Proteomics, nanotechnology and molecular diagnostics

Sequencing of the human genome opened the way to the exploration of the proteome and this has lead to the identification of large numbers of proteins in complex biological samples. The identification of diagnostic patterns in samples taken from patients to aid diagnosis is in the early stages of development. The solution to many of the technical challenges in proteomics and protein based molecular diagnostics will be found in new applications of nanomaterials. This review describes some of the physical and chemical principles underlying nanomaterials and devices and outlines how they can be used in proteomics; developments which are establishing nanoproteomics as a new field. Nanoproteomics will provide the platform for the discovery of next generation biomarkers. The field of molecular diagnostics will then come of age.

[1]  P. Tempst,et al.  Automated serum peptide profiling , 2006, Nature Protocols.

[2]  Y. Wada,et al.  Requirements for laser-induced desorption/ionization on submicrometer structures. , 2005, Analytical chemistry.

[3]  M. Hegner,et al.  Advanced biosensing using micromechanical cantilever arrays. , 2004, Methods in molecular biology.

[4]  P. Davidsson,et al.  Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples , 2005, Proteomics.

[5]  Yu-Chie Chen,et al.  Molecularly imprinted TiO2-matrix-assisted laser desorption/ionization mass spectrometry for selectively detecting alpha-cyclodextrin. , 2004, Analytical chemistry.

[6]  Joachim Klose,et al.  Two‐dimensional electrophoresis of proteins: An updated protocol and implications for a functional analysis of the genome , 1995, Electrophoresis.

[7]  C. Lieber,et al.  Nanowire Nanosensors for Highly Sensitive and Selective Detection of Biological and Chemical Species , 2001, Science.

[8]  Nicole Pamme,et al.  Magnetism and microfluidics. , 2006, Lab on a chip.

[9]  F. Švec.  Less common applications of monoliths: I. Microscale protein mapping with proteolytic enzymes immobilized on monolithic supports , 2006, Electrophoresis.

[10]  Yee Lam,et al.  Using microcantilever deflection to detect HIV-1 envelope glycoprotein gp120. , 2006, Nanomedicine : nanotechnology, biology, and medicine.

[11]  Laurie L. Wood,et al.  New biochip technology for label-free detection of pathogens and their toxins. , 2003, Journal of microbiological methods.

[12]  Gengfeng Zheng,et al.  Multiplexed electrical detection of cancer markers with nanowire sensor arrays , 2005, Nature Biotechnology.

[13]  R. Colton,et al.  The BARC biosensor applied to the detection of biological warfare agents. , 2000, Biosensors & bioelectronics.

[14]  V. Bhandari,et al.  Proteomic Profiling of the Amniotic Fluid to Detect Inflammation, Infection, and Neonatal Sepsis , 2007, PLoS medicine.

[15]  M. Natan,et al.  Glass-Coated, Analyte-Tagged Nanoparticles: A New Tagging System Based on Detection with Surface-Enhanced Raman Scattering , 2003 .

[16]  A. Alivisatos.  Semiconductor Clusters, Nanocrystals, and Quantum Dots , 1996, Science.

[17]  A. Görg,et al.  Current two‐dimensional electrophoresis technology for proteomics , 2004, Proteomics.

[18]  Elisabeth Verpoorte,et al.  Fast, high-efficiency peptide separations on a 50-microm reversed-phase silica monolith in a nanoLC-MS set-up. , 2006, Journal of chromatography. A.

[19]  Y. P. Bao,et al.  Detection of protein analytes via nanoparticle-based bio bar code technology. , 2006, Analytical chemistry.

[20]  T. Hunkapiller,et al.  Peptide mass maps: a highly informative approach to protein identification. , 1993, Analytical biochemistry.

[21]  A. Alivisatos,et al.  Nanocrystals: Building blocks for modern materials design , 1997 .

[22]  W. Cho,et al.  Oncoproteomics: current trends and future perspectives , 2007, Expert review of proteomics.

[23]  C. Mirkin,et al.  Nanoparticle-Based Bio-Bar Codes for the Ultrasensitive Detection of Proteins , 2003, Science.

[24]  Hiroaki Sato,et al.  Matrix-free laser desorption/ionization-mass spectrometry using self-assembled germanium nanodots. , 2007, Analytical chemistry.

[25]  J L West,et al.  A whole blood immunoassay using gold nanoshells. , 2003, Analytical chemistry.

[26]  Elisabetta Gianazza,et al.  Protein stains for proteomic applications: Which, when, why? , 2006, Proteomics.

[27]  R. Dasari,et al.  Ultrasensitive chemical analysis by Raman spectroscopy. , 1999, Chemical reviews.

[28]  C. Watanabe,et al.  Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Mauro Ferrari,et al.  Fractionation of serum components using nanoporous substrates. , 2006, Bioconjugate chemistry.

[30]  H. Craighead,et al.  Mechanical resonant immunospecific biological detector , 2000 .

