Proteomics: A Challenge for Technology and Information Science. What is proteomics?

Size: px
Start display at page:

Download "Proteomics: A Challenge for Technology and Information Science. What is proteomics?"

Transcription

1 Proteomics: A Challenge for Technology and Information Science CBCB Seminar, November 21, 2005 Tim Griffin Dept. Biochemistry, Molecular Biology and Biophysics tgriffin@umn.edu What is proteomics? Proteomics includes not only the identification and quantification of proteins, but also the determination of their localization, modifications, interactions, activities, and, ultimately, their function. -Stan Fields in Science,

2 Genomics vs. Proteomics Similarities: Large datasets, tools needed for annotation and interpretation of results Differences: Genomics generally mature technologies, data processing methods, questions asked usually involve quantitative changes in RNA transcripts (microarrays) Proteomics still evolving, complexity of protein biochemical properties: expression changes, modifications, interactions, activities many questions to ask and data to interpret, methods changing, different approaches (mass spec, arrays etc.), Genomics, Proteomics, and Systems Biology genomics proteomics computational biology genomic DNA mrna protein products functional protein system mature prototype emerging sequencing arrays 3D structure quantitative profiling protein cataloguing catalytic activity sub cellular location Protein Modifications Protein dynamics protein phosphorylation descriptive protein interaction maps interactions between components identify system components measure and define properties 2

3 Shotgun identification of proteins in mixtures by LC-MS/MS Liquid chromatography coupled to tandem mass spectrometry (MS/MS) Protein(s) peptides peptide fragments Digestion µlc separation ( um) Ionization: MALDI or Electrospray Isolation Fragmentation Mass Analysis Tandem mass spectrum (thousands in a matter of hours) Peptide sequence determination from MS/MS spectra Collision-induced dissociation (CID) creates two prominent ion series: y-series: y 14 y 13 y 12 y 11 y 10 y 9 y 8 y 7 y 6 y 5 y 4 y 3 y 2 y 1 2 N-N--S--G--D--I--V--N--L--G--S--I--A--G--R-COO b-series: b 1 b 2 b 3 b 4 b 5 b 6 b 7 b 8 b 9 b 10 b 11 b 12 b 13 b 14 Relative Abundance

4 Peptide sequence identifies the protein Relative Abundance GDIVNLGSIAGR DIVNLGSIAGR IVNLGSIAGR VNLGSIAGR NLGSIAGR LGSIAGR GSIAGR SIAGR IAGR AGR GR R 2 N-NSGDIVNLGSIAGR-COOCOO YMR134W, yeast protein involved in iron metabolism igh-throughput protein identification by LC-MS/MS and automated sequence database searching Raw MS/MS spectrum Relative Abundance Protein sequence and/or DNA sequence database search Direct identification of 1000 proteins from complex mixtures Peptide sequence match Relative Abundance GDIVNLGSIAGR DIVNLGSIAGR IVNLGSIAGR VNLGSIAGR NLGSIAGR LGSIAGR GSIAGR SIAGR IAGR AGR GR R 2 N-NSGDIVNLGSIAGR-COOCOO Protein identification 4

5 Dealing with the data 1. Data acquisition Experimental information, metadata capture Integrated workflow? 2. Peak analysis 3. Knowledge annotation and interpretation Sequence database searching Quantitative analysis Database mining Assignment of function, pathway, localization etc. Output for database archiving, publication 1. Data acquisition: capturing experimental information Proteomics Experimental Data Repository (PEDRo) Proposed schema Similar to genomic needs, but experimental info a bit different 5

6 ProFound Mascot PepSea MS-Fit MOWSE Peptident Multident Sequest PepFrag MS-Tag 2. Peak Analysis Computational algorithms for searching MS/MS spectra against protein sequence databases, mrna sequences, DNA sequences Relative Abundance Protein identification need cpu horsepower (parallel computing) 2. Peak Analysis: data formats Format 1 Format 2 Format 3?? Output 1 Output 2 Output 3 Lack of flexibility Slow to evolve Lack of incorporation of competing products, methods 6

