Richard D. Smith | |
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Born | |
Nationality | American |
Alma mater | University of Utah |
Known for | Ion funnel, Electrospray ionization, Mass spectrometry, Capillary electrophoresis-mass spectrometry, Proteomics |
Awards | 2003 ACS Award for Analytical Chemistry; 2009 HUPO Discovery Award in Proteomics Sciences; R&D Magazine Scientist of the Year (2010); 2013 American Society for Mass Spectrometry Distinguished Contribution in Mass Spectrometry Award |
Scientific career | |
Fields | Chemistry Proteomics |
Institutions | Pacific Northwest National Laboratory |
Thesis | Studies in ion cyclotron resonance mass spectrometry (1975) |
Doctoral advisor | Jean Futrell |
Richard Dale Smith is a chemist and a Battelle Fellow and chief scientist within the biological sciences division, as well as the director of proteomics research at the Pacific Northwest National Laboratory (PNNL). Smith is also director of the NIH Proteomics Research Resource for Integrative Biology, an adjunct faculty member in the chemistry departments at Washington State University and the University of Utah, and an affiliate faculty member at the University of Idaho and the Department of Molecular Microbiology & Immunology, Oregon Health & Science University. [1] He is the author or co-author of approximately 1100 peer-reviewed publications and has been awarded 70 US patents. [2]
Smith obtained his B.S. in chemistry in 1971 from Lowell Technological Institute (currently the University of Massachusetts Lowell). [1] [3] He then received his PhD in the field of Physical Chemistry from the University of Utah in 1975. [4]
Starting in the 1970s Smith published peer-reviewed papers on several subjects, including mass spectrometry, ion cyclotron resonance mass spectrometry, ion-molecule reactions, molecular assemblies, and supercritical fluid solutions. [5] [6] [7] [8] [9] This early work has led him to be considered an internationally recognized expert in mass spectrometry and separation techniques, and his research has led to advancements in instrumentation for the medical and environmental analysis fields, as well as biological research. [10]
In the medical field, Smith's work has produced benefits in the areas of drug testing, analysis of pharmaceuticals and medical diagnostics in the clinical arena. His most successful invention has been the combination of capillary electro-phoresis with mass spectrometry. By the end of the 1990s, Smith's achievements included the electrodynamic ion funnel and a micro-dialysis device for the rapid purification of samples analyzed using mass spectrometry. Other notable contributions have been in the fields of supercritical fluids and related reverse micelle phenomena.
On August 22, 2000, Smith demonstrated and patented [11] the electrodynamic ion funnel [12] [13] for highly efficient capture and focusing of ions in gases. He applied it for increasing the sensitivity of ESI-MS. [14] His group has continued to refine and extend ion funnel technology, which is now widely applied in mass spectrometry and ion mobility instrumentation. [13] [15]
In the late 1990s, Smith's group was also extensively involved in the development and application of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry, which provided the basis for much greater MS resolution and mass measurement accuracy, and particularly in the development of these technologies for applications in proteomics. [16] [17] More recent work has centered on extending application of these proteomics technologies to mammalian systems, which pose additional challenges due to their much greater complexity. One early focus has been the human blood plasma proteome due to its broad biomedical applications. Plasma proteome measurements potentially can provide the basis for discovery of protein biomarkers or signatures for virtually every disease state. [16]
In September 1999, R&D Magazine picked the top 40 technologies of all time based on their impact on society, industry and commercial applications. The Top 40 were selected from a list of 3,600 past R&D 100 Awards. Smith was the recipient of one of these awards, for the development of capillary electrophoresis-mass spectrometry. [10]
Since the Human Genome Project developed a blueprint of all human genes in our chromosomes, proteomics researchers have pushed to understand how that blueprint creates life. Diseases and infections are often the result of proteins going wrong, and finding the aberrant one requires sifting through thousands of other proteins. In addition, many problem proteins have not been given names yet or are too rare to find easily.
In the last few years, Smith and his team have led work that has reduced analytical steps from hours to minutes. This increased speed has enabled many samples to be processed faster in high-throughput experiments. Smith has led other advances in sensitivity and accuracy that have improved the ability to find rare proteins, bringing proteomics technology to the doorstep of clinical researchers.
Smith and collaborators have applied the technology to liver disease and cancer in the hopes of finding rare markers of disease in blood, making diagnosis or treatment safer and faster. In 2007, Scientific American magazine listed Smith and his collaborator Desmond Smith as one of the top 50 researchers for work to understand the origins of Parkinson's disease by mapping where proteins amass in diseased mouse brains.
