Advances in shotgun proteomics and the analysis of membrane proteomes.

The emergence of shotgun proteomics has facilitated the numerous biological discoveries made by proteomic studies. However, comprehensive proteomic analysis remains challenging and shotgun proteomics is a continually changing field. This review details the recent developments in shotgun proteomics and describes emerging technologies that will influence shotgun proteomics going forward. In addition, proteomic studies of integral membrane proteins remain challenging due to the hydrophobic nature in integral membrane proteins and their general low abundance levels. However, there have been many strategies developed for enriching, isolating and separating membrane proteins for proteomic analysis that have moved this field forward. In summary, while shotgun proteomics is a widely used and mature technology, the continued pace of improvements in mass spectrometry and proteomic technology and methods indicate that future studies will have an even greater impact on biological discovery.

[1]  Linfeng Wu,et al.  A Systematic Characterization of Mitochondrial Proteome from Human T Leukemia Cells*S , 2005, Molecular & Cellular Proteomics.

[2]  S. Nie,et al.  Proteomic analysis of mouse liver plasma membrane: Use of differential extraction to enrich hydrophobic membrane proteins , 2005, Proteomics.

[3]  P. Lehner,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture and Differential Plasma Membrane Proteome Quantitation Identify New Substrates for the MARCH9 Transmembrane E3 Ligase , 2009, Molecular & Cellular Proteomics.

[4]  D. B. Weatherly,et al.  Glycoproteomics of Trypanosoma cruzi trypomastigotes using subcellular fractionation, lectin affinity, and stable isotope labeling. , 2006, Journal of proteome research.

[5]  D. Wessel,et al.  A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. , 1984, Analytical biochemistry.

[6]  Christine C. Wu,et al.  Shotgun analysis of integral membrane proteins facilitated by elevated temperature. , 2007, Analytical chemistry.

[7]  P. Andrews,et al.  Quantitative Proteomics Analysis of Cell Cycle-regulated Golgi Disassembly and Reassembly* , 2010, The Journal of Biological Chemistry.

[8]  Florian Gnad,et al.  Precision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints , 2010, Cell.

[9]  Michael J MacCoss,et al.  Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics. , 2008, Analytical chemistry.

[10]  K. Medzihradszky.  Characterization of protein N-glycosylation. , 2005, Methods in enzymology.

[11]  Xian-hui He,et al.  Quantitative Proteomics Analysis of Chondrogenic Differentiation of C3H10T1/2 Mesenchymal Stem Cells by iTRAQ Labeling Coupled with On-line Two-dimensional LC/MS/MS* , 2009, Molecular & Cellular Proteomics.

[12]  Norman Pavelka,et al.  Delayed Correlation of mRNA and Protein Expression in Rapamycin-treated Cells and a Role for Ggc1 in Cellular Sensitivity to Rapamycin* , 2009, Molecular & Cellular Proteomics.

[13]  Liang Li,et al.  Microwave-assisted acid hydrolysis of proteins combined with liquid chromatography MALDI MS/MS for protein identification , 2005, Journal of the American Society for Mass Spectrometry.

[14]  B. Persson,et al.  Quantitative membrane proteomics applying narrow range peptide isoelectric focusing for studies of small cell lung cancer resistance mechanisms , 2008, Proteomics.

[15]  D. Tabb,et al.  Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry. , 2008, Journal of proteome research.

[16]  Jean-Claude Martinou,et al.  Proteomic Analysis of the Mouse Liver Mitochondrial Inner Membrane* , 2003, Journal of Biological Chemistry.

[17]  J. Dolan.  Temperature selectivity in reversed-phase high performance liquid chromatography. , 2002, Journal of chromatography. A.

[18]  Michael Hecker,et al.  A Comprehensive Proteomics and Transcriptomics Analysis of Bacillus subtilis Salt Stress Adaptation , 2009, Journal of bacteriology.

[19]  Ruedi Aebersold,et al.  Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry , 2003, Nature Biotechnology.

