Proteomic LC-MS systems using nanoscale liquid chromatography with tandem mass spectrometry.

Current nano-scale liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) approaches in proteome research are reviewed from an analytical perspective. For comprehensive analysis of cellular proteins, analytical methods with higher resolution, sensitivity, and wider dynamic range are required. Miniaturized LC coupled with tandem mass spectrometry is currently one of the most versatile techniques. In this review, the current status of nanoLC-MS/MS systems as well as data management systems is addressed. In addition, the future prospects for complete proteomics are discussed.

[1]  A. Stensballe,et al.  Characterization of phosphoproteins from electrophoretic gels by nanoscale Fe(III) affinity chromatography with off‐line mass spectrometry analysis , 2001, Proteomics.

[2]  T. Veenstra,et al.  The Human Plasma Proteome , 2004, Molecular & Cellular Proteomics.

[3]  Wayne F. Patton,et al.  Two-dimensional gel electrophoresis; better than a poke in the ICAT? , 2002, Current opinion in biotechnology.

[4]  Liang Li,et al.  Continuous-flow matrix-assisted laser desorption ionization mass spectrometry , 1993 .

[5]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[6]  Magnus Palmblad,et al.  Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry. , 2002, Analytical chemistry.

[7]  Naoki Asakawa,et al.  Highly robust stainless steel tips as microelectrospray emitters. , 2002, Rapid communications in mass spectrometry : RCM.

[8]  T. Niwa,et al.  Stepwise gradient elution using switching valves in micro high-performance liquid chromatography , 1987 .

[9]  B. Cargile,et al.  Immobilized pH gradients as a first dimension in shotgun proteomics and analysis of the accuracy of pI predictability of peptides , 2004, Electrophoresis.

[10]  Nilsson,et al.  Capillary liquid chromatography interfaced to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using an on-line coupled piezoelectric flow-through microdispenser , 2000, Journal of mass spectrometry : JMS.

[11]  Ruedi Aebersold,et al.  Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. , 2002, Journal of proteome research.

[12]  Soga,et al.  Performance of a monolithic silica column in a capillary under pressure-driven and electrodriven conditions , 2000, Analytical chemistry.

[13]  M. Karas,et al.  Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. , 1988, Analytical chemistry.

[14]  S. Ito,et al.  Nanoflow gradient generator for capillary high-performance liquid chromatography. , 2004, Analytical chemistry.

[15]  N. Smith,et al.  The analysis of pharmaceutical compounds using electrochromatography , 1994 .

[16]  Frank J. Yang.  Fused-silica narrow-bore microparticle-packed-column high-performance liquid chromatography , 1982 .

[17]  T. S. Stevens,et al.  Porous ceramic bed supports for fused silica packed capillary columns used in liquid chromatography , 1987 .

[18]  S. Gygi,et al.  Automation of nanoscale microcapillary liquid chromatography-tandem mass spectrometry with a vented column. , 2002, Analytical chemistry.

[19]  F. Cross,et al.  Accurate quantitation of protein expression and site-specific phosphorylation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Koichi Tanaka,et al.  Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry , 1988 .

[21]  J. Yates,et al.  Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. , 1998, Analytical biochemistry.

[22]  J. Fenn,et al.  Electrospray ion source: another variation on the free-jet theme , 1984 .

[23]  M. Mann,et al.  Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[24]  N. Ishioka,et al.  Automated tandem high-performance liquid chromatographic system for separation of extremely complex peptide mixtures. , 1985, Journal of chromatography.

[25]  T. Takeuchi,et al.  Ultra-micro high-performance liquid chromatography , 1980 .

[26]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[27]  H. Meiring,et al.  Nanoscale LC–MS(n): technical design and applications to peptide and protein analysis , 2002 .

[28]  J. Jorgenson,et al.  Preparation and evaluation of slurry-packed liquid chromatography microcolumns with inner diameters from 12 to 33 μm , 1996 .

[29]  Ruedi Aebersold,et al.  The study of macromolecular complexes by quantitative proteomics , 2003, Nature Genetics.

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

[31]  T. Lee,et al.  Low flow high-performance liquid chromatography solvent delivery system designed for tandem capillary liquid chromatography-mass spectrometry , 1995, Journal of the American Society for Mass Spectrometry.

