Autoantibodies and Biomarker Discovery - Proteomic and Metabolomic Approaches to Biomarker Discovery - page 357

TABLE 2 Comparison of Different Technologies for Autoantibody Discovery

Neoantigens from
alternative splicing/
mutation/translocation

Post-translational
modi Antigen sources Proteome coverage cations

cDNA expression

Phage plaque Low. Limited by bacterial

expression and minimal
coverage of low abundance
proteins. Truncations and
frame shifts are prevalent.

Yes No

Phage display & microarray Low. Same as above. Yes No

Bacterial expression &
microarray

Medium. Limited by
bacterial expression and
minimal coverage of low
abundance proteins.

Yes No

Cell lysates

2D Western Medium. Only proteins

compatible with 2D gel.

Yes Yes

Natural protein array Medium. Only proteins

compatible with
multidimensional column-
based separation.

Yes Yes

Recombinant proteins

Puri ed proteins High. Limited by

ORFeome.

No if without prior
knowledge and intention
to include a particular
neoantigen.

No

In vitro expression
mixtures

High. Limited by
ORFeome.

No No

On-chip synthesized proteins High No No in the standard format.

Possible to study certain
PTMs.

Synthetic peptides

Synthetic peptides/peptoids
on arrays

N/A Maybe. If a synthetic

peptide happens to have
the same sequence.

No

Synthetic human peptidome &
phage display

High No No

Microbial surface display Low to medium Maybe No