7 2. Peak Analysis: need general, flexible, in-house solutions Format 1 Format 2 Format 3 reverse engineering of data formats General tools for analysis of multiple data formats 2. Peak Analysis; reverse engineering data formats 7

8 2. Peak analysis: quality control of protein matches filtering Unfiltered 10 5 matches (lots of noise and junk) Filtered thousands of true matches Statistical analysis of database results (tools are available) 2. Peak Analysis: Quantitative analysis State 1 State 2 N = normal isotope label N combine, proteolyze and isolate labeled peptides = heavy isotopic label (e.g. 2, 13 C, 15 N) N analyze peptides by mass spectrometry External chemical labeling Metabolic labeling (SILAC) Enzymatic incorporation (O 16 /O 18 ) intensity N Δm relative protein abundance = [intensity of N-labeled peptide] [intensity of -labeled peptide] mass-to-charge () Flexibility is key need tools to handle different quantitative methods 8

9 2. Peak Analysis: Quantitative analysis T O F M S : 2 0 M C A sca n s fro m m m _ sa m p le.w iff a= e-004, t0= e Relative intensity = relative protein abundance Sample Max counts Sample , amu Evolving methodologies: itraq Sample: Digest to peptides Digest to peptides Digest to peptides itraq label: Digest to peptides Multidimensional separation MS/MS spectrum Intensity Diagnostic ions used for quantitative analysis Peptide fragments used for sequence identification 4-way multiplexing: simultaneous comparison of multiple states, replicates 9

10 old Need for changeable tools new TOF MS: 20 MCA scans from mm_sample.wiff a= e-004, t0= e Sample Relative intensity = relative protein abundance Sample Max counts , amu Intensity Automated analysis tools? 3. Knowledge annotation: making sense of lists of data 10

11 3. Knowledge annotation: mining proteomic/genomic databases 3. Knowledge annotation: needs Annotation: accession numbers and protein names Functional assignments (functional degeneracy?) Pathway assignments Subcellular localization Disease implications Comparison of different proteomic datasets (i.e. expression profiles compared to modification state profiles, other protein properties) Automated and streamlined?? Publication and deposit in databases Visualization of complex phenomena, interpretation of biological relevance Modeling, integration with genomics data computational and systems biology 11

Proteomics and some of its Mass Spectrometric Applications

Proteomics and some of its Mass Spectrometric Applications Proteomics and some of its Mass Spectrometric Applications What? Large scale screening of proteins, their expression, modifications and interactions by using high-throughput approaches 2 1 Why? The number

More information

Proteomics. Proteomics is the study of all proteins within organism. Challenges

Proteomics. Proteomics is the study of all proteins within organism. Challenges Proteomics Proteomics is the study of all proteins within organism. Challenges 1. The proteome is larger than the genome due to alternative splicing and protein modification. As we have said before we

More information

Computing with large data sets

Computing with large data sets Computing with large data sets Richard Bonneau, spring 2009 Lecture 14 (week 8): genomics 1 Central dogma Gene expression DNA RNA Protein v22.0480: computing with data, Richard Bonneau Lecture 14 places

More information

MRMPilot Software: Accelerating MRM Assay Development for Targeted Quantitative Proteomics

MRMPilot Software: Accelerating MRM Assay Development for Targeted Quantitative Proteomics Product Bulletin MRMPilot Software: Accelerating MRM Assay Development for Targeted Quantitative Proteomics With Unique QTRAP System Technology Overview Targeted peptide quantitation is a rapidly growing

More information

Strategies for Quantitative Proteomics. Atelier "Protéomique Quantitative" La Grande Motte, France - June 26, 2007

Strategies for Quantitative Proteomics. Atelier Protéomique Quantitative La Grande Motte, France - June 26, 2007 Strategies for Quantitative Proteomics Atelier "Protéomique Quantitative", France - June 26, 2007 Bruno Domon, Ph.D. Institut of Molecular Systems Biology ETH Zurich Zürich, Switzerland OUTLINE Introduction