[31]  Igor L. Medintz,et al.  Multiplexed toxin analysis using four colors of quantum dot fluororeagents. , 2004, Analytical chemistry.

[32]  Peter Nordlander,et al.  Plasmonic nanostructures: artificial molecules. , 2007, Accounts of chemical research.

[33]  Peter Horvatovich,et al.  Biomarker discovery by proteomics: challenges not only for the analytical chemist. , 2006, The Analyst.

[34]  M. Bawendi,et al.  Synthesis and characterization of nearly monodisperse CdE (E = sulfur, selenium, tellurium) semiconductor nanocrystallites , 1993 .

[35]  Guang-Zhong Yang,et al.  ProteomeGRID: towards a high‐throughput proteomics pipeline through opportunistic cluster image computing for two‐dimensional gel electrophoresis , 2004, Proteomics.

[36]  Daniel L Graham,et al.  Magnetoresistive-based biosensors and biochips. , 2004, Trends in biotechnology.

[37]  Mark A. Atwater,et al.  Extinction coefficient of gold nanoparticles with different sizes and different capping ligands. , 2007, Colloids and surfaces. B, Biointerfaces.

[38]  Olga Lyandres,et al.  Real-time glucose sensing by surface-enhanced Raman spectroscopy in bovine plasma facilitated by a mixed decanethiol/mercaptohexanol partition layer. , 2005, Analytical chemistry.

[39]  C. Mirkin,et al.  Scanometric DNA array detection with nanoparticle probes. , 2000, Science.

[40]  Jinwoo Cheon,et al.  Heterostructured magnetic nanoparticles: their versatility and high performance capabilities. , 2007, Chemical communications.

[41]  Li Zhang,et al.  Immobilized carbon nanotubes as matrix for MALDI-TOF-MS analysis: Applications to neutral small carbohydrates , 2005, Journal of the American Society for Mass Spectrometry.

[42]  H. Rothuizen,et al.  Translating biomolecular recognition into nanomechanics. , 2000, Science.

[43]  Y. Ozaki,et al.  Surface-Enhanced Raman Spectroscopy , 2005 .

[44]  C. Mirkin,et al.  Photoinduced Conversion of Silver Nanospheres to Nanoprisms , 2001, Science.

[45]  M. Porter,et al.  Femtomolar detection of prostate-specific antigen: an immunoassay based on surface-enhanced Raman scattering and immunogold labels. , 2003, Analytical chemistry.

[46]  Prem Gurnani,et al.  Pegylated, steptavidin-conjugated quantum dots are effective detection elements for reverse-phase protein microarrays. , 2005, Bioconjugate chemistry.

[47]  Hao Zeng,et al.  Bio-functionalization of monodisperse magnetic nanoparticles and their use as biomolecular labels in a magnetic tunnel junction based sensor. , 2005, The journal of physical chemistry. B.

[48]  Robert L. White,et al.  Towards a magnetic microarray for sensitive diagnostics , 2005 .

[49]  Bing Xu,et al.  Biofunctional magnetic nanoparticles for protein separation and pathogen detection. , 2006, Chemical communications.

[50]  Chad A Mirkin,et al.  The bio-barcode assay for the detection of protein and nucleic acid targets using DTT-induced ligand exchange , 2006, Nature Protocols.

[51]  R. McDermott,et al.  Ultrasensitive magnetic biosensor for homogeneous immunoassay. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[52]  C. Huck,et al.  Mass Spectrometric Identification of Serum Peptides Employing Derivatized Poly(glycidyl methacrylate/divinyl benzene) Particles and μ-HPLC , 2007 .

[53]  Shuming Nie,et al.  Bioconjugated quantum dots for multiplexed and quantitative immunohistochemistry , 2007, Nature Protocols.

[54]  Young-wook Jun,et al.  The President and Society for Analytical Chemistry Gold Medallist , 1973 .

[55]  W. Cho,et al.  Contribution of oncoproteomics to cancer biomarker discovery , 2007, Molecular Cancer.

[56]  Marilyne Sousa,et al.  Investigating the molecular mechanisms of in-plane mechanochemistry on cantilever arrays. , 2007, Journal of the American Chemical Society.

[57]  T. Thundat,et al.  Bioassay of prostate-specific antigen (PSA) using microcantilevers , 2001, Nature Biotechnology.

[58]  Naomi J. Halas,et al.  Nanoengineering of optical resonances , 1998 .

[59]  J. Clifton,et al.  Use of monolithic supports in proteomics technology. , 2007, Journal of chromatography. A.

[60]  Weihong Tan,et al.  Aptamer-modified gold nanoparticles for colorimetric determination of platelet-derived growth factors and their receptors. , 2005, Analytical chemistry.

[61]  A. Lisitsa,et al.  AFM fishing nanotechnology is the way to reverse the Avogadro number in proteomics , 2007, Proteomics.

