Aiping Lu. Key Laboratory of System Biology Chinese Academic Society
|
|
- Felicia Baldwin
- 8 years ago
- Views:
Transcription
1 Aiping Lu Key Laboratory of System Biology Chinese Academic Society
2 Proteome and Proteomics PROTEin complement expressed by genome Marc Wilkins Electrophoresis (7): proteomics is the principle to study the proteome
3 Proteomics in broad sense Two-Dimentional Electrophoresis large-scale two-hybrid assays Protein Microarrays Proteomics in normal sense high-throughput protein production and crystallization Mass spectrometry based proteomics
4 Workflow of MS-based proteomics Protein seperation digestion Peptide seperation Protein lysate Peptide MS and MS/MS acquisition Bioinformatics analysis MS and MS/MS acquisition Top-down Database search Bottom-up
5 Studying targets Tissues Body fluid Cell lines Cell organelles
6 Sample preparation is critical for proteomic analysis Protein extraction Soluble proteins Membrane proteins Recovery Protein digestion Trypsin Lys-C Suitable for MS analysis Protein/peptide separation IEF Multiple dimensional HILIC SCX SAX RP-HPLC SDS-PAGE + RP-HPLC Dynamic range Sensitivity
7 Mass spectrometry is the basis of proteomics Ion Source Ion from solution to gas Mass Analyzer Acquire mass-to-charge value Detector Electron multiplier orbitrap Quadrupole Electrospray Ionization Continuous dynode electron multiplier Time-of-Flight FT-ICR:Fourier transform ion cyclotron resonance Matrix-Assisted Laser Desorption/Ionization Microchannel plate detectors Linear quadrupole ion trap
8 Pros and Cons of Different Analyzer Accuracy Resolution Sensitivity Dynamic Range FT-ICR 1 ppm High Low High Orbitrap 5 ppm High Low High TOF 50 ppm Medium Medium Medium Quadrupole 500 ppm Low High Low Ion trap 500 ppm Low High Low Hybrid instrument
9 Tandem mass spectrometer Tandem in space Collision Cell Ion Source Mass Analyzer C C Mass Analyzer Detector e.g. QQQ, Q-TOF, TOF-TOF Tandem in time Ion Source Mass Analyzer Detector e.g. ion trap, LTQ, FT-ICR, orbitrap
10 Peptide fragmentation and nomenclature Low energy collision High energy collision
11 MS data interpretation Isotopic Cluster Mass Resolution Dynamic Range m/z FWHH Mass Accuracy FWHH:full width at the half-height Signal-to-noise ratio
12 MS data - an example Precursor ion mass Precursor ion charge state Sample information Total Ion Current / Base Peak Current Retention time Fragment ion m/z Fragment ion intensity MS MS/MS Database search
13 Search Engine Mascot Sequest In short, SEQUEST performs automated peptide/protein sequencing via database searching of MS/MS spectra User friendly interpretation Straightforward search
14 Search mechanism Real Identical mass within MMD Theoretical m/z m/z Compare and scoring SEQUEST MASCOT X!tandem ProbID m/z NCBI Swiss-Prot IPI Ensembl Theoretical digestion SFATFDIMAETLK DILSVDYTDIMK Theoretical fragment ladders identification
15 Significant identification Mascot Probability based scoring Compute the probability that the observed match between the experimental data and mass values calculated from a candidate peptide sequence is a random event. The correct match has a very low probability. Ion score = -10Log 10 (P), P = p/n, (p : prosibility threshold, N: database entries of the precursor ions ) Sequest a two-tiered scoring scheme 1. the preliminary score (Sp), is an empirically derived score that restricts the number of sequences analyzed in the correlation analysis. 2. XCorr is independent of database size and reflects the quality of the match between spectrum and sequence, whereas ΔCn is database dependent and reflects the quality of the match relative to near misses. 3. normalize XCorr for spectral noise and peptide size target /Reversed FDR: NT NT + NR FPR: NT NT + 2 X NR NT: Number of peptide in target database NR: Number of peptide in reversed database
16 Qualitative and Quantitative Proteomics Qualitative proteomics Quantitative proteomics Protein identifications PTM analysis Biomarker Protein dynamics Protein interaction partners
17 Quantitative approaches 15 N, SILAC ICAT, itraq Bantscheff M. et al. Anal Bioanal Chem (2007) 389:
18 Labeling reagents SILAC: 2 H 4 -Lys, 13 C 6 15 N 2 -Lys, 13 C 6 -Arg, 13 C 6 15 N 4 -Arg 2 H 3 -Leu Mann M. MCP 2002 ICAT: Aebersold R. Nat. Biotechnol itraq: Pappin D.J. MCP, 2004