More information

SGN-6106 Computational Systems Biology I

SGN-6106 Computational Systems Biology I SGN-6106 Computational Systems Biology I A View of Modern Measurement Systems in Cell Biology Kaisa-Leena Taattola 21.2.2007 1 The cell a complex system (Source: Lehninger Principles of Biochemistry 4th

More information

Basic protein and peptide science for proteomics. Henrik Johansson

Basic protein and peptide science for proteomics. Henrik Johansson Basic protein and peptide science for proteomics Henrik Johansson Proteins are the main actors in the cell Membranes Transport and storage Chemical factories DNA Building proteins Structure Proteins mediate

More information

Advances in analytical biochemistry and systems biology: Proteomics

Advances in analytical biochemistry and systems biology: Proteomics Advances in analytical biochemistry and systems biology: Proteomics Brett Boghigian Department of Chemical & Biological Engineering Tufts University July 29, 2005 Proteomics The basics History Current

More information

Key questions of proteomics. Bioinformatics 2. Proteomics. Foundation of proteomics. What proteins are there? Protein digestion

Key questions of proteomics. Bioinformatics 2. Proteomics. Foundation of proteomics. What proteins are there? Protein digestion s s Key questions of proteomics What proteins are there? Bioinformatics 2 Lecture X roteomics How much is there of each of the proteins? - Absolute quantitation - Stoichiometry What (modification/splice)

More information

Quantitative mass spec based proteomics

Quantitative mass spec based proteomics Quantitative mass spec based proteomics Tuula Nyman Institute of Biotechnology tuula.nyman@helsinki.fi THE PROTEOME The complete protein complement expressed by a genome or by a cell or a tissue type (M.

More information

Outline and learning objectives. From Proteomics to Systems Biology. Integration of omics - information

Outline and learning objectives. From Proteomics to Systems Biology. Integration of omics - information From to Systems Biology Outline and learning objectives Omics science provides global analysis tools to study entire systems How to obtain omics - What can we learn Limitations Integration of omics - In-class

More information

Agilent Software Tools for Mass Spectrometry Based Multi-omics Studies

Agilent Software Tools for Mass Spectrometry Based Multi-omics Studies Agilent Software Tools for Mass Spectrometry Based Multi-omics Studies Technical Overview Introduction The central dogma for biological information flow is expressed as a series of chemical conversions

More information

From Proteomics to Systems Biology. Integration of omics - information

From Proteomics to Systems Biology. Integration of omics - information From Proteomics to Systems Biology Integration of omics - information Outline and learning objectives Omics science provides global analysis tools to study entire systems How to obtain omics - data What

More information

Spectrum Mill MS Proteomics Workbench. Comprehensive tools for MS proteomics

Spectrum Mill MS Proteomics Workbench. Comprehensive tools for MS proteomics Spectrum Mill MS Proteomics Workbench Comprehensive tools for MS proteomics Meeting the challenge of proteomics data analysis Mass spectrometry is a core technology for proteomics research, but large-scale

More information

Proteomics and Cancer

Proteomics and Cancer Proteomics and Cancer Japan Society for the Promotion of Science (JSPS) Science Dialogue Program at Niitsu Senior High School Niitsu, Niigata September 4th 2006 Vladimir Valera, M.D, PhD JSPS Postdoctoral

More information

Towards unbiased biomarker discovery

Towards unbiased biomarker discovery Towards unbiased biomarker discovery High-throughput molecular profiling technologies are routinely applied for biomarker discovery to make the drug discovery process more efficient and enable personalised

More information

timstof Innovation with Integrity Powered by PASEF TIMS-QTOF MS

timstof Innovation with Integrity Powered by PASEF TIMS-QTOF MS timstof Powered by PASEF Innovation with Integrity TIMS-QTOF MS timstof The new standard for high speed, high sensitivity shotgun proteomics The timstof Pro with PASEF technology delivers revolutionary

More information

Improving Productivity with Applied Biosystems GPS Explorer

Improving Productivity with Applied Biosystems GPS Explorer Product Bulletin TOF MS Improving Productivity with Applied Biosystems GPS Explorer Software Purpose GPS Explorer Software is the application layer software for the Applied Biosystems 4700 Proteomics Discovery

More information

Proteomics And Cancer Biomarker Discovery. Dr. Zahid Khan Institute of chemical Sciences (ICS) University of Peshawar. Overview. Cancer.

