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].