19 SILAC stable isotopic labeling of amino acid in cell culture
20 How to analyze long list of protein?
21 Bioinformatics for qualitative proteomics Chanchal Kumar & Matthias Mann. FEBS Letters 583 (2009)
22 Bioinformatics for quantitative proteomics Chanchal Kumar & Matthias Mann. FEBS Letters 583 (2009)
23 Useful bioinformatics tools Qualitative analysis: BINGO Quantitative analysis: CLUSTER & PCA Biological analysis: KEGG
24 Tool Bingo Qualitative analysis of overrepresented groups Entrez Gene Biological Process Cellular Component Molecular Function Control database
25 Result display of Bingo
26 Tool Cluster
27 Result display of cluster
28 Different samples Tool PCA Principal component analysis involves a mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components Different proteins Intensity Matrix
29 Tool KEGG Kyoto Encyclopedia of Genes and Genomes
30 Pathway display of KEGG
31 Proteomics is not the end of a story Immunohistochemistry candidates Fluorescent Knock-out animal model ChIP
32
泛 用 蛋 白 質 體 學 之 質 譜 儀 資 料 分 析 平 台 的 建 立 與 應 用 Universal Mass Spectrometry Data Analysis Platform for Quantitative and Qualitative Proteomics
泛 用 蛋 白 質 體 學 之 質 譜 儀 資 料 分 析 平 台 的 建 立 與 應 用 Universal Mass Spectrometry Data Analysis Platform for Quantitative and Qualitative Proteomics 2014 Training Course Wei-Hung Chang ( 張 瑋 宏 ) ABRC, Academia
More informationProteomics in Practice
Reiner Westermeier, Torn Naven Hans-Rudolf Höpker Proteomics in Practice A Guide to Successful Experimental Design 2008 Wiley-VCH Verlag- Weinheim 978-3-527-31941-1 Preface Foreword XI XIII Abbreviations,
More informationIntroduction to Proteomics 1.0
Introduction to Proteomics 1.0 CMSP Workshop Tim Griffin Associate Professor, BMBB Faculty Director, CMSP Objectives Why are we here? For participants: Learn basics of MS-based proteomics Learn what s
More informationGlobal and Discovery Proteomics Lecture Agenda
Global and Discovery Proteomics Christine A. Jelinek, Ph.D. Johns Hopkins University School of Medicine Department of Pharmacology and Molecular Sciences Middle Atlantic Mass Spectrometry Laboratory Global
More informationTutorial for Proteomics Data Submission. Katalin F. Medzihradszky Robert J. Chalkley UCSF
Tutorial for Proteomics Data Submission Katalin F. Medzihradszky Robert J. Chalkley UCSF Why Have Guidelines? Large-scale proteomics studies create huge amounts of data. It is impossible/impractical to
More informationQuantitative proteomics background
Proteomics data analysis seminar Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post transcriptional regulation of key cellular processes de Groot, M., Daran
More informationIntroduction to Proteomics
Introduction to Proteomics Åsa Wheelock, Ph.D. Division of Respiratory Medicine & Karolinska Biomics Center asa.wheelock@ki.se In: Systems Biology and the Omics Cascade, Karolinska Institutet, June 9-13,
More informationChallenges in Computational Analysis of Mass Spectrometry Data for Proteomics
Ma B. Challenges in computational analysis of mass spectrometry data for proteomics. SCIENCE AND TECHNOLOGY 25(1): 1 Jan. 2010 JOURNAL OF COMPUTER Challenges in Computational Analysis of Mass Spectrometry
More informationMass Spectrometry Based Proteomics
Mass Spectrometry Based Proteomics Proteomics Shared Research Oregon Health & Science University Portland, Oregon This document is designed to give a brief overview of Mass Spectrometry Based Proteomics
More informationMRMPilot Software: Accelerating MRM Assay Development for Targeted Quantitative Proteomics
MRMPilot Software: Accelerating MRM Assay Development for Targeted Quantitative Proteomics With Unique QTRAP and TripleTOF 5600 System Technology Targeted peptide quantification is a rapidly growing application
More informationLa Protéomique : Etat de l art et perspectives
La Protéomique : Etat de l art et perspectives Odile Schiltz Institut de Pharmacologie et de Biologie Structurale CNRS, Université de Toulouse, Odile.Schiltz@ipbs.fr Protéomique et Spectrométrie de Masse
More informationIntroduction to mass spectrometry (MS) based proteomics and metabolomics
Introduction to mass spectrometry (MS) based proteomics and metabolomics Tianwei Yu Department of Biostatistics and Bioinformatics Rollins School of Public Health Emory University September 10, 2015 Background
More informationProteomic data analysis for Orbitrap datasets using Resources available at MSI. September 28 th 2011 Pratik Jagtap
