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Chemistry Techniques, AnalyticalAccess restricted to Stanford unless otherwise noted

  • Prof. Mark Reimers covers the best ways to design and interpret microarray gene expression experiments, including experiment design, pre-processing, exploratory analysis, normalization and statistical testing.
  • Introduction: Proteins analysis using mass spectrometry. -- Molecular scanner development: toward clinical molecular scanner for proteome research: parallel protein chemical processing before and during western-blot. -- Quantitation during electroblotting step: enhanced protein recovery after electrotransfer using square wave alternating voltage. -- Signal traitment and virtual imaging (1/2): a molecular scanner to highly automated research and to display proteome images. -- Signal traitment and virtual imaging (2/2): visualization and analysis of molecular scanner peptide mass spectra. -- Improvement in the peptide mass fingerprint protein identification (1/2): hydrogen/deuterium exchange for higher specificity of protein identification by peptide mass fingerprinting. -- Improvement in the peptide mass fingerprint protein identification (2/2): MALDI-MS/MS with high resolution and sensitivity for identification and characterization of proteins. -- Proteomic and mass spectrometry: some aspects and recent developments. -- Conclusions and perspectives.
  • pt. A. Small molecule sensing -- pt. B. Macromolecular sensing.
  • IR spectroscopy has become without any doubt a key technique to answer questions raised when studying the interaction of proteins or peptides with solid surfaces for a fundamental point of view as well as for technological applications. Principle, experimental set ups, parameters and interpretation rules of several advanced IR-based techniques; application to biointerface characterisation through the presentation of recent examples, will be given in this book. It will describe how to characterise amino acids, protein or bacterial strain interactions with metal and oxide surfaces, by using infrared spectroscopy, in vacuum, in the air or in an aqueous medium. Results will highlight the performances and perspectives of the technique. Description of the principles, expermental setups and parameter interpretation, and the theory for several advanced IR-based techniques for interface characterisation. Contains examples which demonstrate the capacity, potential and limits of the IR techniques. Helps finding the most adequate mode of analysis. Contains examples. Contains a glossary by techniques and by keywords.
  • Biological mass spectrometry 2005, ScienceDirect
  • Overview of Capillary Electrophoresis in Pharmaceutical Analysis -- Theoretical Consideration in Performance of Various Modes of CE -- Equipment Considerations for Capillary Electrophoresis -- Method Development for Pharmaceutical Analysis -- Role of CE in Drug Substance and Drug Product Development -- General Considerations to Improve Performance of CE Methods -- Overview of Current Regulatory Guidance -- Qualification of CE Instrumentation -- Robustness Testing of CE Methods -- Validation of Analytical Methods Using Capillary Electrophoresis-- The Need for CE Methods in Pharmacopeial Monographs -- CE in Impurity Profiling of Drugs -- Ion Analysis Using Capillary Electrophoresis -- Role of CE in Biopharmaceutical Development and Quality Control -- Capillary Electrophoresis and Bioanalysis -- CE as an Orthogonal Technique to Chromatography -- Capillary Electrochromatography of Pharmaceuticals -- Coupling CE and Chip-based Devices and Mass Spectrometry.
  • Chemical genomics 2005, Springer Protocols
  • Circadian rhythms 2007, Springer Protocols
    Basic protocols for drosophila S2 cell line: maintenance and transfection / M. Fernanda Ceriani -- Co-immunoprecipitation on drosophila cells in culture / M. Fernanda Ceriani -- Basic protocols for zebrafish cell lines: maintenance and transfection / Daniela Vallone ... [et al.] -- Manipulation of mammalian cell lines for circadian studies / Filippo Tamanini -- Reporter assays / M. Fernanda Ceriani -- Use of firefly luciferase activity assays to monitor circadian molecular rhythms in vivo and in vitro / Wangjie Yu and Paul E. Hardin -- Suprachiasmatic nucleus cultures that maintain rhythmic properties in vitro / K. Tominaga-Yoshino, T. Ueyama, and H. Okamura -- RNA in situ hybridizations on drosophila whole mounts / Corinna Wulbeck and Charlotte Helfrich-Forster -- In situ hybridization of suprachiasmatic nucleus slices / Horacio O. de la Iglesia -- Immunohistochemistry in drosophila: sections and whole mounts / Charlotte Helfrich-Forster -- Immunocytochemistry on suprachiasmatic nucleus slices / Marta Muñoz Llamosas -- Immunofluorescence analysis of circadian protein dynamics in cultured mammalian cells / Filippo Tamanini.Light, photoreceptors, and circadian clocks / Russell G. Foster, Mark W. Hankins, and Stuart N. Peirson -- Statistical analysis of biological rhythm data / Harold B. Dowse -- Rhythmic conidiation in Neurospora crassa / Cas Kramer -- Monitoring and analyzing drosophila circadian locomotor activity / Mauro A. Zordan, Clara Benna, and Gabriella Mazzotta -- Automated video image analysis of larval zebrafish locomotor rhythms / Gregory M. Cahill -- Locomotor activity in rodents / Gianluca Tosini -- Analysis of circadian leaf movement rhythms in Arabidopsis thaliana / Kieron D. Edwards and Andrew J. Millar -- Detection of rhythmic bioluminescence from luciferase reporters in cyanobacteria / Shannon R. Canales ... [et al.] -- Analysis of rhythmic gene expression in adult drosophila using the firefly-luciferase reporter gene / Ralf Stanewsky -- Monitoring circadian rhythms in Arabidopsis thaliana using luciferase reporter genes / Anthony Hall and Paul Brown -- Specialized techniques for site-directed mutagenesis in cyanobacteria / Eugenia M. Clerico, Jayna L. Ditty, and Susan S. Golden -- Novel strategies for the identification of clock genes in neurospora with insertional mutagenesis / Kruno Sveric ... [et al.] -- Mutagenesis with drosophila / Patrick Emery -- Mutagenesis in arabidopsis / Jodi Maple and Simon G. Moller -- Yeast two-hybrid screening / Jodi Maple and Simon G. Moller --Microarrays: quality control and hybridization protocol / Ken-ichiro Uno and Hiroki R. Ueda -- Microarrays: statistical methods for circadian rhythms / Rikuhiro Yamada and Hiroki R. Ueda -- Identification of clock genes using difference gel electrophoresis / Natasha A. Karp and Kathryn S. Lilley -- Isolation of total RNA from Neurospora mycelium / Cas Kramer -- RNA extraction from drosophila heads / Patrick Emery -- Extraction of plant RNA / Michael G. Salter and Helen E. Conlon -- RNA extraction from mammalian tissues / Stuart N. Peirson and Jason N. Butler -- Northern analysis of sense and antisense fequency RNA in Neurospora crassa / Cas Kramer -- RNase protection assay / Patrick Emery -- Quantitative polymerase chain reaction / Stuart N. Peirson and Jason N. Butler -- Protein extraction, fractionation, and purification from cyanobacteria / Natalia B. Ivleva and Susan S. Golden -- Protein extraction from drosophila heads / Patrick Emery -- Plant protein extraction / Helen E. Conlon and Michael G. Salter -- Protein extraction from mammalian tissues / Choogon Lee -- Western blotting / Choogon Lee -- Co-immunoprecipitation assay / Choogon Lee -- In vitro phosphorylation and kinase assays in Neurospora crassa / Lisa Franchi and Giuseppe Macino --
  • Model and molecule. -- An overview of protein crystallography. -- Protein crystals. -- Collecting diffraction data. -- From diffraction data to electron density. -- Obtaining phases. -- Obtaining and judging the molecular model. -- A user's guide to crystallographic models. -- Other diffraction methods. -- Other kinds of macromolecular models. -- Tools for studying macromolecules. -- Appendix: Viewing stereo images.
  • Current Protocols in Chemical Biology provides validated protocols and overviews about specialized chemical techniques and tools for studies of biology and drug design. These tools include small-molecule design, synthesis, derivatization, handling, and detection as well as advances in laboratory automation, robotics, and medicinal chemistry as applied to high-throughput screening (HTS). Methods for modification of proteins, nucleic acids, carbohydrates and lipids for their use as tools in the study of particular biological systems are also included
  • DNA arrays 2002, CRCnetBASE
  • DNA microarrays. Part A-B pt. A-B, 2006., ScienceDirect
    pt. B, 2006 ScienceDirect
    Pt. A. Array platforms and wet-bench protocols -- pt. B. Databases and statistics.
  • pt. B ScienceDirect
    Part A. 40 years of FCS: how it all began / Elliot L. Elson -- Brief introduction to fluorescence correlation spectroscopy / Elliot L. Elson -- Dual-color fluorescence cross-correlation spectroscopy with continuous laser excitation in a confocal setup / Thomas Weidemann and Petra Schwille -- Brightness analysis / Patrick Macdonald, Jolene Johnson, Elizabeth Smith, Yan Chen, and Joachim D. Mueller -- Time-integrated fluorescence cumulant analysis and its application in living cells / Bin Wu, Robert H. Singer, and Joachim D. Mueller -- Raster image correlation spectroscopy and number and brightness analysis / Michelle A. Digman, Milka Stakic, and Enrico Gratton -- Global analysis in fluorescence correlation spectroscopy and fluorescence lifetime microscopy / Neil Anthony and Keith Berland -- Dual-focus fluorescence correlation spectroscopy / Christoph Pieper, Kerstin Weiss, Ingo Gergor, and Jörg Enderlein -- Pulsed interleaved excitation: principles and applications / Jelle Hendrix and Don C. Lamb -- Image correlation spectroscopy: mapping correlations in space, time, and reciprocal space / Paul W. Wiseman.Part B. FCS in STED microscopy : studying the nanoscale of lipid membrane dynamics / Veronika Mueller ... [et al.] -- Analyzing Förster resonance energy transfer with fluctuation algorithms / Suren Felekyan ... [et al.] -- Fluorescence fluctuation spectroscopy approaches to the study of receptors in live cells / David M. Jameson, Nicholas G. James, and Joseph P. Albanesi -- Studying the protein corona on nanoparticles by FCS / G. Ulrich Nienhaus, Pauline Maffre, and Karin Nienhaus -- Studying antibody-antigen interactions with fluorescence fluctuation spectroscopy / Sergey Y. Tetin, Qiaoqiao Ruan, and Joseph P. Skinner -- Fluorescence fluctuation approaches to the study of adhesion and signaling / Alexia I. Bachir, Kristopher E. Kubow, and Alan R. Horwitz -- Interactions in gene expression networks studied by two-photon fluorescence fluctuation spectroscopy / Nathalie Declerck and Catherine A. Royer-- Studying ion exchange in solution and at biological membranes by FCS / Jerker Widengren -- Fluctuation analysis of acivity biosensor images for the study of information flow in signaling pathways / Marco Vilela ... [et al.] -- Probing the plasma membrane organization in living cells by spot variation fluorescence correlation spectroscopy / Cyrille Billaudeau ... [et al.].