[20]  Bradford W. Gibson,et al.  Characterization of the human heart mitochondrial proteome , 2003, Nature Biotechnology.

[21]  S. Sugano,et al.  Cell Surface Labeling and Mass Spectrometry Reveal Diversity of Cell Surface Markers and Signaling Molecules Expressed in Undifferentiated Mouse Embryonic Stem Cells *S , 2005, Molecular & Cellular Proteomics.

[22]  C. Fenselau,et al.  Integration of Jacobson's pellicle method into proteomic strategies for plasma membrane proteins. , 2004, Journal of proteome research.

[23]  S. Liang,et al.  Proteomic analysis of low-abundant integral plasma membrane proteins based on gels , 2006, Cellular and Molecular Life Sciences.

[24]  J. Yates,et al.  Quantitative proteomic analysis of primary neurons reveals diverse changes in synaptic protein content in fmr1 knockout mice , 2008, Proceedings of the National Academy of Sciences.

[25]  D. Stolz,et al.  Examination of transcellular membrane protein polarity of bovine aortic endothelial cells in vitro using the cationic colloidal silica microbead membrane-isolation procedure. , 1992, Journal of cell science.

[26]  J. Klose.  Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues , 1975, Humangenetik.

[27]  Hwee Tong Tan,et al.  Membrane proteins and membrane proteomics , 2008, Proteomics.

[28]  V. Bafna,et al.  Proteogenomics to discover the full coding content of genomes: a computational perspective. , 2010, Journal of proteomics.

[29]  Allan Stensballe,et al.  Proteomic Analysis of Glycosylphosphatidylinositol-anchored Membrane Proteins* , 2003, Molecular & Cellular Proteomics.

[30]  M. Baker,et al.  A combination of immobilised pH gradients improves membrane proteomics. , 2008, Journal of proteome research.

[31]  E. Heinzle,et al.  Two-dimensional reversed-phase x ion-pair reversed-phase HPLC: an alternative approach to high-resolution peptide separation for shotgun proteome analysis. , 2007, Journal of proteome research.

[32]  Ten-Yang Yen,et al.  Proteins at membrane surfaces-a review of approaches. , 2007, Molecular bioSystems.

[33]  M. Fountoulakis,et al.  Enrichment of low-copy-number gene products by hydrophobic interaction chromatography. , 1999, Journal of chromatography. A.

[34]  Stephen Barnes,et al.  High throughput two‐dimensional blue‐native electrophoresis: A tool for functional proteomics of mitochondria and signaling complexes , 2002, Proteomics.

[35]  M. Dunn,et al.  Comparative analysis of OFFGel, strong cation exchange with pH gradient, and RP at high pH for first‐dimensional separation of peptides from a membrane‐enriched protein fraction , 2009, Proteomics.

[36]  David W. Speicher,et al.  Comparison of Extensive Protein Fractionation and Repetitive LC-MS/MS Analyses on Depth of Analysis for Complex Proteomes , 2009, Journal of proteome research.

[37]  W. Holt,et al.  Global profiling of surface plasma membrane proteome of oviductal epithelial cells. , 2006, Journal of proteome research.

[38]  J. Bruce,et al.  Profiling the membrane proteome of Shewanella oneidensis MR-1 with new affinity labeling probes. , 2007, Journal of proteome research.

[39]  F. Krause.  Detection and analysis of protein–protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (Membrane) protein complexes and supercomplexes , 2006, Electrophoresis.

[40]  Y. She,et al.  Identification of the hydrophobic glycoproteins of Caenorhabditis elegans. , 2005, Glycobiology.

[41]  G. McAlister,et al.  Decision tree–driven tandem mass spectrometry for shotgun proteomics , 2008, Nature Methods.

[42]  J I Garrels,et al.  Transformation-sensitive and growth-related changes of protein synthesis in REF52 cells. A two-dimensional gel analysis of SV40-, adenovirus-, and Kirsten murine sarcoma virus-transformed rat cells using the REF52 protein database. , 1989, The Journal of biological chemistry.