Proteomic data analysis for Orbitrap datasets using Resources available at MSI. September 28 th 2011 Pratik Jagtap The Minnesota http://www.mass.msi.umn.edu/ Proteomics workflow Trypsin Protein Peptides
More informationAdvantages of the LTQ Orbitrap for Protein Identification in Complex Digests
Application Note: 386 Advantages of the LTQ Orbitrap for Protein Identification in Complex Digests Rosa Viner, Terry Zhang, Scott Peterman, and Vlad Zabrouskov, Thermo Fisher Scientific, San Jose, CA,
More informationMultiQuant Software 2.0 for Targeted Protein / Peptide Quantification
MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification Gold Standard for Quantitative Data Processing Because of the sensitivity, selectivity, speed and throughput at which MRM assays can
More informationSession 1. Course Presentation: Mass spectrometry-based proteomics for molecular and cellular biologists
Program Overview Session 1. Course Presentation: Mass spectrometry-based proteomics for molecular and cellular biologists Session 2. Principles of Mass Spectrometry Session 3. Mass spectrometry based proteomics
More informationApplication Note # LCMS-81 Introducing New Proteomics Acquisiton Strategies with the compact Towards the Universal Proteomics Acquisition Method
Application Note # LCMS-81 Introducing New Proteomics Acquisiton Strategies with the compact Towards the Universal Proteomics Acquisition Method Introduction During the last decade, the complexity of samples
More informationResearch-grade Targeted Proteomics Assay Development: PRMs for PTM Studies with Skyline or, How I learned to ditch the triple quad and love the QE
Research-grade Targeted Proteomics Assay Development: PRMs for PTM Studies with Skyline or, How I learned to ditch the triple quad and love the QE Jacob D. Jaffe Skyline Webinar July 2015 Proteomics and
More informationError Tolerant Searching of Uninterpreted MS/MS Data
Error Tolerant Searching of Uninterpreted MS/MS Data 1 In any search of a large LC-MS/MS dataset 2 There are always a number of spectra which get poor scores, or even no match at all. 3 Sometimes, this
More informationProtein Prospector and Ways of Calculating Expectation Values
Protein Prospector and Ways of Calculating Expectation Values 1/16 Aenoch J. Lynn; Robert J. Chalkley; Peter R. Baker; Mark R. Segal; and Alma L. Burlingame University of California, San Francisco, San
More informationIncreasing the Multiplexing of High Resolution Targeted Peptide Quantification Assays
Increasing the Multiplexing of High Resolution Targeted Peptide Quantification Assays Scheduled MRM HR Workflow on the TripleTOF Systems Jenny Albanese, Christie Hunter AB SCIEX, USA Targeted quantitative
More informationPreprocessing, Management, and Analysis of Mass Spectrometry Proteomics Data
Preprocessing, Management, and Analysis of Mass Spectrometry Proteomics Data M. Cannataro, P. H. Guzzi, T. Mazza, and P. Veltri Università Magna Græcia di Catanzaro, Italy 1 Introduction Mass Spectrometry
More informationQuantitative mass spec based proteomics
Quantitative mass spec based proteomics Tuula Nyman Institute of Biotechnology tuula.nyman@helsinki.fi Proteomics is the large-scale study of proteins Proteomics provides information on: -protein expression
More informationAB SCIEX TOF/TOF 4800 PLUS SYSTEM. Cost effective flexibility for your core needs
AB SCIEX TOF/TOF 4800 PLUS SYSTEM Cost effective flexibility for your core needs AB SCIEX TOF/TOF 4800 PLUS SYSTEM It s just what you expect from the industry leader. The AB SCIEX 4800 Plus MALDI TOF/TOF
More informationCONTENTS. PART I INSTRUMENTATION 1 1 DEFINITIONS AND EXPLANATIONS 3 Ann Westman-Brinkmalm and Gunnar Brinkmalm References 13
CONTENTS FOREWORD CONTRIBUTORS xiii xv PART I INSTRUMENTATION 1 1 DEFINITIONS AND EXPLANATIONS 3 Ann Westman-Brinkmalm and Gunnar Brinkmalm References 13 2 A MASS SPECTROMETER S BUILDING BLOCKS 15 Ann
More informationThe Scheduled MRM Algorithm Enables Intelligent Use of Retention Time During Multiple Reaction Monitoring
The Scheduled MRM Algorithm Enables Intelligent Use of Retention Time During Multiple Reaction Monitoring Delivering up to 2500 MRM Transitions per LC Run Christie Hunter 1, Brigitte Simons 2 1 AB SCIEX,
More informationIn-Depth Qualitative Analysis of Complex Proteomic Samples Using High Quality MS/MS at Fast Acquisition Rates
In-Depth Qualitative Analysis of Complex Proteomic Samples Using High Quality MS/MS at Fast Acquisition Rates Using the Explore Workflow on the AB SCIEX TripleTOF 5600 System A major challenge in proteomics
More informationPeptidomicsDB: a new platform for sharing MS/MS data.