  • Fluorescence spectroscopy 2008, ScienceDirect
    A method in enzymology for measuring hydrolytic activities in live cell environments / Beverly Z. Packard and Akira Komoriya -- Heterogeneity of fluorescence determined by the method of area-normalized time-resolved emission spectroscopy / N. Periasamy -- Multiparametric probing of microenvironment with solvatochromic fluorescent dyes / Andrey S. Klymchenko and Alexander P. Demchenko -- Site-selective red-edge effects / Alexander P. Demchenko -- Fluorescence approaches to quantifying biomolecular interactions / Catherine A. Royer and Suzanne F. Scarlata -- Forster resonance energy transfer measurements of transmembrane helix dimerization energetics / Mikhail Merzlyakov and Kalina Hristova -- Application of single-molecule spectroscopy in studying enzyme kinetics and mechanism / Jue Shi ... [et al.] -- Ultrafast fluorescence spectroscopy via upconversion : applications to biophysics / Jianhua Xu and Jay R. Knutson -- Use of fluorescence resonance energy transfer (FRET) in studying protein-induced DNA bending / Anatoly I. Dragan and Peter L. Privalov --Fluorescent pteridine probes for nucleic acid analysis / Mary E. Hawkins -- Single-molecule fluorescence methods for the analysis of RNA folding and ribonucleoprotein assembly / Goran Pljevaljčić and David P. Millar -- Using fluorophore-labeled oligonucleotides to measure affinities of protein-DNA interactions / Brian J. Anderson ... [et al.] -- Identifying small pulsatile signals within noisy data : a fluorescence application / Michael L. Johnson ... [et al.] -- Determination of zinc using carbonic anhydrase-based fluorescence biosensors / Rebecca Bozym ... [et al.] -- Instrumentation for fluorescence-based fiber optic biosensors / Richard B. Thompson ... [et al.]
  • Gene mapping, discovery, and expression 2006, Springer Protocols
    Analysis of allele-specific gene expression / Julian C. Knight -- Construction of microRNA-containing vectors for expression in mammalian cells / Yoko Fukuda, Hiroaki Kawasaki, and Kazunari Taira -- Mining microarray data at NCBI's gene expression omnibus (GEO) / Tanya Barrett and Ron Edgar -- The Stanford microarray database: a user's guide / Jeremy Gollub, Catherine A. Ball, and Gavin Sherlock -- Detecting nucleosome ladders on unique DNA sequences in mouse liver nuclei / Tomara J. Fleury, Alfred Cioffi, and Arnold Stein -- DNA methyltransferase probing of DNA-protein interactions / Scott A. Hoose and Michael P. Kladde -- Protein binding microarrays (PBMS) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins / Michael F. Berger and Martha L. Bulyk -- Quantitative profiling of protein-DNA binding on microarrays / Jiannis Ragoussis, Simon Field, and Irina A. Udalova -- Analysis of protein-DNA binding by streptavidin-agarose pulldown / Kenneth K. Wu -- Isolation and mass spectrometry of specific DNA binding proteins / Mariana Yaneva and Paul Tempst -- Isolation of transcription factor complexes by in vivo biotinylation tagging and direct binding to streptavidin beads / Patrick Rodriguez ... [et al.].Use of genome browsers to locate your favorite genes / Minou Bina -- Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes / Razi Khaja ... [et al.] -- Identification and mapping of paralogous genes on a known genomic DNA sequence / Minou Bina -- Quantitative DNA fiber mapping in genome research and construction of physical maps / Heinz-Ulrich G. Weier and Lisa W. Chu -- PRINS for mapping single copy genes / Avirachan T. Tharapel and Stephen S. Wachtel -- VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes / Inna Dubchak and Dmitriy V. Ryaboy -- Computational prediction of cis-Regulatory modules from multispecies alignments using galaxy, table browser, and GALA / Laura Elnitski, David King, and Ross C. Hardison -- Comparative promoter analysis in vertebrate genomes with the CORG workbench / Christoph Dieterich and Martin Vingron -- cis-Regulatory region analysis using BEARR / Vinsensius Berlian Vega -- A database of 9-Mers from promoter region of human protein-coding genes / Minou Bina, Phillip Wyss, and Syed Rehan Shah -- A program toolkit for the analysis of regulatory regions of genes / Phillip Wyss, Sheryl A. Lazarus, and Minou Bina --
  • Generation of cDNA libraries 2003, Springer Protocols
  • Handbook of thermal analysis and calorimetry v. 1-5, 1998-2008., ScienceDirect
    As a new field of interdisciplinary macromolecular science and engineering, polymeric materials will have a profound presence in 21st century chemical, pharmaceutical, biomedical, manufacturing, infrastructure, electronic, optical and information technologies. The origin of this field derived from an area of polymer science and engineering encompassing plastic technologies. The field is rapidly expanding to incorporate new interdisciplinary research areas such as biomaterials, macromolecular biology, novel macromolecular structures, environmental macromolecular science and engineering, innovative and nano-fabrications of products, and is translating discoveries into technologies.
  • Aqueous Normal-Phase Chromatography -- Application of the Calculated Physicochemical Property, Log D, to Hydrophilic Interaction Chromatography in the Bioanalytical Laboratory -- HILIC Behavior of Reversed-Phase/Ion-Exchange Mixed-Mode Stationary Phases and Their Applications -- Mechanisms Controlling the Separation and Retention of Proanthocyanidins and Other Plant Polyphenols in Hydrophilic Interaction Chromatography -- Applications of Hydrophilic Interaction Chromatography to Food Analysis -- Hydrophilic Interaction Liquid Chromatography-Mass Spectrometry (HILIC-MS) of Paralytic Shellfish Poisoning Toxins, Domoic Acid and Assorted Cyanobacterial Toxins -- Application of HILIC for Polar Environmental Contaminants (Including Pharmaceuticals) in Aquatic Systems -- Hydrophilic Interaction Chromatography-Mass Spectrometry -- Clinical Applications of Hydrophilic Interaction Liquid Chromatography -- Dimethylarginine Analysis by HILIC-MS/MS and Its Applications in Clinical Chemistry and In Vivo Animal Models -- Polar Functional Groups for HILIC Method -- Analysis of Pharmaceutical Impurities Using Hydrophilic Interaction Liquid Chromatography -- Fast In-Process Method for the Determination of Ioversol and Related Polar Compounds by Hydrophilic Interaction Chromatography (HILIC) and UPLC -- Retention Behavior of Hydrazine Derivatives in HILIC Mode -- HILIC Retention Behavior and Method Development for Highly Polar Basic Compounds Used in Pharmaceutical Synthesis -- Retention of Polar Acidic and Basic Drugs by HILIC -- Retention and Selectivity of Polar Stationary Phases for Hydrophilic Interaction Chromatography -- HILIC-MS/MS for the Determination of Polar Bioactive Substances -- Method Development and Analysis of Mono- and Diphosphorylated Nucleotides by HILIC HPLC-ESI-MS -- Hydrophilic Interaction Liquid Chromatography-Based Enrichment Protocol Coupled to Mass Spectrometry for Glycoproteome Analysis -- Development and Application of Methods for Separation of Carbohydrates by Hydrophilic Interaction Liquid Chromatography -- Hydrophilic Interaction Liquid Chromatography in the Characterization of Glycoproteins -- Analysis of Protein Glycosylation and Phosphorylation Using HILIC-MS.
