NDLI: Quantitative Imaging: How to Extract the Most of Your Experiments

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(P4) Technologies for Reading and Writing Omes

(P1) Technology Development in a Multidisciplinary Center

(P3) Boosting Proteome Complexity by N-terminal Acetylation of Proteins

(P2) Academic Entrepreneurship: What is Needed from us?

Targeted Methylation Sequencing of Population Cohorts

Statistical Experimental Design for Mass Spectrometry Studies Using Labeling

Computational Analysis and Comparison of Continuous and Count-based Label-free Quantitative Proteomic Data

Combining Search Engines for Comparative Proteomics

Large-scale Protein Fitness Data Reveal Fundamental Protein Properties

Genome-wide Mapping of Nucleosome Positioning and DNA Methylation Within Individual DNA Molecules

Function, Mechanism of Action, and Regulation of HDACs

Probing Protein Structure in Vivo with FRET

Mass Spectrometry in an Interdisciplinary Technology Development Center: The Yeast Resource Center

Targeted Strategy for Selective Identification of Secreted Breast Tumor Proteins in Plasma Using Mouse Xenograft Models

Methods for Measuring Fractional Synthetic Rates of Secretory Protein Analysis by Triple Quadrupole Mass Spectrometry

A Metagenomic Interrogation of Primates

Determination of Protein Turnover in Human Infants and Alveolar Type 2 Cells

Eukaryotic Marker Gene Studies: Challenges and Considerations for Microbial Taxa With a Nucleus

An Ultrastable AFM for Biophysics

AFM Force Spectroscopy of Protein Interaction

Nanoscale Video Imaging of Proteins in Action by High-speed AFM

Metagenomic-derived Insights of Microbial Communities Between Soil Biomes

Molecular Imaging of Tissue Sections by Mass Spectrometry: Looking Beyond the Microscope

The Creation of a Microbial Rosetta Stone by Seeing Microbial Interactions

Nanoscale Chemical Imaging of Biomaterials with Mass Spectrometry

Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

Clinical DNA Sequencer for Ultra-Low Cost Testing

Genapsys 100X Solution: Label-free Fully-integrated “Personal Genomixer”

Rapid, Direct Quantification of Viruses in Solution Using the ViroCyt Virus Counter

Cryo Transmission Electron Microscopy as an Orthogonal Tool for Characterization of Biopharmaceuticals

Nanopore-based Sensors for Multi-parameter Characterization of Nanoparticles and Viruses

Job Opportunities in Pharma and Biotech: What Makes a Future Employee Stand Out?

NARG 2011–12 Study: Evaluating DNA Methylation Profiles Across Degraded Samples

ABRF-sPRG 2011–2012 Study: Development and Characterization of a Comprehensive Standard for Analysis of Post-translational Modifications Followed by Evaluation of the Standard by Study Participants

The Perfect Antibody: Does it Exist and How Do You Find It?

GVRG 2012 Research Study Survey: A Current Snapshot of Core Services

A Methodology Study for Metagenomics Using Next Generation Sequencers

(gPRG) 2012 Quantitative Glycoprotein Study

GVRG 2011–2012 Research Study Conclusion: Evaluation of DNA Whole Genome Amplification Technologies for Genotyping

Point Spread Functions, Spectral Calibration and Beyond

iPRG 2012 Study: Detecting Modified Peptides in a Complex Mixture

(PERG) 2012 Study

(LMRG): Microscope Resolution, Objective Quality, Spectral Accuracy and Spectral Un-mixing

Protein Sequencing Research Group (PSRG): Results of the PSRG 2012 Study Year 1: Terminal Sequencing of Fusion Proteins

The 2012 PRG Study: Assessing Longitudinal Variability in Routine Peptide LC-MS/MS Analysis

Genotyping on High Throughput Sequencers: Preparation and Analysis of Reduced Representation Genomic Libraries

Genotyping on High Throughput Sequencers: Preparation and Analysis of Reduced Representation Genomic Libraries

What are the Problems with Experiment Design for Quantitative Proteomics and How Do We Get Past Them?