PeptidomicsDB: a new platform for sharing MS/MS data. Federica Viti, Ivan Merelli, Dario Di Silvestre, Pietro Brunetti, Luciano Milanesi, Pierluigi Mauri NETTAB2010 Napoli, 01/12/2010 Mass Spectrometry
More informationPep-Miner: A Novel Technology for Mass Spectrometry-Based Proteomics
Pep-Miner: A Novel Technology for Mass Spectrometry-Based Proteomics Ilan Beer Haifa Research Lab Dec 10, 2002 Pep-Miner s Location in the Life Sciences World The post-genome era - the age of proteome
More informationProteinScape. Innovation with Integrity. Proteomics Data Analysis & Management. Mass Spectrometry
ProteinScape Proteomics Data Analysis & Management Innovation with Integrity Mass Spectrometry ProteinScape a Virtual Environment for Successful Proteomics To overcome the growing complexity of proteomics
More informationProteomic Analysis using Accurate Mass Tags. Gordon Anderson PNNL January 4-5, 2005
Proteomic Analysis using Accurate Mass Tags Gordon Anderson PNNL January 4-5, 2005 Outline Accurate Mass and Time Tag (AMT) based proteomics Instrumentation Data analysis Data management Challenges 2 Approach
More informationEffects of Intelligent Data Acquisition and Fast Laser Speed on Analysis of Complex Protein Digests
Effects of Intelligent Data Acquisition and Fast Laser Speed on Analysis of Complex Protein Digests AB SCIEX TOF/TOF 5800 System with DynamicExit Algorithm and ProteinPilot Software for Robust Protein
More informationusing ms based proteomics
quantification using ms based proteomics lennart martens Computational Omics and Systems Biology Group Department of Medical Protein Research, VIB Department of Biochemistry, Ghent University Ghent, Belgium
More informationChapter 14. Modeling Experimental Design for Proteomics. Jan Eriksson and David Fenyö. Abstract. 1. Introduction
Chapter Modeling Experimental Design for Proteomics Jan Eriksson and David Fenyö Abstract The complexity of proteomes makes good experimental design essential for their successful investigation. Here,
More informationChoices, choices, choices... Which sequence database? Which modifications? What mass tolerance?
Optimization 1 Choices, choices, choices... Which sequence database? Which modifications? What mass tolerance? Where to begin? 2 Sequence Databases Swiss-prot MSDB, NCBI nr dbest Species specific ORFS
More informationQuantitative mass spectrometry in proteomics: a critical review
Anal Bioanal Chem (2007) 389:1017 1031 DOI 10.1007/s00216-007-1486-6 REVIEW Quantitative mass spectrometry in proteomics: a critical review Marcus Bantscheff & Markus Schirle & Gavain Sweetman & Jens Rick
More informationSimultaneous qualitative and quantitative analysis using the Agilent 6540 Accurate-Mass Q-TOF
Simultaneous qualitative and quantitative analysis using the Agilent 654 Accurate-Mass Q-TOF Technical Overview Authors Pat Perkins Anabel Fandino Lester Taylor Agilent Technologies, Inc. Santa Clara,
More informationShotgun Proteomic Analysis. Department of Cell Biology The Scripps Research Institute
Shotgun Proteomic Analysis Department of Cell Biology The Scripps Research Institute Biological/Functional Resolution of Experiments Organelle Multiprotein Complex Cells/Tissues Function Expression Analysis
More informationMass Spectrometry Signal Calibration for Protein Quantitation
Cambridge Isotope Laboratories, Inc. www.isotope.com Proteomics Mass Spectrometry Signal Calibration for Protein Quantitation Michael J. MacCoss, PhD Associate Professor of Genome Sciences University of
More informationInterpretation of MS-Based Proteomics Data
Interpretation of MS-Based Proteomics Data Yet-Ran Chen, 陳 逸 然 Agricultural Biotechnology Research Center Academia Sinica Brief Overview of Protein Identification Workflow Protein Sample Specific Protein
More informationLaboration 1. Identifiering av proteiner med Mass Spektrometri. Klinisk Kemisk Diagnostik
Laboration 1 Identifiering av proteiner med Mass Spektrometri Klinisk Kemisk Diagnostik Sven Kjellström 2014 kjellstrom.sven@gmail.com 0702-935060 Laboration 1 Klinisk Kemisk Diagnostik Identifiering av
More informationProteomics in general deals with the large-scale
Mass spectrometry-based proteomics Ruedi Aebersold* & Matthias Mann *Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, USA (e-mail: raebersold@systemsbiology.org) Center