  • V. 1. Acebutolol -- Dapsone -- v. 2. Dauromycin -- Indigotin Disulfonate -- v. 3. Indole-3-Acetic Acid -- Phendimetrazine -- v. 4. Phenelzine -- Zoxazolamine -- v. 5. Raman spectra data -- Mass spectra of pesticides -- Mass spectra of derivatized drugs -- Gas chromatography/infrared spectra of drugs -- v. 6. Standard KBr infrared spectra and standard NMR solvent spectra -- Supplemental infrared spectra -- Supplemental NMR spectra -- Ultraviolet absorption maxima -- Infrared index -- Mass spectra indices of drugs -- Mass spectra indices of pesticides -- Molecular formula index -- Gas chromatographic data -- Index to specific compounds.
  • Journal of chromatography library v. 1-70, 1973-2005., ScienceDirect
  • ch. 1 Introduction, p. 1-5 -- ch. 2 Liquid Chromatography, p. 7-31 -- ch. 3 Mass Spectrometry, p. 33-74 -- ch. 4 Interface Technology, p. 75-127 -- ch. 5 Applications of High Performance Liquid Chromatography-Mass Spectrometry, p. 129-234.
  • Mass spectrometry imaging 2010, Springer Protocols
    Imaging mass spectrometry : viewing the future / Sarah A. Schwartz and Richard M. Caprioli -- A mass spectrometry primer for mass spectrometry imaging / Stanislav S. Rubakhin and Jonathan V. Sweedler -- Imaging of metals, metalloids, and non-metals by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) in biological tissues / J. Sabine Becker and J. Susanne Becker -- Lipid detection, identification, and imaging single cells with SIMS / Michael L. Heien ... [et al.] -- The application and potential of ion mobility mass spectrometry in imaging MS with a focus on lipids / Amina S. Woods and Shelley N. Jackson -- Quantitative imaging of chemical composition in single cells by secondary ion mass spectrometry : cisplatin affects calcium stores in renal epithelial cells / Subhash Chandra -- Imaging MALDI mass spectrometry of sphingolipids using an oscillating capillary nebulizer matrix application system / Yanfeng Chen ... [et al.] -- Mapping pharmaceuticals in rat brain sections using MALDI imaging mass spectrometry / Yunsheng Hsieh, Fangbiao Li, and Walter A. Korfmacher -- Laser ablation electrospray ionization for atmospheric pressure molecular imaging mass spectrometry / Peter Nemes and Akos Vertes -- Matrix-assisted laser desorption/ionization and nanoparticle-based imaging mass spectrometry for small metabolites : a practical protocol / Yuki Sugiura and Mitsutoshi Setou -- Cellular imaging using matrix-enhanced and metal-assisted SIMS / A.F. Maarten Altelaar and Sander R. Piersma -- Tandem mass spectrometric methods for phospholipid analysis from brain tissue / Timothy J. Garrett and Richard A. Yost -- Chemical imaging with desorption electrospray ionization mass spectrometry / Vilmos Kertesz and Gary J. Van Berkel -- Mass spectrometry imaging of small molecules using matrix-enhanced surface-assisted laser desorption/ionization mass spectrometry (ME-SALDI-MS) / Qiang Liu, Yongsheng Xiao, and Lin He -- Preparation of single cells for imaging mass spectrometry / Elena S.F. Berman, Susan L. Fortson, and Kristen S. Kulp -- Applying imaging ToF-SIMS and PCA in differentiation of tissue types / Ligang Wu, James S. Felton, and Kuang Jen J. Wu -- Direct molecular analysis of whole-body animal tissue sections by MALDI imaging mass spectrometry / Michelle L. Reyzer ... [et al.] -- MALDI direct analysis and imaging of frozen versus FFPE tissues : what strategy for which sample? / Maxence Wisztorski ... [et al.] -- On tissue protein identification improvement by N-terminal peptide derivatization / Julien Franck ... [et al.] -- Specific MALDI-MSI : TAG-MASS / Jonathan Stauber ... [et al.] -- Structurally selective imaging mass spectrometry by imaging ion mobility-mass spectrometry / John A. McLean, Larissa S. Fenn, and Jeffrey R. Enders -- Tutorial : multivariate statistical treatment of imaging data for clinical biomarker discovery / Sören-Oliver Deininger, Michael Becker, and Detlev Suckau -- Applications of MALDI-MSI to pharmaceutical research / Brendan Prideaux, Dieter Staab, and Markus Stoeckli -- Tissue preparation for the in situ MALDI MS imaging of proteins, lipids, and small molecules at cellular resolution / Nathalie Y.R. Agar ... [et al.] -- Imaging of similar mass neuropeptides in neuronal tissue by enhanced resolution MALDI MS with an ion trap-Orbitrap hybrid instrument / Peter D.E.M. Verhaert ... [et al.] -- Mass spectrometric imaging of neuropeptides in decapod crustacean neuronal tissues / Ruibing Chen ... [et al.] -- Mass spectrometry imaging using the stretched sample approach / Tyler A. Zimmerman, Stanislav S. Rubakhin, and Jonathan V. Sweedler.
