Author(s): Harini Chandra 1 , Panga Jaipal Reddy 1 , Sanjeeva Srivastava [[dagger]] 2
gold nanoparticles; label-based detection; label-free detection; microcantilevers; protein microarrays; quantum dots; SELDI-TOF; surface plasmon resonance
The study of the proteome, which encompasses the entire protein complement expressed by the genome of an organism at a given time, can be a daunting task due to the extremely large number of proteins present. The classical proteomics approach, which utilizes gel-based 2D electrophoresis and analytical mass spectrometry (MS) techniques, presents an important platform for the analysis and identification of proteins  . However, owing to many inherent drawbacks associated with gel-based methods, including lack of reproducibility and high-throughput (HT) analysis, numerous gel-free protein microarray techniques have been developed in recent years that carry out rapid functional analysis with economic use of samples and reagents. Protein microarrays are miniaturized 2D arrays, typically printed on functionalized glass slides, which consist of thousands of immobilized proteins that can be simultaneously studied and analyzed in a HT manner. Several microarray formats like capture arrays, reverse-phase arrays, tissue microarrays, small-molecule microarrays [2,3] and microarrays generated by cell-based and cell-free techniques  have emerged over the years in order to suit the needs of various applications (Figure 1). These microarrays provide a versatile platform for many diverse applications, such as biomarker identification, protein interaction studies, immunological profiling and vaccine development, among others.
Along with the advancement of microarray technologies, the development of sensitive and reliable detection systems has also been imperative. Sophisticated label-based and label-free detection techniques have successfully kept pace with the increasing demands of protein microarrays in studying large numbers of proteins, their interactions and functions (Figure 1). Label-based systems involve the use of a tag for the query molecule in the form of conventional fluorescent dyes and radioisotopes, among others [5,6] , or more recently, substances like inorganic quantum dots (QDs), gold nanoparticles (NPs), Raman dye-labeled carbon nanotubes  or silica NPs  . On the other hand, label-free detection techniques, including surface plasmon resonance (SPR), carbon nanotubes, microelectromechanical cantilevers and SELDI-TOF-mass spectrometry (MS) measure an inherent property of the query molecule, such as mass, dielectric or optical properties  . Several of these novel detection platforms have facilitated sensitive, specific, HT and rapid analysis of protein microarrays, thereby finding several applications in proteomics.
For any proteomics study to be successful, these emerging protein microarray platforms must be effectively coupled with sensitive and robust detection systems. This article provides an overview of the various protein microarray technologies and a comprehensive analysis on the progress of various protein microarray detection techniques, their merits, challenges and applications.
An overview of protein microarrays
Protein microarrays provide a valuable platform for both classical and functional proteome analysis and offer many advantages, the most important being HT analysis of thousands of proteins simultaneously. The construction of protein arrays is a significantly greater challenge compared with DNA microarrays due to: the lack of a PCR-equivalent amplification process, which can generate large amounts of protein; the wide variety of binding chemistries and specificities; the need to...