Introducing Inexperienced Users to Label-free Quantitative Proteomics

Statistical Considerations for Quantitative Proteomics Data

Nanoscopy – Pushing the Limits of Light Microscopy

Molecular Profiling of Selected Cell Populations in Tissues by On-chip MALDI MS

Tissue Proteomics Workshop

The PAXgene® Tissue System for Long-Term Storage of Tissue and the Simultaneous Preservation of Tissue Morphology and Biomolecules

ABRF Affiliates and Chapters

ARG: The Perfect Antibody: Does it Exist and How Do You Find It?

iPRG 2012 Study: Detecting Modified Peptides in a Complex Mixture

ABRF Core Administrators Network Survey: Developing a Database of Core Administrators

LMRG: Resolution and Quality Control of Confocal Microscopy Optics: Measuring and Interpreting Point Spread Functions

NARG 2011-12 Study: Evaluating DNA Methylation Profiles Across Degraded Samples

DSRG Metagenomics Study: Next-Generation Techniques and Data Analysis

Protein Sequencing Research Group (PSRG): Results of the PSRG 2012 Study Year 1: Terminal Sequencing of Fusion Proteins

GVRG 2011-2012 Research Study Conclusion: Evaluation of DNA Whole Genome Amplification Technologies for Genotyping

GVRG 2012 Research Study Survey: A Current Snapshot of Core Services

Antibody Purification with AssayMAP, a High Throughput Microchromatography Platform

ABRF-sPRG 2011-2012 Study: Development and Characterization of a Comprehensive Standard for Analysis of Post-translational Modifications followed by Evaluation of the Standard by Study Participants

The 2012 PRG study: Assessing Longitudinal Variability in Routine Peptide LC-MS/MS Analysis

Implementing Label-free Biomolecular Interaction Analyses in an Antibody and Protein Core Setting

Integrating de Novo Sequencing and Database Search for Peptide Identification

Site-specific Labeling of Antibody N-glycans using a Click Chemistry-mediated Chemoenzymatic Approach

Bionformatical Comparative Study of Human Ubiquitinome

Transcriptomic Profiling of Ribosomal Protein Pseudogenes in Diverse Human Tissues

High Performance Protein Enrichment Using Streptavidin Magnetic Beads

A Novel Experimental Scheme to Fully Separate Permethylated Glycans and Allow Online RP-LC-MS with Simplified ESI-MS Analysis

IFNbeta-1b Treatment Alters the Composition of Circulating B Cell Subsets and Leads to Changes in the B Cell Cytokine Secretion Profile in an Ex-vivo Stimulation Assay for Patients with Relapsing-Remitting Multiple Sclerosis

Proteomics Profiling of Human Melanoma, Breast Cancer, Glioblastoma, Lung carcinoma, Osteosarcoma and Cervical Cancer Cell Lines

Methods for Tracking Core-contributed Publications and Increasing Acknowledgment and Authorship Compliance

Automated Glycan Structural Isomer Differentiation Using Bioinformatics Tool

Development of a Fast HPAE-PAD Sialic Acid Analysis Method

Expanding and Enhancing Access to the Sequence Read Archive (SRA) Through a Complementary New Web-based Mirror

Sensitivity of Single Molecule Sequencing Technology (SMRT) to Impurities in DNA Libraries

Help Us Help You! The Cytometry Interest Research Group Bridging the Gap Between Sample Purification and Downstream Applications

Universal NGS Library Preparation on the Apollo 324 TM System: Automated Ion Torrent Personal Genome Machine Library Preparation

ScriptSeq V2 Library Preparation Method: A Rapid and Efficient Method for Preparing Directional RNA-Seq Libraries

Eliminating Ultracentrifugation in the Deep Sequencing of Ribosome-Protected mRNA Fragments Using Polysomes and Monosomes

Improvement of PCR-free NGS Library Preparation to Obtain Uniform Read Coverage of Genome with Extremely High AT Content

Gene Expression Profiling of Picogram Amounts of Mouse Universal Reference RNA Amplified Using the Miltenyi Biotec μMACS SuperAmp Technology

Quality Control of DNA from Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Tissues Prior to Targeted-Enrichment and Next Generation Sequencing

Sample Quality Control Within Various Next Generation Sequencing Workflows Using the New Agilent 2200 TapeStation

Automating Creation of Next Generation Sequencing Libraries

Next Generation Sequencing for the Rest of Us

Complementary DNA Shearing and Size-selection Tools for Mate-pair Library Construction

Two Methods for High-Throughput NGS Template Preparation for Small and Degraded Clinical Samples Without Automation

An Improved Workflow for miRNA Expression Profiling Using Ion Semiconductor Sequencing

Apples with Oranges: Comparing the GS-FLX vs Ion Torrent Platforms for 16S Metagenomics Studies

Simple Automated NGS Library Construction Using Optimized NEBNext(R) Reagents and a Caliper Sciclone