More informationBuilding innovative drug discovery alliances. Evotec Munich. Quantitative Proteomics to Support the Discovery & Development of Targeted Drugs
Building innovative drug discovery alliances Evotec Munich Quantitative Proteomics to Support the Discovery & Development of Targeted Drugs Evotec AG, Evotec Munich, June 2013 About Evotec Munich A leader
More informationProteinPilot Report for ProteinPilot Software
ProteinPilot Report for ProteinPilot Software Detailed Analysis of Protein Identification / Quantitation Results Automatically Sean L Seymour, Christie Hunter SCIEX, USA Pow erful mass spectrometers like
More informationQuan%ta%ve proteomics. Maarten Altelaar, 2014
Quan%ta%ve proteomics Maarten Altelaar, 2014 Proteomics Altelaar et al. Nat Rev Gen 14, 2013, 35-48 Quan%ta%ve proteomics Quan%ta%ve proteomics Control Diseased, s%mulated, Knock down, etc. How quan%ta%ve
More informationMaxQuant User s Guide Version 1.2.2.5
MaxQuant User s Guide Version 1.2.2.5 Jűrgen Cox and Matthias Mann Nature Biotechnology 26, 1367-1372 (2008) Sara ten Have 2012 http://www.lamondlab.com/ http://greproteomics.lifesci.dundee.ac.uk/ References
More informationitraq Tips and Tricks
itraq Tips and Tricks Darryl Pappin Cold Spring Harbor Laboratory Patrick Emery Matrix Science Ltd. 1 Good morning. Unfortunately Darryl Pappin is unable to attend the Matrix Science workshop and the ASMS
More informationIntroduction to Proteomics
Introduction to Proteomics Why Proteomics? Same Genome Different Proteome Black Swallowtail - larvae and butterfly Biological Complexity Yeast - a simple proteome 6,113 proteins = 344,855 tryptic peptides
More informationPrinciples of Mass Spectrometry-Based Proteomics. Steven Gygi Department of Cell Biology Harvard Medical School, Boston, MA
Principles of Mass Spectrometry-Based Proteomics Steven Gygi Department of Cell Biology Harvard Medical School, Boston, MA The Flow of Information The Flow of Information Networks Complexes Proteins Genes
More informationMaster course KEMM03 Principles of Mass Spectrometric Protein Characterization. Exam
Exam Master course KEMM03 Principles of Mass Spectrometric Protein Characterization 2010-10-29 kl 08.15-13.00 Use a new paper for answering each question! Write your name on each paper! Aids: Mini calculator,
More informationStatistical Analysis Strategies for Shotgun Proteomics Data
Statistical Analysis Strategies for Shotgun Proteomics Data Ming Li, Ph.D. Cancer Biostatistics Center Vanderbilt University Medical Center Ayers Institute Biomarker Pipeline normal shotgun proteome analysis
More informationA Tool To Visualize and Evaluate Data Obtained by Liquid Chromatography-Electrospray Ionization-Mass Spectrometry
Anal. Chem. 2004, 76, 3856-3860 A Tool To Visualize and Evaluate Data Obtained by Liquid Chromatography-Electrospray Ionization-Mass Spectrometry Xiao-jun Li,* Patrick G. A. Pedrioli, Jimmy Eng, Dan Martin,
More informationThermo Scientific PepFinder Software A New Paradigm for Peptide Mapping
Thermo Scientific PepFinder Software A New Paradigm for Peptide Mapping For Conclusive Characterization of Biologics Deep Protein Characterization Is Crucial Pharmaceuticals have historically been small
More informationBiopharmaceutical Glycosylation Analysis
Biopharmaceutical Glycosylation Analysis Glycosylation Analysis: Product Offering Molecular model of erythropoietin with complex N-linked glycans. Courtesy of M.R Wormald and R.A Dwek, Oxford Glycobioloy
More informationIntegrated Data Mining Strategy for Effective Metabolomic Data Analysis
The First International Symposium on Optimization and Systems Biology (OSB 07) Beijing, China, August 8 10, 2007 Copyright 2007 ORSC & APORC pp. 45 51 Integrated Data Mining Strategy for Effective Metabolomic
More informationMASCOT Search Results Interpretation
The Mascot protein identification program (Matrix Science, Ltd.) uses statistical methods to assess the validity of a match. MS/MS data is not ideal. That is, there are unassignable peaks (noise) and usually
More informationSimGlycan Software*: A New Predictive Carbohydrate Analysis Tool for MS/MS Data
SimGlycan Software*: A New Predictive Carbohydrate Analysis Tool for MS/MS Data Automated Data Interpretation for Glycan Characterization Jenny Albanese 1, Matthias Glueckmann 2 and Christof Lenz 2 1 AB
More informationOverview. Triple quadrupole (MS/MS) systems provide in comparison to single quadrupole (MS) systems: Introduction