  • Molecular weight determination of peptides and proteins by ESI and MALDI / Kerstin Strupat -- Batch introduction techniques / Connie R. Jiménez -- In-solution digestion of proteins for mass spectrometry / Katalin F. Medzihradszky -- Identification of phosphorylation sites using microimmobilized metal affinity chromatography / Garry L. Corthals, Reudi Aebersold, and David R. Goodlett -- Mapping posttranslational modifications of proteins by MS-based selective detection : application to phosphoproteomics / Steven A. Carr, Roland S. Annan, and Michael J. Huddleston -- Characterization of protein N-glycosylation / Katalin F. Medzihradszky -- Methods in enzymology : O-glycosylation of proteins / Jasna Peter-Katalinić -- Analysis of glycosylphosphatidylinositol protein anchors : the prion protein / Michael A. Baldwin -- Comprehensive mass spectrometric analysis of the 20S proteasome complex / Lan Huang and A.L. Burlingame -- The analysis of multiprotein complexes : the yeast and the human spliceosome as case studies / Gitte Neubauer -- The use of mass spectrometry to identify antigens from proteasome processing / Odile Burlet-Schiltz ... [et al.] -- Glycosphingolipid structural analysis and glycosphingolipidomics / Steven B. Levery -- Mapping bacterial glycolipid complexity using capillary electrophoresis and electrospray mass spectrometry / J. Li ... [et al.]
  • Metabolomics 2006, Springer Protocols
    Metabolite profiling in blood plasma / Oliver Fiehn and Tobias Kind -- Nonsupervised construction and application of mass spectral and retention time index libraries from time-of-flight GC/MS metabolite profiles / Alexander Erban ... [et al.] -- Metabolomic profiling of natural volatiles: head space trapping-GC/MS / Yury M. Tikunov, Francel W. A. Verstappen, and Robert D. Hall -- Integrative profiling of metabolites and proteins: improving pattern recognition and biomarker selection for systems-level approaches / Katja Morgenthal ... [et al.] -- Integrating profiling data: using linear correlation to reveal coregulation of transcript and metabolites / Ewa Urbanczyk-Wochniak, Lothar Willmitzer, and Alisdair R. Fernie -- Visualization and analysis of molecular data / Matthias Scholz and Joachim Selbig -- A gentle guide to the analysis of metabolomic data / Ralf Steuer ... [et al.] -- CE-MS for metabolomics / Tomoyoshi Soga -- Application of LC/MS analysis in metabolomics: reversed-phase monolithic capillary chromatography and hydrophilic chromatography coupled to electrospray ionization mass spectrometry / Vladimir V. Tolstikov, Oliver Fiehn, and Nobuo Tanaka -- HPLC-separations coupled with coulometric-electrode array detectors: a unique approach to metabolomics / Bruce S. Kristal ... [et al.] -- Determination of metabolic flux ratios from 13C-experiments and GC/MS data: protocol and principles / Annik Nanchen, Tobias Fuhrer, and Uwe Sauer -- Understanding the roadmap of metabolism by pathway analysis / Stefan Schuster, Axel von Kamp, and Mikhail Pachkov -- Revealing the metabolome of animal tissues using 1H NMR spectroscopy / Mark R. Viant -- NMR metabonomics: methods for drug discovery and development / Karl-Heinz Ott and Nelly Aranibar.
  • A comprehensive analysis of the effect of microarray data preprocessing methods on differentially expressed transcript selection -- Differentiation detection in microarray normalization -- Preprocessing and normalization for Affymetrix GeneChip expression microarrays -- Spatial detrending and normalization methods for two-channel DNA and protein microarray data -- A survey of cDNA microarray normalization and a comparison by k-NN classification -- Technical variation in modeling the joint expression of several genes -- Biological interpretation for microarray normalization selection -- Methodology of functional analysis for omics data normalization -- Exon array analysis for the detection of alternative splicing -- Normalization of array CGH data -- SNP array-based analysis for the detection of chromosomal aberrations and copy number variations.
  • Microarray data analysis 2007, Springer Protocols
  • Manufacturing of microarrays -- Technological platforms for microarray gene expression profiling -- Principles of gene microarray data analysis -- Gaining weights ... and feeling good about it! -- Complementary techniques -- Microarrays for cancer diagnosis and classification -- Gene profiling for the prediction of tumor response to treatment: the case of immunotherapy -- Identification of molecular determinants of tumor sensitivity and resistance to anticancer drugs -- SNP and mutation analysis -- Cancer development and progression -- Gene expression profiling in malignant lymphomas -- Tumor immunology.
  • Microarrays in clinical diagnostics 2005, Springer Protocols
  • Microarrays. 2nd ed. v. 1-2, 2007., Springer Protocols
    v.2, 2009 Springer Protocols
    v. 1. Synthesis methods -- v. 2. Applications and data analysis.
  • Microchip capillary electrophoresis 2006, Springer Protocols
  • Microchip-based assay systems 2007, Springer Protocols
    Microchip electrophoresis for DNA separation by wire-imprinted microchannels on PMMA substrates / Shu-Hui Chen -- Fabrication of porous polymer monoliths in microfluidic chips for selective nucleic acid concentration and purification / Jay A.A. West and Brent C. Satterfield -- Rapid electrical lysis of bacterial cells in a microfluidic device / Hsiang-Yu Wang ... [et al.] -- On-chip bioassay using immobilized sensing bacteria in three-dimensional microfluidic network / Hirofumi Tani, Koji Maehana, and Tamio Kamidate -- Microchip-based enumeration of human white blood cells / Pierre Floriano ... [et al.] -- Microchip for the diagnosis of cervical cancer / Anja Gulliksen and Frank Karlsen -- DNA microchips toward molecular signatures in cervical cancers / Yick F. Wong ... [et al.] -- Impedimetric detection for DNA hybridization within microfluidic biochips / Louise Lingerfelt ... [et al.] -- Applications of functional protein microarrays: identifying protein/protein interactions in an array format / Matthew A. Coleman ... [et al.] -- A microchip-based assay for interleukin-6 / Nicolaos Christodoulides ... [et al.] -- Allergen microarrays for the diagnosis of specific IgE against components of cow milk and hen egg in a multiplex biochip-based immunoassay / Christian Harwanegg, Sabine Hutter, and Reinhard Hiller -- Surface plasmon resonance imaging on polypyrrole protein chips: application to streptavidin immobilization and immunodetection / Emilie Mercey ... [et al.] -- Protein array-based multiplexed cytokine assays / Cheng C. Wang -- Lectin microarrays for glycoprotein analysis / Lara K. Mahal and Kanoelani Pilobello -- Interaction of HIV RNA with peptides detected by acoustic shear wave sensor operated in an on-line format / Anil Deisingh ... [et al.] -- Microchip-based electrochemical enzyme immunoassays / Madhu Prakash Chatrathi, Greg Collins, and Joseph Wang.