[43]  M. Washburn,et al.  Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors , 2006, Proceedings of the National Academy of Sciences.

[44]  L. Snyder.  Changing reversed-phase high performance liquid chromatography selectivity. Which variables should be tried first? , 1997, Journal of chromatography. B, Biomedical sciences and applications.

[45]  F. Levander,et al.  Membrane protein identification: N-terminal labeling of nontryptic membrane protein peptides facilitates database searching. , 2008, Journal of proteome research.

[46]  G. Bensi,et al.  Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome , 2006, Nature Biotechnology.

[47]  A. Gooley,et al.  Proteomic analysis of the Escherichia coli outer membrane. , 2000, European journal of biochemistry.

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

[49]  Beatrix Ueberheide,et al.  Protein identification using sequential ion/ion reactions and tandem mass spectrometry. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[50]  Alexey I Nesvizhskii,et al.  Investigation of neutral loss during collision-induced dissociation of peptide ions. , 2005, Analytical chemistry.

[51]  M. Baker,et al.  Characterization of the rat liver membrane proteome using peptide immobilized pH gradient isoelectric focusing. , 2008, Journal of proteome research.

[52]  Bernard Monsarrat,et al.  A Label-free Quantitative Proteomics Strategy to Identify E3 Ubiquitin Ligase Substrates Targeted to Proteasome Degradation* , 2009, Molecular & Cellular Proteomics.

[53]  David L. Tabb,et al.  A proteomic view of the Plasmodium falciparum life cycle , 2002, Nature.

[54]  Daniel B. McClatchy,et al.  Comparisons of mass spectrometry compatible surfactants for global analysis of the mammalian brain proteome. , 2008, Analytical chemistry.

[55]  D. Wolters,et al.  The two‐phase partitioning system – a powerful technique to purify integral membrane proteins of Corynebacterium glutamicum for quantitative shotgun analysis , 2009, Proteomics.

[56]  D. Wolters,et al.  Physiological adaptation of Corynebacterium glutamicum to benzoate as alternative carbon source – a membrane proteome‐centric view , 2009, Proteomics.

[57]  Albert J R Heck,et al.  Quantitative erythrocyte membrane proteome analysis with Blue-native/SDS PAGE. , 2010, Journal of proteomics.

[58]  Bernhard Kuster,et al.  Profiling Core Proteomes of Human Cell Lines by One-dimensional PAGE and Liquid Chromatography-Tandem Mass Spectrometry*S , 2003, Molecular & Cellular Proteomics.

[59]  R. Carrozzo,et al.  Functional assays in high‐resolution clear native gels to quantify mitochondrial complexes in human biopsies and cell lines , 2007, Electrophoresis.

[60]  M. Kubbutat,et al.  Workflow comparison for label-free, quantitative secretome proteomics for cancer biomarker discovery: method evaluation, differential analysis, and verification in serum. , 2010, Journal of proteome research.

[61]  Masaru Tomita,et al.  Unbiased Quantitation of Escherichia coli Membrane Proteome Using Phase Transfer Surfactants* , 2009, Molecular & Cellular Proteomics.

[62]  Ying Zhang,et al.  Effect of dynamic exclusion duration on spectral count based quantitative proteomics. , 2009, Analytical chemistry.

[63]  A. Makarov,et al.  The Orbitrap: a new mass spectrometer. , 2005, Journal of mass spectrometry : JMS.

[64]  R. Beavis,et al.  Lectin affinity as an approach to the proteomic analysis of membrane glycoproteins. , 2004, Journal of proteome research.

[65]  S. Gygi,et al.  Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[66]  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.

[67]  P. O’Farrell.  High resolution two-dimensional electrophoresis of proteins. , 1975, The Journal of biological chemistry.

[68]  C. Fenselau,et al.  Unbiased examination of changes in plasma membrane proteins in drug resistant cancer cells. , 2005, Journal of proteome research.

