StudiesProtein Microarrays: Technology Adoption and Utilization As protein arrays have become increasingly consistent and reliable, more scientists have recently begun to incorporate them into their proteomics experiments. Researchers are attracted by the technology’s ability to detect protein expression quicker and easier than traditional approaches such as 2D gel electrophoresis and mass spectrometry. By allowing scientists to look at multiple protein interactions simultaneously, the seemingly insurmountable challenge of characterizing an organism’s entire collection of proteins (i.e., proteome) is within reach. While there is tremendous excitement about the potential of protein arrays to further our understanding about protein expression, function and structure on a microscopically global level, there is also hesitancy on behalf of many scientists to adopt a technology that is often still perceived as unstable and irreproducible. This study, sponsored by The Science Advisory Board, examines the most critical factors related to protein microarray performance as specified by 675 current and future protein microarray users: Although no longer considered a new technology, 47% of survey respondents have only been using protein microarrays in their research for six months or less suggesting a relatively slow rate of adoption since its emergence in the late 1990s—until relatively recently. However, this statistic and the fact that 69% of future users plan on using protein arrays within 12 months or less suggest that scientists might now be more receptive to the technology than they were even a year ago. “The value of protein microarrays is in the tremendous volume of useful information that one can gain from the massively parallel observations that can be obtained rapidly and with relative ease. To help lower the "barrier" to entry-level users, I would emphasize the availability of expert technical support, optimized protocols, and relevant analytical and relational database software and LIMS. Customer access to these tools is critical to successful widespread market acceptance of protein microarrays.” -Principal Investigator, North America Protein Microarray Content Protein microarray can be generally divided into two main categories: capture arrays and interaction arrays. Capture arrays have immobilized molecules such as antibodies or chemically treated surfaces, which bind to target proteins. Interaction arrays have immobilized biological moieties such as proteins or peptides, which are used to identify functions or determine interactions with other proteins or small molecules. For all study respondents currently using protein microarrays, antibody:antigen binding is the most popular type of array content. In contrast, for academic reserachers planning on using protein microarrays, protein:protein interactions will dictate much of the array content. And for industrial scientists planning on using protein microarrays, ligand:receptor and antibody:antigen binding will constitute the majority of array content along with protein:protein interactions. Antibody:antigen content constitutes the archetypal capture arrays, while protein-protein array interactions make up the classic interaction array. Science Advisory Board members demonstrate the following product preferences based upon whether or not they are already using protein microarray technology in their research: Applicability of Protein Arrays One-third of respondents have the most trouble with sample preparation of proteins that are to be interrogated. This stumbling block could be a factor in why the number of samples currently arrayed is relatively modest: 48% of respondents array 10 or fewer samples per month. In contrast, once arrayed, sample labeling and probing are the least problematic steps. After arraying, the next biggest challenge respondents face is analyzing their data. Besides needing to better master the technology, researchers who participated in this study are also looking for guidance on how best to apply it. Demonstrating "proof of concept" for new applications would be the most desired improvement. Given the potential to use protein microarrays to facilitate expression profiling, studies of protein-protein and protein-drug interactions and activity measurements, it is understandable that some scientists are overwhelmed at their options and wonder, “What is the technology particularly appropriate for—especially as it relates to my own research objectives?” While the major focus of the scientists using protein microarrays is basic proteomics research, there is currently a smaller subset of people using the technology for drug discovery and development and diagnostics. This emphasis will be slightly overshadowed as even more basic researchers embrace protein microarrays in the near future. On expanding the applicability of protein microarrays: “[Suppliers should] Give specific cases in which protein microarrays has help to get unexpected but important discoveries.” -Graduate Student, North America Experimental Parameters Before adopting the technology, scientists want protein microarray performance to be validated and demonstrated by the ways and means that are familiar to them: peer-reviewed articles and/or a colleague’s recommendation. Signal-to-noise ratio and reproducibility are key parameters by which scientists will evaluate both self-printed and commercial array performance. Future users of the technology will be different than current users in many respects. There will be a need for suppliers to increase the range of product offerings from arrays with less than 100 proteins printed to arrays that have somewhere in the range of 51 to 1,000 proteins printed. In addition to density, scientists will expect increasing array complexity as the types of interactions they want to investigate via protein microarrays become more nuanced and intricate. Researchers are more and more interested in assessing proteins that traditionally have been difficult to array such as membrane-bound proteins. For these types of interactions, protein orientation and conformation will be of the utmost importance. When asked how best to convince scientists to use protein microarrays, one respondent replied “[A] Free demonstration and validation of a specific application.” -Lab Director, North America Another scientist replied, “Protein microarrays have the potential to provide all this data compared to the much more limited data available using traditional techniques such as 2D-gel electrophoresis or ELISAs. This is the benefit of protein microarrays!” -Staff Scientist, North America One emerging trend in array content is comprehensive proteome arrays, which represent all the major proteins of a target organism. While in their early stages, these so-called whole proteome arrays will forge high-throughput analysis and comprehensive measurements into a powerful tool for deciphering a panoply of proteins. Despite their promise of omnipotence, the demand for them has been unknown. This study assessed scientists’ level of interest in whole proteome arrays and found that only 2% of current users and 3% of future users of the technology would not be receptive to them. The majority of respondents, in fact, would prefer whole proteome arrays of human and/or mouse. A major challenge scientists face will be to ensure that the majority of meaningful biological problems that can be answered with a whole proteome array can be done so quantitatively and with real-time measurements. ### To find out what your colleagues would do if they were a "protein microarray" spokesperson for a life science supplier please click here. Other articles on Protein microarrays on The Science Advisory Board Web site can be found at: The Tools and Techniques of Protein Science: Protein Biomolecular Interactions (in vitro methods) Protein chip technology is a novel and powerful tool for high throughput assays of protein expression profiling, protein-protein interaction and enzyme activity. Currently only 8% of protein scientists employ this technology, although 41% have plans to use it within 12 months. The Tools and Techniques of Plant Biotechnology Two-thirds of the study respondents use molecular biology techniques and most work on food plants. Some of these techniques are real-time PCR (27% of respondents), RNAi (24% of respondents), confocal microscopy (61% of respondents), and protein microarrays (15% of respondents). To find out how more about your colleagues' experience with protein microarrays, please click here. [ View Current & Future Studies ] [ View Past Studies ] |
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