The Complete Sequence of the 90.1-kb Virulence Plasmid, pO145-NM, Carried in Shiga Toxin-Producing Escherichia coli (STEC) O145:NM 83-75

Whole Genome mtDNA Sequencing on the Ion Torrent PGM

Standardization of Flow Cytometry Instrumentation for the Analysis of Microparticles

Proteomics with Undergraduates: The Vermont Genetics Network Proteomics Module

Acquisition Rates Effect on Multiparametric Rare Event Analysis: a Look at Data Consistency

DNA Target Enrichment and Background Depletion for Detection of Rare Sequences

Using Microsatellites to Identify Yeast Strains in Beer

Comparative microRNA Profiling by TaqMan Low Density Arrays and Affymetrix GeneChip miRNA 2.0 Arrays: An Evaluation of Platform Performance

Identification of a Network of Inflammatory Genes Associated with Differences in Skin Tumor Promotion Susceptibility

GHigh Throughput DNA Damage Assay Based on High Density Cell Array

Potential Susceptibility Variants for Obesity and Type 2 Diabetes in the TALLYHO Mouse

Pathogenic Orphan Transduction Created by a Non-reference LINE-1 Retrotransposon

Column Purification of Histidine-Tagged Proteins from Unclarified Samples

200 μm ID Chip Based Columns for Increased Throughput Peptide Quantitation with NanoLC/MS

Automated Method Development for Online 2D RP/RP for Peptides

Rapid Analysis of Intact Protein Using Liquid Chromatography Coupled with Mass Spectrometry

Chemical Cross-linking and MALDI-TOF/TOF to Investigate Protein Interacting Domains

Increasing Protein Identifications On a Q-TOF Mass Spectrometer

Improving nanoLC-MS Duty Cycle: Investigating Dual Column Capabilities and its Benefits

Optimization of Tryptic Digestion Methods for LC-MS/MS Analysis of Chimeric Immunoglobulin G

Isobaric Labeling and Data Normalization without Requiring Protein Quantification

Optimization of Whole-body Zebrafish Sectioning Methods for Mass Spectrometry Imaging

Working Towards AutoTune for NanoESI Spray Optimization: Investigating the Key Parameters which affect Spray Stability on a 4000 QTRAP Interface

Application of MALDI MS for Study of 5-bromouridine Photo-dissociation Rate Dependency on DNA Tertiary Structure

Robust, Quantitative, Label-free Phosphoproteomics Platform: Automated Enrichment and 2D-LC/MS/MS

The Use of Solid Supports to Facilitate Peptide Chemistry for Analytical Purposes Including Phosphorylation Analysis

Evaluation of LC Parameters on Peptide Identifications using Data-Dependent Acquisition on an LTQ Orbitrap Velos Mass Spectrometer

Comparison of Different Phosphopeptide Enrichment Strategies In Phosphoprotein Analysis

Yale Protein Expression Database 2.0

A Miniaturized Nanospray Probe Source for High Sensitivity NanoLC-MS

Metabolite Profiling of Methanosarcina Acetivorans (MA) with Direct Infusion to FT-ICR

Use of Ion Mobility and Fragment Ions to Increase Coverage in Hydrogen-Deuterium Exchange

Identification of Hypoxia-induced Metabolic Changes in Human Intestinal Epithelial Cells

Down-regulation of Bioenergetics in a Cellular Model of Friedreich's Ataxia: Frataxin Deficiency Affects Formation of Respiratory Supercomplexes and Glycolysis

Quality Control in a Metabolomics Laboratory: Back to Basics

Quantum Dot Uptake in Fathead Minnows, Pimephales Promelas, Ovarian Explant Cultures

Comparison of Agilent 2100 Bioanalyzer and Caliper Life Sciences GX II in Functionality, Total RNA Scoring Algorithms and Reproducibility to Evaluate Total RNA Integrity

Resolution and Quality Control of Confocal Microscopy Optics: Measuring and Interpreting Point Spread Functions

A Comparative Study of Peptide Storage Conditions Over an Extended Time Frame

Bacterial Apoa-1 Purification for the Deliverance of an Anticancer Drug Delivery System

Proteomics and Mass Spectrometry of Tragopogon Polyploid Evolution

N-terminal Top-Down Protein Sequencing of the ABRF-PSRG2012 Study Samples by ETD-UHR-TOF Mass Spectrometry

Creation of a Proteomics and Informatics Collaborative Group to Enhance Biomedical Research at Ethnically Diverse Institutions

Effect of the Presence of Carbohydrates during Acid Hydrolysis upon the Subsequent Recovery Free Amino Acids