Among other work, Smith and colleagues at PNNL have looked at how bacteria and viruses might cause illness. They've learned breast cancer leaves traces behind in the blood that doctors might exploit someday. Smith led early studies for DOE into possible roles for microbes in making biofuels. In other DOE studies, he's examined how large environmental communities of microbes function in our ecosystem and affect our environment. An intimate understanding of how microbes work will let researchers employ them to trap radioactive contaminants or greenhouse gases. [18]
In other recent work he has been leading the development of structures for lossless ion manipulations (SLIM) and their application for very high speed sample processing, reactions, separations, and other manipulations of ions in the gas phase, and particularly their use for ion mobility spectrometry (IMS) separations in conjunction with mass spectrometry. Smith and colleagues at PNNL, including Drs. Yehia Ibrahim and Sandilya Gerimella, have extended the range of SLIM technologies to include the use of travel wave electric fields for SLIM IMS. This has enabled extremely high resolution separations based on 'multi-pass" separations, and has enabled the separation of ions previously impractical, such as isotopomers and isotopologues.
Smith a principal investigator at NIH Biomedical Technology Resource Center for Integrative Biology [19] and the U.S. Department of Energy High Throughput Proteomics Facility at PNNL. [20] He is an adjunct faculty member in the chemistry departments at Washington State University and the University of Utah and an affiliate faculty member Department of Chemistry at the University of Idaho and the Department of Molecular Microbiology & Immunology, Oregon Health & Science University. Smith serves on the Board of Scientific Counselors, [21] Office of Public Health Preparedness and Response of the Centers for Disease Control and Prevention. He is also a Fellow of the American Association for the Advancement of Science, [22] and has been elected to the Washington State Academy of Sciences. [23]
In 2011, Discover Magazine selected a peer-reviewed paper on Lyme disease that he coauthored with immunologist Steven Schutzer of the University of Medicine and Dentistry of New Jersey as one of the top 100 articles of the year, placing it at number 90. [24] [25] He was the recipient of the 2003 ACS award in Analytical Chemistry, [26] the 2009 Human Proteome Organization (HUPO) Discovery Award in Proteomics Sciences, and was selected by R&D Magazine as the 2010 R&D Scientist of the Year. [18] He has also received ten R&D 100 Awards: Combined Orthogonal Mobility & Mass Evaluation Technology (2013); Ion Mobility Spectrometer on a Microchip (2010); Ultrasensitive Electrospray Ionization Mass Spectrometry Source and Interface (2009); FT-MS Proteome Express (2003); Electrodynamic Ion Funnel (1999); Rapid Microdialyzer (1998); MICLEAN/MICARE Process (1998); Rapid Expansion of Supercritical Fluid Solutions Process (1988); Capillary Electrophoresis-Electrospray Ionization-MS (1988); and Supercritical Fluid Chromatography-MS (1983). He was the recipient of the 2013 Award for a Distinguished Contribution in Mass Spectrometry. [27]
Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules because it overcomes the propensity of these molecules to fragment when ionized. ESI is different from other ionization processes since it may produce multiple-charged ions, effectively extending the mass range of the analyser to accommodate the kDa-MDa orders of magnitude observed in proteins and their associated polypeptide fragments.
Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more stages of analysis using one or more mass analyzer are performed with an additional reaction step in between these analyses to increase their abilities to analyse chemical samples. A common use of tandem MS is the analysis of biomolecules, such as proteins and peptides.
Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles. The metabolome represents the complete set of metabolites in a biological cell, tissue, organ, or organism, which are the end products of cellular processes. Messenger RNA (mRNA), gene expression data, and proteomic analyses reveal the set of gene products being produced in the cell, data that represents one aspect of cellular function. Conversely, metabolic profiling can give an instantaneous snapshot of the physiology of that cell, and thus, metabolomics provides a direct "functional readout of the physiological state" of an organism. There are indeed quantifiable correlations between the metabolome and the other cellular ensembles, which can be used to predict metabolite abundances in biological samples from, for example mRNA abundances. One of the ultimate challenges of systems biology is to integrate metabolomics with all other -omics information to provide a better understanding of cellular biology.
In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy-absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of biomolecules and various organic molecules, which tend to be fragile and fragment when ionized by more conventional ionization methods. It is similar in character to electrospray ionization (ESI) in that both techniques are relatively soft ways of obtaining ions of large molecules in the gas phase, though MALDI typically produces far fewer multi-charged ions.