  • Microfluidic techniques 2005, Springer Protocols
    Overview of advances in microfluidics and microfabrication / Shelley D. Minteer and Christine M. Moore -- Introduction to microfabrication techniques / Rabih Zaouk, Benjamin Y. Park, and Marc J. Madou -- Fabrication ofpolydimethylsiloxane microfluidics using SU-8 molds / Rabih Zaouk, Benjamin Y. Park, and Marc J. Madou -- Fabrication of microelectrodes using the lift-off technique / Benjamin Y. Park, Rabih Zaouk, and Marc J. Madou -- Laser ablation as a fabrication technique for microfluidic devices / Emanual A. Waddell -- Reversible, room temperature bonding of glass devices for microfluidics / Loranelle L. Lockyear -- Solid phase extraction in packed beds on glass microdevices / Loranelle L. Lockyear -- Fabrication of micromachined magnetic particle separators for bioseparation in microfluidic systems / Jin-Woo Choi -- Hydrogel-immobilized antibodies for microfluidic immunoassays: hydrogel immunoassay / Gloria Thomas ... [et al.] --Polymerase chain reaction in miniaturized systems : big progress in little devices / Kalee D. Spitzack and Victor M. Ugaz -- Polymerase chain reaction on microchips / Maria C. Carles and Nikolaus J. Sucher -- A sensitive sandwich DNA array using fluorescent nanoparticle probes / Xiajun Zhao, David T. Pierce, and Yanfu Huan -- Microfluidic ethanol biobatteries on a microchip / Shelley D. Minteer and Christine M. Moore -- Microfluidic chambers for cell migration and neuroscience research / Anne M. Taylor, Seog Woo Rhee, and Noo Li Jeon -- Microtextured polydimethylsiloxane substrates for culturing mesenchymal stem cells / Erik T.K. Peterson and Ian Papautsky -- Contraction study of a single cardiac muscle cell in the microfluidic chip / Xiujun (James) Li and Paul C.H. Li -- Microscale inegrated sperm sorter / Yaokuang Chung ... [et al.].
  • New and emerging proteomic techniques 2006, Springer Protocols
    On-chip protein synthesis for making microarrays / Niroshan Ramachandran ... [et al.] -- RCA-enhanced protein detection arrays / Brian B. Haab and Paul M. Lizardi -- Antibody microarrays using resonance light-scattering particles for detection / Bernhard H. Geierstanger, Petri Saviranta, and Achim Brinker -- Chemical proteomics profiling of proteasome activity / Martijn Verdoes ... [et al.] -- Two-dimensional difference gel electrophoresis / Terence L. Wu -- Oligomeric states of proteins determined by size-exclusion chromatography coupled with light scattering, absorbance, and refractive index detectors / Ewa Folta-Stogniew -- Surface plasmon resonance imaging measurements of protein interactions with biopolymer microarrays / Terry T. Goodrich ... [et al.] --Surface plasmon resonance mass spectrometry for protein analysis / Dobrin Nedelkov and Randall W. Nelson -- High-throughput affinity mass spectrometry / Urban A. Kiernan ... [et al.] -- Isotope-coded affinity tags for protein quantification / Christopher M. Colangelo and Kenneth R. Williams -- Proteomic analysis by multidimensional protein identification technology / Laurence Florens and Michael P. Washburn -- Isolation of glycoproteins and identification of their N-linked glycosylation sites / Hui Zhang and Ruedi Aebersold -- N-Glycosylation analysis using the StrOligo algorithm / Martin Ethier, Daniel Foigeys, and Hélène Perreault -- MALDI-MS data analysis for disease biomarker discovery / Weichuan Yu ... [et al.] -- Using the global proteome machine for protein identification / Ronald C. Beavis.