Advantages of Using Triple Quadrupole over Single Quadrupole Mass Spectrometry to Quantify and Identify the Presence of Pesticides in Water and Soil Samples André Schreiber AB SCIEX Concord, Ontario (Canada)
More informationALGORITHMS FOR SHOTGUN PROTEOMICS SPECTRAL IDENTIFICATION AND QUALITY ASSESSMENT. Ze-Qiang Ma
ALGORITHMS FOR SHOTGUN PROTEOMICS SPECTRAL IDENTIFICATION AND QUALITY ASSESSMENT By Ze-Qiang Ma Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment
More informationAccurate calibration of on-line Time of Flight Mass Spectrometer (TOF-MS) for high molecular weight combustion product analysis
Accurate calibration of on-line Time of Flight Mass Spectrometer (TOF-MS) for high molecular weight combustion product analysis B. Apicella*, M. Passaro**, X. Wang***, N. Spinelli**** mariadellarcopassaro@gmail.com
More informationComparison of Spectra in Unsequenced Species
Comparison of Spectra in Unsequenced Species Freddy Cliquet 1,2, Guillaume Fertin 1, Irena Rusu 1,Dominique Tessier 2 1 LINA, UMR CNRS 6241 Université de Nantes, 2 rue de la Houssinière, 44322, Nantes,
More informationDevelopment of computational methods for analysing proteomic data for genome annotation
Development of computational methods for analysing proteomic data for genome annotation University of Cambridge Darwin College A thesis submitted for the degree of Doctor of Philosophy Markus Brosch The
More informationSub menu of functions to give the user overall information about the data in the file
Visualize The Multitool for Proteomics! File Open Opens an.ez2 file to be examined. Import from TPP Imports data from files created by Trans Proteomic Pipeline. User chooses mzxml, pepxml and FASTA files
More informationProSightPC 3.0 Quick Start Guide
ProSightPC 3.0 Quick Start Guide The Thermo ProSightPC 3.0 application is the only proteomics software suite that effectively supports high-mass-accuracy MS/MS experiments performed on LTQ FT and LTQ Orbitrap
More informationNUVISAN Pharma Services
NUVISAN Pharma Services CESI MS Now available! 1st CRO in Europe! At the highest levels of quality. LABORATORY SERVICES Equipment update STATE OF THE ART AT NUVISAN CESI MS Now available! 1st CRO in Europe!
More informationMass Spectra Alignments and their Significance
Mass Spectra Alignments and their Significance Sebastian Böcker 1, Hans-Michael altenbach 2 1 Technische Fakultät, Universität Bielefeld 2 NRW Int l Graduate School in Bioinformatics and Genome Research,
More informationMass spectrometry. Dr. Kevin R. Tucker
Mass spectrometry Dr. Kevin R. Tucker What is mass spectrometry? A versatile analytical technique used to determine the composition of chemical samples either at the atomic or molecular level. Ionic forms
More informationComputational analysis of unassigned high-quality MS/MS spectra in proteomic data sets
2712 DOI 10.1002/pmic.200900473 Proteomics 2010, 10, 2712 2718 TECHNICAL BRIEF Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets Kang Ning 1, Damian Fermin 1 and Alexey
More informationSupplementary Materials and Methods (Metabolomics analysis)
Supplementary Materials and Methods (Metabolomics analysis) Metabolite extraction and mass spectrometry analysis. 12 Vldlr-/- knock out and 12 wild type (WT) retinas were separately frozen at -80 ºC in
More informationInvestigating Biological Variation of Liver Enzymes in Human Hepatocytes
Investigating Biological Variation of Liver Enzymes in Human Hepatocytes MS/MS ALL with SWATH Acquisition on the TripleTOF Systems Xu Wang 1, Hui Zhang 2, Christie Hunter 1 1 AB SCIEX, USA, 2 Pfizer, USA
More informationContents. Preface to the Second Edition List of Contributors XIII
Contents Preface to the Second Edition List of Contributors XIII XI 1 The MALDI Process and Method 1 Franz Hillenkamp, Thorsten W. Jaskolla, and Michael Karas 1.1 Introduction 1 1.2 Analyte Incorporation
More informationOvercoming Challenges of Shotgun Proteomics
DISSERTATION ZUR ERLANGUNG DES DOKTORGRADES DER FAKULTÄT FÜR CHEMIE UND PHARMAZIE DER LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Overcoming Challenges of Shotgun Proteomics von Annette Michalski aus Hildesheim
More informationSoftware for protein identification and quantitative analysis of mass spectrometry data used for protein characterization and proteomics Version 5.
