Sample Depletion, Fractionation, and Enrichment for Biomarker Discovery - Proteomic and Metabolomic Approaches to Biomarker Discovery - page 232

22 PROTEINS COMPRISE 99% OF THE PROTEIN MASS IN SERUM!

Lipoprotein(a)
Factor H
Ceruloplasmin
C4 Complement
Complement Factor B
Prealbumin
C9 Complement
C1q Complement
C8 Complement

Fibrinogen

lgA Total
Alpha-2-Macroglobulin
lgM Total
Alpha-1-Antitrypsin
C3 Complement
Haptoglobin

Transferrin

lgG Total

1%

10%

Alpha-1-acid Glycoprotein

Apolipoprotein A-1

Albumin

Apolipoprotein B

90% 10%

FIGURE 1 Schematic of serum proteome.

at the protein or peptide level as indicated in
Figure 2 . The properties of proteins make
them amenable to different electrophoretic and
chromatographic fractionation approaches. The

the proteins into peptides prior to fractionation
by liquid chromatography owing to their
increased solubility in buffers and solvents
commonly used for both reversed-phase and
strong cation exchange (SCX) chromatography
( Table 1 ).

first step in most proteome published studies,
after extraction or depletion, is the digestion of

FIGURE 2 Schematic of proteome
fractionation procedures at the protein
or peptide level.

Serum Proteins

Trypsin digestion Fractionation

Proteins

Peptides

X-Fractions

SCX-Fractionation

2D SDS PAGE

Trypsin digestion

X-Fractions

Spots excised

SCX Fractionation

Trypsin digestion

RP-HPLC/MS/MS

RP-HPLC/MS/MS

RP-HPLC/MS/MS

Protein identification by data base searching