtraction is the most effective means for simplifying the serum proteome while maintaining reasonable sample throughput. The reported dataset is publicly available and provides a standard against which emergent technologies can be compared and evaluated for their contribution to serum-based biomarker discovery.
authors.affiliation: Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109-1024, USA.
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Whiteaker
authors.forename: Heidi
authors.initials: H
authors.lastname: Zhang
authors.forename: Jimmy K
authors.initials: JK
authors.lastname: Eng
authors.forename: Ruihua
authors.initials: R
authors.lastname: Fang
authors.forename: Brian D
authors.initials: BD
authors.lastname: Piening
authors.forename: Li-Chia
authors.initials: LC
authors.lastname: Feng
authors.forename: Travis D
authors.initials: TD
authors.lastname: Lorentzen
authors.forename: Regine M
authors.initials: RM
authors.lastname: Schoenherr
authors.forename: John F
authors.initials: JF
authors.lastname: Keane
authors.forename: Ted
authors.initials: T
authors.lastname: Holzman
authors.forename: Matthew
authors.initials: M
authors.lastname: Fitzgibbon
authors.forename: ChenWei
authors.initials: C
authors.lastname: Lin
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.forename: Kelly
authors.initials: K
authors.lastname: Cooke
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: David G
authors.initials: DG
authors.lastname: Camp
authors.forename: Leigh
authors.initials: L
authors.lastname: Anderson
authors.forename: Julian
authors.initials: J
authors.lastname: Watts
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.forename: Martin W
authors.initials: MW
authors.lastname: McIntosh
authors.forename: Amanda G
authors.initials: AG
authors.lastname: Paulovich
mesh_terms: D001798:Blood Proteins / Q000737:chemistry* / Q000302:isolation & purification; D002853:Chromatography, Liquid; D006020:Glycopeptides / Q000097:blood / Q000737:chemistry / Q000302:isolation & purification; D006801:Humans; D008297:Male; D013058:Mass Spectrometry; D010446:Peptide Fragments / Q000097:blood / Q000737:chemistry / Q000302:isolation & purification; D040901:Proteomics / Q000379:methods; D021241:Spectrometry, Mass, Electrospray Ionization; D014357:Trypsin
chemical_list: D001798:Blood Proteins; D006020:Glycopeptides; D010446:Peptide Fragments; D014357:Trypsin