[62]  D. A. Stuart,et al.  In vivo glucose measurement by surface-enhanced Raman spectroscopy. , 2006, Analytical chemistry.

[63]  D. L. Jeanmaire,et al.  Surface raman spectroelectrochemistry: Part I. Heterocyclic, aromatic, and aliphatic amines adsorbed on the anodized silver electrode , 1977 .

[64]  Diandra L. Leslie-Pelecky,et al.  Magnetic Properties of Nanostructured Materials , 1996 .

[65]  A K Chakraborty,et al.  Origin of nanomechanical cantilever motion generated from biomolecular interactions. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[66]  M. Apuzzo,et al.  Toward the Emergence of Nanoneurosurgery: Part II—Nanomedicine: Diagnostics and Imaging at the Nanoscale Level , 2006, Neurosurgery.

[67]  Juewen Liu,et al.  Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. , 2005, Angewandte Chemie.

[68]  N. Anderson,et al.  The Human Plasma Proteome , 2002, Molecular & Cellular Proteomics.

[69]  F Tokumasu,et al.  Development and application of quantum dots for immunocytochemistry of human erythrocytes , 2003, Journal of microscopy.

[70]  Gil U. Lee,et al.  A biosensor based on magnetoresistance technology. , 1998, Biosensors & bioelectronics.

[71]  A. J. Nijdam,et al.  Nanoporous surfaces as harvesting agents for mass spectrometric analysis of peptides in human plasma. , 2006, Journal of proteome research.

[72]  Shuming Nie,et al.  Quantum dot-encoded beads. , 2005, Methods in molecular biology.

[73]  A. Lu,et al.  Magnetic nanoparticles: synthesis, protection, functionalization, and application. , 2007, Angewandte Chemie.

[74]  Igor L. Medintz,et al.  Proteolytic activity monitored by fluorescence resonance energy transfer through quantum-dot–peptide conjugates , 2006, Nature materials.

[75]  Denis Hochstrasser,et al.  How shall we use the proteomics toolbox for biomarker discovery? , 2007, Journal of proteome research.

[76]  Shimon Weiss,et al.  Synthesis and Properties of Biocompatible Water-Soluble Silica-Coated CdSe/ZnS Semiconductor Quantum Dots† , 2001 .

[77]  F. Švec.  Less common applications of monoliths: preconcentration and solid-phase extraction. , 2006, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[78]  Gengfeng Zheng,et al.  Nanowire sensors for medicine and the life sciences. , 2006, Nanomedicine.

[79]  Nancy H. Finkel,et al.  Ordered silicon nanocavity arrays in surface-assisted desorption/ionization mass spectrometry. , 2005, Analytical chemistry.

[80]  J. McLean,et al.  Size-selected (2-10 nm) gold nanoparticles for matrix assisted laser desorption ionization of peptides. , 2005, Journal of the American Chemical Society.

[81]  S. Fonash,et al.  Desorption-ionization mass spectrometry using deposited nanostructured silicon films. , 2001, Analytical chemistry.

[82]  M. Stevens,et al.  Protease-triggered dispersion of nanoparticle assemblies. , 2007, Journal of the American Chemical Society.

[83]  T. Kinumi,et al.  Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using an inorganic particle matrix for small molecule analysis , 2000, Journal of mass spectrometry : JMS.

[84]  Anja Boisen,et al.  Fabrication and characterization of nanoresonating devices for mass detection , 2000 .

[85]  Chad A Mirkin,et al.  Nanostructures in biodiagnostics. , 2005, Chemical reviews.

[86]  L. Huber,et al.  Zooming in: Fractionation strategies in proteomics , 2004, Proteomics.

[87]  S. L. Westcott,et al.  Infrared extinction properties of gold nanoshells , 1999 .

[88]  D. Zhao,et al.  Preparation of highly ordered mesoporous WO3–TiO2 as matrix in matrix-assisted laser desorption/ionization mass spectrometry , 2005 .

[89]  P. Selby,et al.  Key clinical issues in renal cancer: a challenge for proteomics , 2007, World Journal of Urology.

[90]  Junefredo V. Apon,et al.  Desorption/ionization on silicon nanowires. , 2005, Analytical chemistry.

[91]  Igor L. Medintz,et al.  Quantum dot bioconjugates for imaging, labelling and sensing , 2005, Nature materials.

[92]  G. Siuzdak,et al.  Desorption–ionization mass spectrometry on porous silicon , 1999, Nature.

[93]  A new analytical material-enhanced laser desorption ionization (MELDI) based approach for the determination of low-mass serum constituents using fullerene derivatives for selective enrichment. , 2007, Journal of proteome research.

[94]  S. Nie,et al.  Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules , 2001, Nature Biotechnology.

[95]  H. Lang,et al.  Multiple label-free biodetection and quantitative DNA-binding assays on a nanomechanical cantilever array , 2002, Proceedings of the National Academy of Sciences of the United States of America.