[69]  M. Molloy,et al.  Membrane proteins and proteomics: Un amour impossible? , 2000, Electrophoresis.

[70]  Manesh B Shah,et al.  Cross-species Global Proteomics Reveals Conserved and Unique Processes in Phytophthora sojae and Phytophthora ramorum*S , 2008, Molecular & Cellular Proteomics.

[71]  C. Emanuelsson,et al.  Aqueous two-phase partitioning for proteomic monitoring of cell surface biomarkers in human peripheral blood mononuclear cells. , 2006, Journal of proteome research.

[72]  M. Washburn,et al.  Multidimensional separations-based shotgun proteomics. , 2007, Chemical reviews.

[73]  B. Franza,et al.  The Ref52 Protein Database , 1988 .

[74]  Lingjun Li,et al.  Comparison of two-dimensional fractionation techniques for shotgun proteomics. , 2008, Analytical chemistry.

[75]  T. Meyer,et al.  Identification of Helicobacter pylori surface proteins by selective proteinase K digestion and antibody phage display. , 2005, Journal of microbiological methods.

[76]  Michael K. Coleman,et al.  Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. , 2006, Journal of proteome research.

[77]  R. Wahl,et al.  Towards defining the urinary proteome using liquid chromatography‐tandem mass spectrometry I.Profiling an unfractionated tryptic digest , 2001, Proteomics.

[78]  Michael Olivier,et al.  Improved method for the analysis of membrane proteins by mass spectrometry. , 2007, Physiological genomics.

[79]  G. Scheele.  Two-Dimensional Gel Analysis of Soluble Proteins , 1975 .

[80]  J. Gebler,et al.  Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions. , 2005, Journal of separation science.

[81]  J. Garrels.  The QUEST system for quantitative analysis of two-dimensional gels. , 1989, The Journal of biological chemistry.

[82]  Christine C. Wu,et al.  Quantitative strategies to fuel the merger of discovery and hypothesis-driven shotgun proteomics. , 2009, Briefings in functional genomics & proteomics.

[83]  R. Aebersold,et al.  Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry , 2001, Nature Biotechnology.

[84]  L. Foster,et al.  Quantitative analysis of proteome coverage and recovery rates for upstream fractionation methods in proteomics. , 2010, Journal of proteome research.

[85]  Lennart Martens,et al.  Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research , 2010, Journal of proteomics.

[86]  H. Schägger,et al.  Blue native PAGE , 2006, Nature Protocols.

[87]  T. Rabilloud,et al.  Two-dimensional gel electrophoresis in proteomics: Past, present and future. , 2010, Journal of proteomics.

[88]  B. Blagoev,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Quantitative Comparison of the Membrane Proteomes of Self-renewing and Differentiating Human Embryonic Stem Cells*S , 2009, Molecular & Cellular Proteomics.

[89]  D. Hochstrasser,et al.  The dynamic range of protein expression: A challenge for proteomic research , 2000, Electrophoresis.

[90]  John R Yates,et al.  Proteomics by mass spectrometry: approaches, advances, and applications. , 2009, Annual review of biomedical engineering.

[91]  J. Coon,et al.  Value of using multiple proteases for large-scale mass spectrometry-based proteomics. , 2010, Journal of proteome research.

[92]  J. Pronk,et al.  A three‐way proteomics strategy allows differential analysis of yeast mitochondrial membrane protein complexes under anaerobic and aerobic conditions , 2009, Proteomics.

[93]  Tabiwang N. Arrey,et al.  Membrane protein analysis using an improved peptic in‐solution digestion protocol , 2009, Proteomics.

[94]  Lewis Y. Geer,et al.  Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry , 2007, Proceedings of the National Academy of Sciences.

[95]  Joseph J. Pereira,et al.  Proteomic analysis of the human colon carcinoma cell line (LIM 1215): Development of a membrane protein database , 2000, Electrophoresis.