Liquid chromatography–mass spectrometry (LC–MS) is an analytical chemistry technique that combines the physical separation capabilities of liquid chromatography with the mass analysis capabilities of mass spectrometry (MS). Coupled chromatography – MS systems are popular in chemical analysis because the individual capabilities of each technique are enhanced synergistically. While liquid chromatography separates mixtures with multiple components, mass spectrometry provides spectral information that may help to identify each separated component. MS is not only sensitive, but provides selective detection, relieving the need for complete chromatographic separation. LC–MS is also appropriate for metabolomics because of its good coverage of a wide range of chemicals. This tandem technique can be used to analyze biochemical, organic, and inorganic compounds commonly found in complex samples of environmental and biological origin. Therefore, LC–MS may be applied in a wide range of sectors including biotechnology, environment monitoring, food processing, and pharmaceutical, agrochemical, and cosmetic industries. Since the early 2000s, LC–MS has also begun to be used in clinical applications.
Ion mobility spectrometry (IMS) It is a method of conducting analytical research that separates and identifies ionized molecules present in the gas phase based on the mobility of the molecules in a carrier buffer gas. Even though it is used extensively for military or security objectives, such as detecting drugs and explosives, the technology also has many applications in laboratory analysis, including studying small and big biomolecules. IMS instruments are extremely sensitive stand-alone devices, but are often coupled with mass spectrometry, gas chromatography or high-performance liquid chromatography in order to achieve a multi-dimensional separation. They come in various sizes, ranging from a few millimeters to several meters depending on the specific application, and are capable of operating under a broad range of conditions. IMS instruments such as microscale high-field asymmetric-waveform ion mobility spectrometry can be palm-portable for use in a range of applications including volatile organic compound (VOC) monitoring, biological sample analysis, medical diagnosis and food quality monitoring. Systems operated at higher pressure are often accompanied by elevated temperature, while lower pressure systems (1–20 hPa) do not require heating.
Surface-enhanced laser desorption/ionization (SELDI) is a soft ionization method in mass spectrometry (MS) used for the analysis of protein mixtures. It is a variation of matrix-assisted laser desorption/ionization (MALDI). In MALDI, the sample is mixed with a matrix material and applied to a metal plate before irradiation by a laser, whereas in SELDI, proteins of interest in a sample become bound to a surface before MS analysis. The sample surface is a key component in the purification, desorption, and ionization of the sample. SELDI is typically used with time-of-flight (TOF) mass spectrometers and is used to detect proteins in tissue samples, blood, urine, or other clinical samples, however, SELDI technology can potentially be used in any application by simply modifying the sample surface.
Protein mass spectrometry refers to the application of mass spectrometry to the study of proteins. Mass spectrometry is an important method for the accurate mass determination and characterization of proteins, and a variety of methods and instrumentations have been developed for its many uses. Its applications include the identification of proteins and their post-translational modifications, the elucidation of protein complexes, their subunits and functional interactions, as well as the global measurement of proteins in proteomics. It can also be used to localize proteins to the various organelles, and determine the interactions between different proteins as well as with membrane lipids.
Shotgun proteomics refers to the use of bottom-up proteomics techniques in identifying proteins in complex mixtures using a combination of high performance liquid chromatography combined with mass spectrometry. The name is derived from shotgun sequencing of DNA which is itself named after the rapidly expanding, quasi-random firing pattern of a shotgun. The most common method of shotgun proteomics starts with the proteins in the mixture being digested and the resulting peptides are separated by liquid chromatography. Tandem mass spectrometry is then used to identify the peptides.
Top-down proteomics is a method of protein identification that either uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry (MS/MS) analysis or other protein purification methods such as two-dimensional gel electrophoresis in conjunction with MS/MS. Top-down proteomics is capable of identifying and quantitating unique proteoforms through the analysis of intact proteins. The name is derived from the similar approach to DNA sequencing. During mass spectrometry intact proteins are typically ionized by electrospray ionization and trapped in a Fourier transform ion cyclotron resonance, quadrupole ion trap or Orbitrap mass spectrometer. Fragmentation for tandem mass spectrometry is accomplished by electron-capture dissociation or electron-transfer dissociation. Effective fractionation is critical for sample handling before mass-spectrometry-based proteomics. Proteome analysis routinely involves digesting intact proteins followed by inferred protein identification using mass spectrometry (MS). Top-down MS (non-gel) proteomics interrogates protein structure through measurement of an intact mass followed by direct ion dissociation in the gas phase.