  • Plant proteomics 2006, Springer Protocols
    Total protein extraction with TCA-acetone / Valérie Méchin, Catherine Damerval, and Michel Zivy -- Phenol extraction of proteins for proteomic studies of recalcitrant plant tissues / Mireille Faurobert, Esther Pelpoir, and Jamila Chaïb -- Protein extraction from cereal seeds / Gérard Branlard and Emmanuelle Blancel -- Protein extraction from xylem and phloem sap / Julia Kehr and Martijn Rep -- Protein extraction from woody plants / Christophe Plomion and Céline Lalanne -- Isolation of chloroplast proteins from Arabidopsis thaliana for proteome analysis / Klaas J. van Wijk, Jean-Benoit Peltier, and Lisa Giacomelli -- Isolation and subfractionation of plant mitochondria for proteomic analysis / Holger Eubel, Joshua L. Heazlewood, and A. Harvey Millar -- Extraction of nuclear proteins from root meristematic cells / Fernando González-Camacho and Francisco Javier Medina -- Isolation of nuclear proteins / Setsuko Komatsu -- Isolation of cell wall proteins from Medicago sativa stems / Bonnie S. Watson and Lloyd W. Sumner -- Plant plasma membrane protein extraction and solubilization for proteomic analysis / Véronique Santoni -- Detergents and chaotropes for protein solubilization before two-dimensional electrophoresis / Thierry Rabilloud ... [et al.] -- Two-dimensional electrophoresis for plant proteomics / Walter Weiss and Angelika Görg -- Visible and fluorescent staining of two-dimensional gels / François Chevalier, Valérie Rofidal, and Michel Rossignol -- Two-dimensional differential in-gel electrophoresis (DIGE) of leaf and roots of Lycopersicon esculentum / Matthew Keeler ... [et al.] -- Quantitative analysis of 2D gels / Michel Zivy -- Multivariate data analysis of proteome data / Kåre Engkilde, Susanne Jacobsen, and Ib Søndergaard -- Edman sequencing of plant proteins from 2D gels / Setsuko Komatsu -- Peptide mass fingerprinting: identification of proteins by MALDI-TOF / Nicolas Sommerer, Delphine Centeno, and Michel Rossignol -- Protein identification using nano liquid chromatography-tandem mass spectrometry / Luc Negroni -- Two-dimensional nanoflow liquid chromatography-tandem mass spectrometry of proteins extracted from rice leaves and roots / Linda Breci and Paul A. Haynes -- Separation, identification, and profiling of membrane proteins by GFC/IEC/SDS-PAGE and MALDI TOF MS / Wojciech Szponarski ... [et al.] -- The PROTICdb database for 2-DE proteomics / Olivier Langella, Michel Zivy, and Johann Joets -- Identification of phosphorylated proteins / Maria V. Turkina and Alexander V. Vener -- Plant proteomics and glycosylation / Anne-Catherine Fitchette ... [et al.] -- Blue-native gel electrophoresis for the characterization of protein complexes in plants / Jesco Heinemeyer, Dagmar Lewejohann, and Hans-Peter Braun -- Electroelution of intact proteins from SDS-PAGE gels and their subsequent MALDI-TOF MS analysis / Zhentian Lei ... [et al.] -- Generation of plant protein microarrays and investigation of antigen-antibody interactions / Birgit Kersten and Tanja Feilner -- Phosphorylation studies using plant protein microarrays / Tanja Feilner and Birgit Kersten.
  • Protein arrays 2004, Springer Protocols
  • Protein chromatography 2011, Springer Protocols
    A digest of protein purification -- Gel-filtration chromatography -- Immunoaffinity chromatography -- Avoiding proteolysis during protein chromatography -- Scale-up of protein purification : Downstream processing issues -- Phage display : A powerful technology for the generation of high specificity affinity reagents from alternative immune sources -- Engineering protein stability -- Microfluidics in protein chromatography -- Tagging recombinant proteins to enhance solubility and aid purification -- Storage and lyophilisation of pure proteins -- Differential precipitation and solubilization of proteins -- Ion-exchange chromatography : Basic principles and application to the partial purification of soluble mammalian prolyl oligopeptidase -- Protein quantitation and analysis of purity -- Purification of proteins fused to glutathione S-transferase -- Purification of proteins fused to maltose-binding protein -- Purification of proteins from baculovirus-infected insect cells -- Purification of poly-histidine-tagged proteins -- Immobilized metal affinity chromatography/reversed-phase enrichment of phosphopeptides and analysis by cid/etd tandem mass spectrometry -- Tag removal by site-specific cleavage of recombinant fusion proteins -- Purification of antibodies using affinity chromatography -- Optimized generation of high-affinity, high-specificity single-chain Fv antibodies from multiantigen immunized chickens -- Measuring protein-protein interactions using biacore -- Ultra-performance liquid chromatography-mass spectrometry of proteins -- Hydrophobic interaction chromatography -- Fast protein liquid chromatography -- Shotgun proteomics : A qualitative approach applying isoelectric focusing on immobilized pH gradient and LC-MS/MS -- Shotgun proteomics : A relative quantitative approach using off-gel electrophoresis and LC-MS/MS -- Clinical proteomics : Liquid chromatography-mass spectrometry purification systems -- Strategies for the purification of membrane proteins -- A multi-step chromatographic strategy to purify three fungal endo-[beta]-glucanases.
  • Quantitation of proteins -- Electrophoresis of proteins and peptides and detection in gels -- Blotting and detection methods -- Chemical modification of proteins and peptide production and purification -- Posttranslational modifications -- Antibody techniques.
  • Protein-ligand interactions 2005, Springer Protocols
  • This book is designed to help scientists without a strong background in analytical chemistry to understand basic analytical principles so they can apply them to proteomics profiling. It will also help researchers with an analytical chemistry background to break into the proteomics field. The title focuses on practical applications for proteomic research so readers are guided to design better experiments and to more easily interpret the resulting data. Bridges the gap between overly specialized courses and books in mass spectrometry, proteomics and analytical chemistryCovers the analytical consequences of protein and peptide modifications that may have a profound effect on how and what researchers actually measure; other books do not discuss such issuesIncludes real life examples illustrating the importance of problems in quantitation and validation of biomarkers from the perspective of analytical chemistry with additional references to other sources Helps in designing and executing proteomic experiments with sound analytics.