Release Notes ProteinPilot Software for protein identification and quantitative analysis of mass spectrometry data used for protein characterization and proteomics Version 5.0 Introduction Thank you for
More informationHigh resolution mass spectrometry (HRMS*) in Graz
High resolution mass spectrometry (HRMS*) in Graz 10.2.2012 * Instruments with high resolution where exact mass measurements can be performed 1 HRMS in Graz s and Ionization Techniques 2 6 3 5 4 1 TU Graz
More informationEvaluation of LC-MS data for the absolute quantitative analysis of marker proteins
Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins Nathanaël Delmotte 1, Bettina Mayr 1, Andreas Leinenbach 1, Knut Reinert 2, Oliver Kohlbacher 3, Christoph Klein 4, and
More informationRetrospective Analysis of a Host Cell Protein Perfect Storm: Identifying Immunogenic Proteins and Fixing the Problem
Retrospective Analysis of a Host Cell Protein Perfect Storm: Identifying Immunogenic Proteins and Fixing the Problem Kevin Van Cott, Associate Professor Dept. of Chemical and Biomolecular Engineering Nebraska
More informationPrinciples and Applications of Proteomics
Principles and Applications of Proteomics Why Proteomics? 2-DE Overview Sample preparation 1 st & 2 nd dimension seperation Data Analysis Sample preparation for Mass Spectrometry Mass Spectrometry MALDI-TOF,
More informationLC-MS/MS for Chromatographers
LC-MS/MS for Chromatographers An introduction to the use of LC-MS/MS, with an emphasis on the analysis of drugs in biological matrices LC-MS/MS for Chromatographers An introduction to the use of LC-MS/MS,
More informationANALYSIS OF PROTEINS AND PROTEOMES BY MASS SPECTROMETRY
Annu. Rev. Biochem. 2001. 70:437 73 Copyright c 2001 by Annual Reviews. All rights reserved ANALYSIS OF PROTEINS AND PROTEOMES BY MASS SPECTROMETRY Matthias Mann, 1,2 Ronald C. Hendrickson, 2 and Akhilesh
More informationOverview. Introduction. AB SCIEX MPX -2 High Throughput TripleTOF 4600 LC/MS/MS System
Investigating the use of the AB SCIEX TripleTOF 4600 LC/MS/MS System for High Throughput Screening of Synthetic Cannabinoids/Metabolites in Human Urine AB SCIEX MPX -2 High Throughput TripleTOF 4600 LC/MS/MS
More informationSimGlycan Software*: A New Predictive Carbohydrate Analysis Tool for MS/MS Data
SimGlycan Software*: A New Predictive Carbohydrate Analysis Tool for MS/MS Data Automated Data Interpretation for Glycan Characterization Jenny Albanese1, Matthias Glueckmann2 and Christof Lenz2 1Applied
More informationAccurate Mass Screening Workflows for the Analysis of Novel Psychoactive Substances
Accurate Mass Screening Workflows for the Analysis of Novel Psychoactive Substances TripleTOF 5600 + LC/MS/MS System with MasterView Software Adrian M. Taylor AB Sciex Concord, Ontario (Canada) Overview
More informationRapidFire High-throughput MS technology. Enhancing Drug Discovery Turning Mass Specs into Plate Readers
RapidFire High-throughput MS technology Enhancing Drug Discovery Turning Mass Specs into Plate Readers 1 Drug Discovery with RapidFire Target Selection High-throughput Target Screening (HTS) Lead Optimization
More informationAgilent 6000 Series LC/MS Solutions CONFIDENCE IN QUANTITATIVE AND QUALITATIVE ANALYSIS
Agilent 6000 Series LC/MS Solutions CONFIDENCE IN QUANTITATIVE AND QUALITATIVE ANALYSIS AGILENT 6000 SERIES LC/MS SOLUTIONS UNRIVALED ACHIEVEMENT AT EVERY LEVEL The Agilent 6000 Series of LC/MS instruments
More informationProtein Hit1, a novel box C/D snornp assembly factor, controls cellular concentration of protein Rsa1p by direct interaction
Supplementary data Protein Hit1, a novel box C/D snornp assembly factor, controls cellular concentration of protein Rsa1p by direct interaction Benjamin Rothé, Jean-Michel Saliou, Marc Quinternet, Régis
More informationAgilent G2721AA/G2733AA Spectrum Mill MS Proteomics Workbench
Agilent G2721AA/G2733AA Spectrum Mill MS Proteomics Workbench Application Guide Agilent Technologies Notices Agilent Technologies, Inc. 2012 No part of this manual may be reproduced in any form or by any