Proteomics and Metabolomics of Arabidopsis Responses to Glucosinolate Perturbation

Quantitation and Validation of Low ng/ml Levels of Calcyclin: a Potential Pre-eclampsia Marker – in Serum by SRM

ProteoRed Multicenter Experiment for Long-term Quality Control Evaluation of Proteomics Core Facilities

Development of Automated SISCAPA Assays for High-Throughput Quantitation of Protein Biomarkers

Quantitative Imaging: How to Extract the Most of Your Experiments

Probing Advantages of Different Selectivity Strategies for Targeted Quantitative Proteomics

Evaluation of the Dynamic Range of Label-free Protein Quantification on an UHR-TOF MS

Redox Protein Characterization and Quantification Using ICAT-MS to Investigate Thiol-based Regulatory Mechanisms Induced by Oxidative Stress in Plants

Tips for Data Processing of iTRAQ Labeling Quantitative Proteomics Using ProteinPilot and its Background Correction Factor

A Label-free Quantitative Proteomics Assessment of Stress-responses in Candida albicans

Quantification of a Model Protein Lysozyme and Peptide MUC5AC-13 in Serum Matrix Using LC-QTOF

Strategies for Incorporating Novel Post-Translational Modification Enrichment Methods in a Quantitative Proteomics Environment

Effects of Protein Modification on Bottom-up Quantitative Proteomic Analyses

Quantitative Proteomics Reveals Dynamic changes in the Plasma Membrane Proteome During Arabidopsis Immune Signaling

A Multi-Centric Study To Assess Reproducibility of Protein Quantification By SRM LC-MS Proteomic Analysis

The Comparison of Secretion and Export of hIGF-1 in Escherichia Coli Strain BL21 and DH5?

Superior rRNA Removal for RNA-Seq Library Preparation

New Low Cost Cell and Tissue Acquisition System (CTAS): Microdissection of Live and Frozen Tissues

Searchable Core Facility Database: Building Resource Bridges

Enhanced Methods To Capture the Entire Small-RNA Transcriptome for RNA-Seq

Use of Ingenuity® iReport to Confirm and Expound Upon Previous Published Data Examining Differences in Gene Expression in Response to Seasonal and Pandemic H1N1 Influenza Infection in Human Type-I Like Alveolar Epithelial Cells

The Instituto Gulbenkian de Ciência and its Outreach

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Quantitative Imaging: How to Extract the Most of Your Experiments

Content Provider	PubMed Central
Author	Anders, Marcusson Svensson, Erika Diez, Roberto
Copyright Year	2012
Abstract	BACKGROUND: 2D-Difference Gel Electrophoresis DIGE is a technique where small changes of proteomes can be analyzed with high reproducibility and statistical significance. The sensitivity of the CyDyes™ combined with excellent normalization possibilities enables accurate monitoring of small protein changes. To reach the highest sensitivity and a broad linear dynamic range it requires imagers that meet these demands. The imaging system used for the analysis has a major impact on the quality of results as will be illustrated with a DIGE experiment. Moreover a set of dyes and stains have been evaluated for sensitivity and dynamic range on scanners and CCD-based imaging systems demonstrating the importance of those two parameters to reach the most of your research. Methods: Control and treated samples were randomly labelled with CyDye DIGE Fluor minimal dyes according to standard procedure. The samples were mixed and subjected to 2-D electrophoresis. The gels were imaged on Typhoon™ laser-based scanner and DeCyder™ 2-D software v 7.2 was used for analysis of differential protein abundances in the control and treated samples. RESULTS: To reach the best possible results of the analyses, optimal performance of the complete set of tools will have to be considered. Fluorescent dyes and stains are recommended for measuring differences in quantities of low abundant proteins, as they are showing higher sensitivity and wider dynamic range. The choice of imager is important; features such as filter options, resolution, and optics all affect image quality. The DIGE experiment demonstrates the importance of a high performance imaging system to reach optimal results. Lastly, the analysis software determines the final quality of the results. CONCLUSIONS: The quality of the results and the amount of information that can be extracted from an experiment is directly correlated to the performance of the imaging system.
Starting Page	53
File Format	PDF
ISSN	19434731
e-ISSN	19434731
Journal	Journal of Biomolecular Techniques : JBT
Issue Number	Suppl
Volume Number	23
Language	English
Publisher	Association of Biomolecular Resource Facilities
Publisher Date	2012-01-01
Access Restriction	Open
Rights Holder	Association of Biomolecular Resource Facilities
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article

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