[32]  E. P. Maziarz,et al.  Polyaniline: A conductive polymer coating for durable nanospray emitters , 2000, Journal of the American Society for Mass Spectrometry.

[33]  L. Licklider,et al.  A microscale electrospray interface incorporating a monolithic, poly(styrene-divinylbenzene) support for on-line liquid chromatography/tandem mass spectrometry analysis of peptides and proteins. , 1998, Analytical chemistry.

[34]  T. Takeuchi,et al.  High-performance micro packed flexible columns in liquid chromatography , 1981 .

[35]  F. McLafferty,et al.  Attomole Protein Characterization by Capillary Electrophoresis-Mass Spectrometry , 1996, Science.

[36]  Blagoy Blagoev,et al.  A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling , 2003, Nature Biotechnology.

[37]  A. Shevchenko,et al.  Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry , 1996, Nature.

[38]  M. Mann,et al.  Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. , 2003, Analytical chemistry.

[39]  Terry D. Lee,et al.  Rapid protein identification using a microscale electrospray LC/MS system on an ion trap mass spectrometer , 1998, Journal of the American Society for Mass Spectrometry.

[40]  L. Deterding,et al.  Coaxial continuous flow fast atom bombardment in conjunction with tandem mass spectrometry for the analysis of biomolecules. , 1989, Analytical chemistry.

[41]  M. Wilm,et al.  Error-tolerant identification of peptides in sequence databases by peptide sequence tags. , 1994, Analytical chemistry.

[42]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[43]  M. Novotny,et al.  Dead-volume free termination for packed columns in microcapillary liquid chromatography. , 1984, Analytical chemistry.

[44]  B. Karger,et al.  On-line MALDI-TOF MS using a continuous vacuum deposition interface. , 1998, Analytical chemistry.

[45]  John I. Clark,et al.  Shotgun identification of protein modifications from protein complexes and lens tissue , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[46]  J. Shabanowitz,et al.  Subfemtomole MS and MS/MS peptide sequence analysis using nano-HPLC micro-ESI fourier transform ion cyclotron resonance mass spectrometry. , 2000, Analytical chemistry.

[47]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[48]  Tohru Natsume,et al.  A direct nanoflow liquid chromatography-tandem mass spectrometry system for interaction proteomics. , 2002, Analytical chemistry.

[49]  J. Jorgenson,et al.  Preparation and evaluation of packed capillary liquid chromatography columns with inner diameters from 20 to 50 μm , 1989 .

[50]  Gusev,et al.  A novel interface for on-line coupling of liquid capillary chromatography with matrix-assisted laser desorption/ionization detection , 1999, Rapid communications in mass spectrometry : RCM.

[51]  M. Goto,et al.  Direct coupling of micro high-performance liquid chromatography with fast atom bombardment mass spectrometry , 1985 .

[52]  J. Stults,et al.  Analysis of protein digests by capillary high-performance liquid chromatography and on-line fast atom bombardment mass spectrometry. , 1990, Analytical biochemistry.

[53]  R. Caprioli,et al.  Capillary electrophoresis combined with matrix-assisted laser desorption/ionization mass spectrometry; continuous sample deposition on a matrix-precoated membrane target. , 1996, Journal of mass spectrometry : JMS.

[54]  M. Novotny,et al.  Separation efficiency of slurry-packed liquid chromatography microcolumns with very small inner diameters. , 1988, Analytical chemistry.

[55]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[56]  Richard D. Smith,et al.  High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. , 2002, Analytical chemistry.

[57]  John R Yates,et al.  Analysis of quantitative proteomic data generated via multidimensional protein identification technology. , 2002, Analytical chemistry.

[58]  T Sasagawa,et al.  Prediction of peptide retention times. , 1988, Journal of chromatography.

[59]  W. T. Moore,et al.  Microbore HPLC/mass spectrometry for the analysis of peptide mixtures using a continuous flow interface. , 1987, Biochemical and biophysical research communications.

[60]  M. Mann,et al.  Trypsin Cleaves Exclusively C-terminal to Arginine and Lysine Residues*S , 2004, Molecular & Cellular Proteomics.