More informationOpenMS A Framework for Quantitative HPLC/MS-Based Proteomics
OpenMS A Framework for Quantitative HPLC/MS-Based Proteomics Knut Reinert 1, Oliver Kohlbacher 2,Clemens Gröpl 1, Eva Lange 1, Ole Schulz-Trieglaff 1,Marc Sturm 2 and Nico Pfeifer 2 1 Algorithmische Bioinformatik,
More informationIn-depth Analysis of Tandem Mass Spectrometry Data from Disparate Instrument Types* S
Research In-depth Analysis of Tandem Mass Spectrometry Data from Disparate Instrument Types* S Robert J. Chalkley, Peter R. Baker, Katalin F. Medzihradszky, Aenoch J. Lynn, and A. L. Burlingame Mass spectrometric
More informationMassMatrix Web Server User Manual
MassMatrix Web Server User Manual Version 2.2.3 or later Hua Xu, Ph. D. Center for Proteomics & Bioinformatics Case Western Reserve University August 2009 Main Navigation Bar of the Site MassMatrix Web
More informationBruker ToxScreener TM. Innovation with Integrity. A Comprehensive Screening Solution for Forensic Toxicology UHR-TOF MS
Bruker ToxScreener TM A Comprehensive Screening Solution for Forensic Toxicology Innovation with Integrity UHR-TOF MS ToxScreener - Get the Complete Picture Forensic laboratories are frequently required
More informationPesticide Analysis by Mass Spectrometry
Pesticide Analysis by Mass Spectrometry Purpose: The purpose of this assignment is to introduce concepts of mass spectrometry (MS) as they pertain to the qualitative and quantitative analysis of organochlorine
More informationPractical Analysis of Proteome Data Using Bioinformatics and Statistics
Practical Analysis of Proteome Data Using Bioinformatics and Statistics Simon Barkow-Oesterreicher Functional Genomics Center Zurich Dr. Jonas Grossmann Functional Genomics Center Zurich 1 Outline Challenges
More information# LCMS-35 esquire series. Application of LC/APCI Ion Trap Tandem Mass Spectrometry for the Multiresidue Analysis of Pesticides in Water
Application Notes # LCMS-35 esquire series Application of LC/APCI Ion Trap Tandem Mass Spectrometry for the Multiresidue Analysis of Pesticides in Water An LC-APCI-MS/MS method using an ion trap system
More informationMolecular Cell Biology. Prof. D. Karunagaran. Department of Biotechnology. Indian Institute of Technology Madras
Molecular Cell Biology Prof. D. Karunagaran Department of Biotechnology Indian Institute of Technology Madras Module 5 Methods in Cell Biology (Methods to Manipulate Protein, DNA and RNA and Methods to
More informationDefinition of the Measurand: CRP
A Reference Measurement System for C-reactive Protein David M. Bunk, Ph.D. Chemical Science and Technology Laboratory National Institute of Standards and Technology Definition of the Measurand: Human C-reactive
More informationWaters Core Chromatography Training (2 Days)
2015 Page 2 Waters Core Chromatography Training (2 Days) The learning objective of this two day course is to teach the user core chromatography, system and software fundamentals in an outcomes based approach.
More informationMass spectrometry based proteomics
Practice-oriented, student-friendly modernization of the biomedical education for strengthening the international competitiveness of the rural Hungarian universities TÁMOP-4.1.1.C-13/1/KONV-2014-0001 Mass
More informationAGILENT S BIOINFORMATICS ANALYSIS SOFTWARE
ACCELERATING PROGRESS IS IN OUR GENES AGILENT S BIOINFORMATICS ANALYSIS SOFTWARE GENESPRING GENE EXPRESSION (GX) MASS PROFILER PROFESSIONAL (MPP) PATHWAY ARCHITECT (PA) See Deeper. Reach Further. BIOINFORMATICS
More informationBrochure More information from http://www.researchandmarkets.com/reports/2172993/
Brochure More information from http://www.researchandmarkets.com/reports/2172993/ Proteomics Today. Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis,and Microarray Technology.
More informationIdentification of Serum Protein Biomarkers for Autistic Spectrum Disorder. Melissa Butkiewicz
Identification of Serum Protein Biomarkers for Autistic Spectrum Disorder by Melissa Butkiewicz Clarkson University Identification of Serum Protein Biomarkers for Autistic Spectrum Disorder A Thesis Proposal
More information