[96]  D. Matthews,et al.  Proteomics Analysis of the Nucleolus in Adenovirus-infected Cells , 2009, Molecular & Cellular Proteomics.

[97]  K. Schey,et al.  Proteolysis and mass spectrometric analysis of an integral membrane: aquaporin 0. , 2004, Journal of proteome research.

[98]  D. Natale,et al.  Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes. , 2010, Journal of proteome research.

[99]  H. Schägger,et al.  Features and applications of blue‐native and clear‐native electrophoresis , 2008, Proteomics.

[100]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[101]  Daniel B. McClatchy,et al.  Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. , 2007, Genome research.

[102]  K. Pfeiffer,et al.  Supercomplexes in the respiratory chains of yeast and mammalian mitochondria , 2000, The EMBO journal.

[103]  R. Schlapbach,et al.  Identification and relative quantification of membrane proteins by surface biotinylation and two‐dimensional peptide mapping , 2005, Proteomics.

[104]  J. Shabanowitz,et al.  Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[105]  J. Clifton,et al.  Mammalian plasma membrane proteomics , 2007, Proteomics.

[106]  Erika L. Lawson,et al.  Use of magnetic beads with immobilized monoclonal antibodies for isolation of highly pure plasma membranes , 2006, Electrophoresis.

[107]  M. Mann,et al.  Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast , 2008, Nature.

[108]  Ronald J. Moore,et al.  Enrichment of integral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry. , 2002, Journal of proteome research.

[109]  T. Kislinger,et al.  Peptide separations by on-line MudPIT compared to isoelectric focusing in an off-gel format: application to a membrane-enriched fraction from C2C12 mouse skeletal muscle cells. , 2009, Journal of proteome research.

[110]  K. Resing,et al.  Mapping protein post-translational modifications with mass spectrometry , 2007, Nature Methods.

[111]  T. Stevens,et al.  Do more complex organisms have a greater proportion of membrane proteins in their genomes? , 2000, Proteins.

[112]  J I Garrels,et al.  The REF52 protein database. Methods of database construction and analysis using the QUEST system and characterizations of protein patterns from proliferating and quiescent REF52 cells. , 1989, The Journal of biological chemistry.

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

[114]  Samuel I. Miller,et al.  Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides. , 2008, Analytical chemistry.

[115]  Daniel B. McClatchy,et al.  Strategies for shotgun identification of integral membrane proteins by tandem mass spectrometry , 2008, Proteomics.

[116]  Christine C. Wu,et al.  Proteomics of Integral Membrane Proteins — Theory and Application , 2007 .

[117]  Yan Li,et al.  Subtractive proteomic mapping of the endothelial surface in lung and solid tumours for tissue-specific therapy , 2004, Nature.

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

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

[120]  M. Mann,et al.  Universal sample preparation method for proteome analysis , 2009, Nature Methods.

[121]  Y. Fujiki,et al.  Isolation of intracellular membranes by means of sodium carbonate treatment: application to endoplasmic reticulum , 1982, The Journal of cell biology.

[122]  B. Jacobson,et al.  Coating cells with colloidal silica for high yield isolation of plasma membrane sheets and identification of transmembrane proteins. , 1983, The Journal of biological chemistry.

[123]  P Berndt,et al.  Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography , 1999, Electrophoresis.

[124]  Ilka Wittig,et al.  High Resolution Clear Native Electrophoresis for In-gel Functional Assays and Fluorescence Studies of Membrane Protein Complexes* , 2007, Molecular & Cellular Proteomics.

[125]  M. Münchbach,et al.  Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. , 2000, Analytical chemistry.

[126]  Alexey I Nesvizhskii,et al.  Analysis and validation of proteomic data generated by tandem mass spectrometry , 2007, Nature Methods.

[127]  T. Griffin,et al.  Quantitative Nuclear Proteomics Identifies mTOR Regulation of DNA Damage Response* , 2009, Molecular & Cellular Proteomics.