Ion mobility spectrometry–mass spectrometry (IMS-MS) is an analytical chemistry method that separates gas phase ions based on their interaction with a collision gas and their masses. In the first step, the ions are separated according to their mobility through a buffer gas on a millisecond timescale using an ion mobility spectrometer. The separated ions are then introduced into a mass analyzer in a second step where their mass-to-charge ratios can be determined on a microsecond timescale. The effective separation of analytes achieved with this method makes it widely applicable in the analysis of complex samples such as in proteomics and metabolomics.
Capillary electrophoresis–mass spectrometry (CE–MS) is an analytical chemistry technique formed by the combination of the liquid separation process of capillary electrophoresis with mass spectrometry. CE–MS combines advantages of both CE and MS to provide high separation efficiency and molecular mass information in a single analysis. It has high resolving power and sensitivity, requires minimal volume and can analyze at high speed. Ions are typically formed by electrospray ionization, but they can also be formed by matrix-assisted laser desorption/ionization or other ionization techniques. It has applications in basic research in proteomics and quantitative analysis of biomolecules as well as in clinical medicine. Since its introduction in 1987, new developments and applications have made CE-MS a powerful separation and identification technique. Use of CE–MS has increased for protein and peptides analysis and other biomolecules. However, the development of online CE–MS is not without challenges. Understanding of CE, the interface setup, ionization technique and mass detection system is important to tackle problems while coupling capillary electrophoresis to mass spectrometry.
Ambient ionization is a form of ionization in which ions are formed in an ion source outside the mass spectrometer without sample preparation or separation. Ions can be formed by extraction into charged electrospray droplets, thermally desorbed and ionized by chemical ionization, or laser desorbed or ablated and post-ionized before they enter the mass spectrometer.
In mass spectrometry, liquid junction interface is an ion source or set-up that couples peripheric devices, such as capillary electrophoresis, to mass spectrometry.
Atmospheric pressure laser ionization is an atmospheric pressure ionization method for mass spectrometry (MS). Laser light in the UV range is used to ionize molecules in a resonance-enhanced multiphoton ionization (REMPI) process. It is a selective and sensitive ionization method for aromatic and polyaromatic compounds. Atmospheric photoionization is the latest in development of atmospheric ionization methods.
In the field of cellular biology, single-cell analysis and subcellular analysis is the study of genomics, transcriptomics, proteomics, metabolomics and cell–cell interactions at the single cell level. The concept of single-cell analysis originated in the 1970s. Before the discovery of heterogeneity, single-cell analysis mainly referred to the analysis or manipulation of an individual cell in a bulk population of cells at a particular condition using optical or electronic microscope. To date, due to the heterogeneity seen in both eukaryotic and prokaryotic cell populations, analyzing a single cell makes it possible to discover mechanisms not seen when studying a bulk population of cells. Technologies such as fluorescence-activated cell sorting (FACS) allow the precise isolation of selected single cells from complex samples, while high throughput single cell partitioning technologies, enable the simultaneous molecular analysis of hundreds or thousands of single unsorted cells; this is particularly useful for the analysis of transcriptome variation in genotypically identical cells, allowing the definition of otherwise undetectable cell subtypes. The development of new technologies is increasing our ability to analyze the genome and transcriptome of single cells, as well as to quantify their proteome and metabolome. Mass spectrometry techniques have become important analytical tools for proteomic and metabolomic analysis of single cells. Recent advances have enabled quantifying thousands of protein across hundreds of single cells, and thus make possible new types of analysis. In situ sequencing and fluorescence in situ hybridization (FISH) do not require that cells be isolated and are increasingly being used for analysis of tissues.
In mass spectrometry, matrix-assisted ionization is a low fragmentation (soft) ionization technique which involves the transfer of particles of the analyte and matrix sample from atmospheric pressure (AP) to the heated inlet tube connecting the AP region to the vacuum of the mass analyzer.
Peter Nemes is a Hungarian-American chemist, who is active in the fields of bioanalytical chemistry, mass spectrometry, cell/developmental biology, neuroscience, and biochemistry.
Probe electrospray ionization (PESI) is an electrospray-based ambient ionization technique which is coupled with mass spectrometry for sample analysis. Unlike traditional mass spectrometry ion sources which must be maintained in a vacuum, ambient ionization techniques permit sample ionization under ambient conditions, allowing for the high-throughput analysis of samples in their native state, often with minimal or no sample pre-treatment. The PESI ion source simply consists of a needle to which a high voltage is applied following sample pick-up, initiating electrospray directly from the solid needle.
Erin Shammel Baker is an American bioanalytical chemist specializing in developing ion mobility-mass spectrometry hybrid instruments for biological and environmental applications. Baker is an expert in the research of perfluoroalkyl and polyfluoroalkyl substances analysis.
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