Head-to-head comparison of serum fractionation techniques.
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.
Whiteaker
Jeffrey R
JR
Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109-1024, USA.
Zhang
Heidi
H
Eng
Jimmy K
JK
Fang
Ruihua
R
Piening
Brian D
BD
Feng
Li-Chia
LC
Lorentzen
Travis D
TD
Schoenherr
Regine M
RM
Keane
John F
JF
Holzman
Ted
T
Fitzgibbon
Matthew
M
Lin
ChenWei
C
Zhang
Hui
H
Cooke
Kelly
K
Liu
Tao
T
Camp
David G
DG
Anderson
Leigh
L
Watts
Julian
J
Smith
Richard D
RD
McIntosh
Martin W
MW
Paulovich
Amanda G
AG
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
D001798:Blood Proteins; D006020:Glycopeptides; D010446:Peptide Fragments; D014357:Trypsin