[128]  A. Varki,et al.  Overview of Glycoconjugate Analysis , 2009, Current protocols in protein science.

[129]  K. Tomer,et al.  Quantitative Proteomics Analysis of Macrophage Rafts Reveals Compartmentalized Activation of the Proteasome and of Proteasome-mediated ERK Activation in Response to Lipopolysaccharide*S , 2009, Molecular & Cellular Proteomics.

[130]  H. Schägger,et al.  Analysis of molecular masses and oligomeric states of protein complexes by blue native electrophoresis and isolation of membrane protein complexes by two-dimensional native electrophoresis. , 1994, Analytical biochemistry.

[131]  Ruedi Aebersold,et al.  Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins , 2009, Nature Biotechnology.

[132]  John R Yates,et al.  Nuclear Membrane Proteins with Potential Disease Links Found by Subtractive Proteomics , 2003, Science.

[133]  J. Gebler,et al.  Orthogonality of separation in two-dimensional liquid chromatography. , 2005, Analytical chemistry.

[134]  Ilka Wittig,et al.  Advantages and limitations of clear‐native PAGE , 2005, Proteomics.

[135]  Albert Sickmann,et al.  Proteomic analysis of the yeast mitochondrial outer membrane reveals accumulation of a subclass of preproteins. , 2005, Molecular biology of the cell.

[136]  J. Yates,et al.  A method for the comprehensive proteomic analysis of membrane proteins , 2003, Nature Biotechnology.

[137]  M. Mann,et al.  Precision proteomics: The case for high resolution and high mass accuracy , 2008, Proceedings of the National Academy of Sciences.

[138]  John D. Venable,et al.  Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples. , 2006, Analytical chemistry.

[139]  G. Heijne,et al.  Genome‐wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms , 1998, Protein science : a publication of the Protein Society.

[140]  Wei Zhang,et al.  Proteomic analysis of integral plasma membrane proteins. , 2004, Analytical chemistry.

[141]  B. Cargile,et al.  Gel based isoelectric focusing of peptides and the utility of isoelectric point in protein identification. , 2004, Journal of proteome research.

[142]  Steven P. Gygi,et al.  Identification of β-Secretase (BACE1) Substrates Using Quantitative Proteomics , 2009, PloS one.

[143]  J. Monshouwer-Kloots,et al.  Identification of cell surface proteins for antibody-based selection of human embryonic stem cell-derived cardiomyocytes. , 2010, Journal of proteome research.

[144]  H. Schägger,et al.  Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. , 1991, Analytical biochemistry.

[145]  Dirk Wolters,et al.  Proteomic survey of metabolic pathways in rice , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[146]  Eberhard Durr,et al.  Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture , 2004, Nature Biotechnology.

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

[148]  E. Friauf,et al.  Proteomic Analysis of Brain Plasma Membranes Isolated by Affinity Two-phase Partitioning*S , 2006, Molecular & Cellular Proteomics.

[149]  Tabiwang N. Arrey,et al.  Elastase Digests , 2009, Molecular & Cellular Proteomics.

[150]  A. Heck,et al.  Orthogonal separation techniques for the characterization of the yeast nuclear proteome. , 2009, Journal of proteome research.

[151]  F. Boisvert,et al.  A Quantitative Proteomics Analysis of Subcellular Proteome Localization and Changes Induced by DNA Damage , 2009, Molecular & Cellular Proteomics.

[152]  Linfeng Wu,et al.  Role of spectral counting in quantitative proteomics , 2010, Expert review of proteomics.

[153]  Alexey I Nesvizhskii,et al.  Quantitative Proteomic Profiling of Prostate Cancer Reveals a Role for miR-128 in Prostate Cancer* , 2009, Molecular & Cellular Proteomics.

[154]  T. Maeda,et al.  Preparative two‐dimensional gel electrophoresis with agarose gels in the first dimension for high molecular mass proteins , 2000, Electrophoresis.