  • Acrylamide: a cysteine alkylating reagent for quantitative proteomics / Illarion V. Turko and Salvatore Sechi -- Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition / Jeffrey A. Ranish, Marjorie Brand, and Ruedi Aebersold -- Stable isotope labeling by amino acids in cell culture for quantitative proteomics / Shao-En Ong and Matthias Mann -- Quantitative proteomics of mouse brain and specific protein-interaction studies using stable isotope labeling / Toshitaka Sato, Yasushi Ishihama, and Yoshiya Oda -- The absolute quantification strategy: application to phosphorylation profiling of human separase serine 1126 / Scott A. Gerber ... [et al.] -- Quantification of proteins and metabolites by mass spectrometry without isotopic labeling / Sushmita Mimi Roy and Christopher H. Becker -- The use of a quantitative cysteinyl-peptide enrichment technology for high-throughput quantitative proteomics / Tao Liu ... [et al.] --An isotope coding strategy for proteomics involving both amine and carboxyl group labeling / Fred E. Regnier -- Proteolytic labeling with ¹⁸O for comparative proteomics studies: preparation of ¹⁸O-labeled peptides and the ¹⁸O/¹⁶O peptide mixture / Catherine Fenselau and Xudong Yao -- Tandem mass spectrometry in the detection of inborn errors of metabolism for newborn screening / František Tureček, C. Ronald Scott, and Michael H. Gelb -- Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags / Yu Lu ... [et al.] -- Computational analysis of quantitative proteomics data using stable isotope labeling / Michael J. MacCoss and Christine C. Wu -- Quantitative proteomic analysis of mammalian organisms using metabolically labeled tissues / Christine C. Wu, and Michael J. MacCoss -- Quantitative proteomic analysis of phosphotyrosine-mediated cellular signaling networks / Yi Zhang, Alejandro Wolf-Yadlin, and Forest M. White.
  • Star polymer surface passivation for single-molecule detection / Jürgen Groll and Martin Moeller -- Azide-specific labeling of biomolecules by Staudinger-Bertozzi ligation: phosphine derivatives of fluorescent probes suitable for single-molecule fluorescence spectroscopy / Anirban Chakraborty ... [et al.] -- Preparation of fluorescent pre-mRNA substrates for an smFRET study of pre-mRNA splicing in yeast / John Abelson, Haralambos Hadjivassiliou and Christine Guthrie -- Nanovesicle trapping for studying weak protein interactions by single-molecule FRET / Jaime J. Benítez, Aaron M. Keller and Peng Chen -- Droplet confinement and fluorescence measurement of single molecules / Lori S. Goldner, Ana M. Jofre and Jianyong Tang -- Single-molecule fluorescence spectroscopy using phospholipid bilayer nanodiscs / Abhinav Nath ... [et al.] -- Single-molecule spectroscopy using microfluidic platforms / Samuel Kim and Richard N. Zare -- Detection of protein-protein interactions in the live cell plasma membrane by quantifying prey redistribution upon bait micropatterning / Julian Weghuber ... [et al.] -- Analysis of complex single-molecule FRET time trajectories / Mario Blanco and Nils G. Walter -- Single-molecule fluorescence studies of intrinsically disordered proteins / Allan Chris M. Ferreon ... [et al.] -- Measuring the energetic coupling of tertiary contacts in RNA folding using single molecule fluorescence resonance energy transfer / Max Greenfield and Daniel Herschlag -- A highly purified, fluorescently labeled in vitro translation system for single-molecule studies of protein synthesis / Jingyi Fei ... [et al.] -- Watching individual proteins acting on single molecules of DNA / Ichiro Amitani ... [et al.] -- DNA curtains for high-throughput single-molecule optical imaging / Eric C. Greene ... [et al.] -- Scanning FCS for the characterization of protein dynamics in live cells / Zdenĕk Petrás̆ek, Jonas Ries and Petra Schwille -- Observing protein interactions and their stoichiometry in living cells by brightness analysis of fluorescence fluctuation experiments / Yan Chen ... [et al.] -- Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes / Arjin Raj and Sanjay Tyagi -- Single mRNA tracking in live cells / Hye Yoon Park, Adina R. Buxbaum and Robert H. Singer -- Single-molecule sequencing: sequence methods to enable accurate quantitation / Christopher Hart ... [et al.] -- Real-time DNA sequencing from single polymerase molecules / Jonas Korlach ... [et al.].
  • v. 2, 2006 Springer
    v. 3, 2006 Springer
    v. 4, 2006 Springer
    v. 5, 2006 Springer
    v. 6, 2006 Springer
    v. 1. Cholestanes, ergostanes, withanolides, stigmastane -- v. 2. Stigmastanes, furostanes, spirtostanes-- v. 3. Spirostanes, bufanolides, cardenolides-- v. 4. Cardenolides and pregnanes -- v. 5. Pregnanes, androstanes, and miscellaneous -- v. 6. Miscellaneous steroids and indexes.
  • Tissue proteomics 2008, Springer protocols
    Capabilities using 2-D DIGE in proteomics research : the new gold standard for 2-D gel electrophoresis / Christine R. Rozanas and Stacey M. Loyland -- Protein carbohydrate analysis : gel-based staining, liquid chromatography, mass spectrometry, and microarray screening / Injae Shin, Alina D. Zamfir, and Bin Ye -- Surface-enhanced laser desorption/ionization mass spectrometry for protein and peptide profiling of body fluids / Audrey Gagnon, Qian Shi, and Bin Ye -- A novel approach using MALDI-TOF mass spectrometry and prestructured sample supports (AnchorChip technology) for proteomic profiling and protein identification / Sau-Mei Leung and Rebecca L. Pitts -- Automated laser capture microdissection for tissue proteomics / Adrianna S. Rodriguez ... [et al.] -- Tissue microarrays : an overview / Rajiv Dhir -- Frozen protein arrays / Stephen M. Hewitt and Robert A. Star -- Reverse phase protein microarrays for theranostics and patient-tailored therapy / Virginia Espina ... [et al.] -- Antibody arrays for determination of relative protein abundances / Grigoriy S. Chaga -- SH2 domain-based tyrosine phosphorylation array / Xin Jiang ... [et al.] -- Immunoregulomics : a serum autoantibody-based platform for transcription factor profiling / Oliver W. Tassinari ... [et al.] -- The "reverse capture" autoantibody microarray : an innovative approach to profiling the autoantibody response to tissue-derived native antigens / Joshua R. Ehrlich ... [et al.] -- Biorepository standards and protocols for collecting, processing, and storing human tissues / Dean Troyer.

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