Proteomics And Cancer Biomarker Discovery. Dr. Zahid Khan Institute of chemical Sciences (ICS) University of Peshawar. Overview. Cancer. Proteomics And Cancer Biomarker Discovery Dr. Zahid Khan Institute of chemical Sciences (ICS) University of Peshawar Overview Proteomics Cancer Aims Tools Data Base search Challenges Summary 1 Overview

More information

What are proteomics? And what can they tell us about seed maturation and germination?

What are proteomics? And what can they tell us about seed maturation and germination? Danseed Symposium Kobæk Strand, Skelskør 14 March, 2017 What are proteomics? And what can they tell us about seed maturation and germination? Ian Max Møller Department of Molecular Biology and Genetics

More information

11/22/13. Proteomics, functional genomics, and systems biology. Biosciences 741: Genomics Fall, 2013 Week 11

11/22/13. Proteomics, functional genomics, and systems biology. Biosciences 741: Genomics Fall, 2013 Week 11 Proteomics, functional genomics, and systems biology Biosciences 741: Genomics Fall, 2013 Week 11 1 Figure 6.1 The future of genomics Functional Genomics The field of functional genomics represents the

More information

LTQ Orbitrap XL Hybrid FT Mass Spectrometer Unrivaled Performance and Flexibility

LTQ Orbitrap XL Hybrid FT Mass Spectrometer Unrivaled Performance and Flexibility m a s s s p e c t r o m e t r y LTQ Orbitrap XL Hybrid FT Mass Spectrometer Unrivaled Performance and Flexibility Part of Thermo Fisher Scientific LTQ Orbitrap XL OFFERING OUTSTANDING MASS ACCURACY, RESOLVING

More information

New Approaches to Quantitative Proteomics Analysis

New Approaches to Quantitative Proteomics Analysis New Approaches to Quantitative Proteomics Analysis Chris Hodgkins, Market Development Manager, SCIEX ANZ 2 nd November, 2017 Who is SCIEX? Founded by Dr. Barry French & others: University of Toronto Introduced

More information

Innovations for Protein Research. Protein Research. Powerful workflows built on solid science

Innovations for Protein Research. Protein Research. Powerful workflows built on solid science Innovations for Protein Research Protein Research Powerful workflows built on solid science Your partner in discovering innovative solutions for quantitative protein and biomarker research Applied Biosystems/MDS

More information

ProteinPilot Report for ProteinPilot Software

ProteinPilot Report for ProteinPilot Software ProteinPilot Report for ProteinPilot Software Detailed Analysis of Protein Identification / Quantitation Results Automatically Sean L Seymour, Christie Hunter SCIEX, USA Powerful mass spectrometers like

More information

Ensure your Success with Agilent s Biopharma Workflows

Ensure your Success with Agilent s Biopharma Workflows Ensure your Success with Agilent s Biopharma Workflows Steve Madden Software Product Manager Agilent Technologies, Inc. June 5, 2018 Agenda Agilent BioPharma Workflow Platform for LC/MS Intact Proteins

More information

Systems Biology and Systems Medicine

Systems Biology and Systems Medicine CHAPTER 5 Systems Biology and Systems Medicine INTRODUCTION A new approach to biology, termed systems biology, has emerged over the past 15 years or so an approach that looks - - have transformed systems

More information

Confident Protein ID using Spectrum Mill Software

Confident Protein ID using Spectrum Mill Software Welcome to our E-Seminar: Confident Protein ID using Spectrum Mill Software Slide 1 Spectrum Mill Informatics Software Start with batches of raw MS data! Sp ec t ru m Mi ll Biologist-friendly answers!