[61]  Y. Ishihama,et al.  Surfactants usable for electrospray ionization mass spectrometry. , 2000, Analytical biochemistry.

[62]  R. Hensel,et al.  Electrospray sample preparation for improved quantitation in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. , 1997, Rapid communications in mass spectrometry : RCM.

[63]  D Figeys,et al.  Nanoflow gradient generator coupled with mu-LC-ESI-MS/MS for protein identification. , 2001, Analytical chemistry.

[64]  Pavel A. Pevzner,et al.  De Novo Peptide Sequencing via Tandem Mass Spectrometry , 1999, J. Comput. Biol..

[65]  M. Mann,et al.  Large-scale Proteomic Analysis of the Human Spliceosome References , 2006 .

[66]  T. Takeuchi,et al.  Continuous gradient elution in micro high-performance liquid chromatography , 1982 .

[67]  M. Dreux,et al.  Ion-pair reversed-phase liquid chromatography-electrospray mass spectrometry for the analysis of underivatized small peptides. , 2002, Journal of chromatography. A.

[68]  R. Henderson,et al.  Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. , 1992, Science.

[69]  J. Yates,et al.  Direct analysis of protein complexes using mass spectrometry , 1999, Nature Biotechnology.

[70]  K. Murray,et al.  Liquid sample introduction for matrix-assisted laser desorption ionization , 1993 .

[71]  David Fenyö,et al.  RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database , 2002, Proteomics.

[72]  R. Kennedy,et al.  Capillary LC-MS2 at the attomole level for monitoring and discovering endogenous peptides in microdialysis samples collected in vivo. , 2001, Analytical chemistry.

[73]  A. Bruins.  Proceedings of the 46th ASMS Conference on Mass Spectrometry and Allied Topics , 1998 .

[74]  T. Veenstra,et al.  Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics. , 2001, Analytical chemistry.

[75]  Neil Hall,et al.  Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry , 2002, Nature.

[76]  J. Shabanowitz,et al.  Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae , 2002, Nature Biotechnology.

[77]  R. Aebersold,et al.  A simplified gradient solvent delivery system for capillary liquid chromatography-electrospray ionization mass spectrometry. , 1998, Analytical biochemistry.

[78]  K. Markides,et al.  A design for low-flow sheathless electrospray emitters. , 1999, Analytical chemistry.

[79]  Joshua E. Elias,et al.  Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. , 2003, Journal of proteome research.

[80]  T. Takeuchi,et al.  Application of ultra-micro high-performance liquid chromatography to trace analysis , 1981 .

[81]  T. Takeuchi,et al.  MICRO HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY , 1982 .

[82]  Scott A. Busby,et al.  Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications. , 2004, Journal of proteome research.

[83]  L. Nyholm,et al.  A simple and robust conductive graphite coating for sheathless electrospray emitters used in capillary electrophoresis/mass spectrometry. , 2001, Rapid communications in mass spectrometry : RCM.

[84]  J. Yates,et al.  An automated multidimensional protein identification technology for shotgun proteomics. , 2001, Analytical chemistry.

[85]  J. Meek.  Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[86]  R. Caprioli,et al.  Micro-electrospray mass spectrometry: Ultra-high-sensitivity analysis of peptides and proteins , 1994, Journal of the American Society for Mass Spectrometry.

[87]  Waltraud X. Schulze,et al.  A Novel Proteomic Screen for Peptide-Protein Interactions* , 2004, Journal of Biological Chemistry.

[88]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[89]  Chris F. Taylor,et al.  A systematic approach to modeling, capturing, and disseminating proteomics experimental data , 2003, Nature Biotechnology.

[90]  M. Wilm,et al.  Electrospray and Taylor-Cone theory, Dole's beam of macromolecules at last? , 1994 .

[91]  A. Heck,et al.  Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. , 2004, Analytical chemistry.

[92]  Gordon A Anderson,et al.  Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. , 2003, Analytical chemistry.

[93]  S. Gygi,et al.  Development of a multiplexed microcapillary liquid chromatography system for high-throughput proteome analysis. , 2002, Analytical chemistry.