4.1 Protein microarray
DNA microarrays were a significant genomics development but couldn’t
predict protein structures or dynamics accurately. Protein microarrays
analyze thousands of proteins or peptides and are valuable for clinical
and functional research. They assess PTMs, quantify target proteins in
fluids, and study protein interactions and autoantibodies in disease
conditions [41]. Protein microarrays allow active exploration of the
human proteome, identifying biomarkers, immune profiles, enzymes, and
quantifying proteins [42]. They offer multiplexed and sensitive
protein analysis, addressing complex proteomes with limited specimens
[43].
Nucleic Acid Programmable Protein Arrays (NAPPA) is a potent method for
biomarker screening and protein-protein interaction investigation.
Unlike traditional protein microarrays, NAPPA uses in vitro
transcription/translation, eliminating the need for costly protein
purification. Proteins are synthesized directly on the array using a DNA
template and coupled with an affinity reagent [43]. Various in situ
expressed microarrays, like PISA and DAPA, exist alongside NAPPA
technology. PISA differs from NAPPA as it uses free DNA templates,
eliminating the need for DNA immobilization [44].
Proto Arrays, designed for analyzing numerous proteins, require small
sample volumes, around 10 μL of serum, making them ideal for
high-throughput screening. They are used in studies like the Parkinson’s
disease biomarker search (ParkCHIP) and systemic erythematosus lupus
(SLE) autoantibody investigations. SLE patients had significantly higher
levels of 446 IgG and 1218 IgM autoantibodies against 9500 antigens,
including novel ones related to the nucleus, cytoplasm, or membrane
[45,46]. Protein microarrays fall into analytical, functional, and
reverse-phase categories [Figure 2].