More information

Medicinal Chemistry of Modern Antibiotics

Medicinal Chemistry of Modern Antibiotics Chemistry 259 Medicinal Chemistry of Modern Antibiotics Spring 2012 Lecture 5: Modern Target Discovery & MOA Thomas Hermann Department of Chemistry & Biochemistry University of California, San Diego Drug

More information

Medicinal Chemistry of Modern Antibiotics

Medicinal Chemistry of Modern Antibiotics Chemistry 259 Medicinal Chemistry of Modern Antibiotics Spring 2008 Lecture 5: Modern Target Discovery & MOA Thomas Hermann Department of Chemistry & Biochemistry University of California, San Diego Drug

More information

A New Strategy for Quantitative Proteomics Using Isotope-Coded Protein Labels

A New Strategy for Quantitative Proteomics Using Isotope-Coded Protein Labels ICPL TM -Isotope Coded Label A New Strategy for Quantitative Proteomics Using Isotope-Coded Labels Alexander Schmidt Department for Max-Planck-Institute of Biochemistry Spotfire User Conference 2004, Cologne

More information

Proteomics. Manickam Sugumaran. Department of Biology University of Massachusetts Boston, MA 02125

Proteomics. Manickam Sugumaran. Department of Biology University of Massachusetts Boston, MA 02125 Proteomics Manickam Sugumaran Department of Biology University of Massachusetts Boston, MA 02125 Genomic studies produced more than 75,000 potential gene sequence targets. (The number may be even higher

More information

The Open2Dprot Proteomics Project for n-dimensional Protein Expression Data Analysis. The Open2Dprot Project. Introduction

The Open2Dprot Proteomics Project for n-dimensional Protein Expression Data Analysis. The Open2Dprot Project. Introduction The Open2Dprot Proteomics Project for n-dimensional Protein Expression Data Analysis http://open2dprot.sourceforge.net/ Revised 2-05-2006 * (cf. 2D-LC) Introduction There is a need for integrated proteomics

More information

Advances in Experimental Medicine and Biology

Advances in Experimental Medicine and Biology Advances in Experimental Medicine and Biology Volume 990 Editorial Board: IRUN R. COHEN, The Weizmann Institute of Science ABEL LAJTHA, N.S. Kline Institute for Psychiatric Research JOHN D. LAMBRIS, University

More information

Protein Valida-on (Sta-s-cal Inference) and Protein Quan-fica-on. Center for Mass Spectrometry and Proteomics Phone (612) (612)

Protein Valida-on (Sta-s-cal Inference) and Protein Quan-fica-on. Center for Mass Spectrometry and Proteomics Phone (612) (612) Protein Valida-on (Sta-s-cal Inference) and Protein Quan-fica-on Terminology Pep-de Spectrum Match Target / Decoy False discovery rate Shared pep-de Parsimony One hit wonders SPECTRUM Rela-ve Abundance

More information

timstof Pro powered by PASEF and the Evosep One for high speed and sensitive shotgun proteomics

timstof Pro powered by PASEF and the Evosep One for high speed and sensitive shotgun proteomics timstof Pro powered by PASEF and the Evosep One for high speed and sensitive shotgun proteomics The Parallel Accumulation Serial Fragmentation (PASEF) method for trapped ion mobility spectrometry (TIMS)

More information

MBios 478: Mass Spectrometry Applications [Dr. Wyrick] Slide #1. Lecture 25: Mass Spectrometry Applications

MBios 478: Mass Spectrometry Applications [Dr. Wyrick] Slide #1. Lecture 25: Mass Spectrometry Applications MBios 478: Mass Spectrometry Applications [Dr. Wyrick] Slide #1 Lecture 25: Mass Spectrometry Applications Measuring Protein Abundance o ICAT o DIGE Identifying Post-Translational Modifications Protein-protein

More information

Application Note TOF/MS

Application Note TOF/MS Application Note TOF/MS New Level of Confidence for Protein Identification: Results Dependent Analysis and Peptide Mass Fingerprinting Using the 4700 Proteomics Discovery System Purpose The Applied Biosystems

More information

Tooling up for Functional Genomics

Tooling up for Functional Genomics Tooling up for Functional Genomics Michael Abberton, Iain Donnison, Phil Morris, Helen Ougham, Mark Robbins, Howard Thomas From model to crop species 6 Genomes and genome mapping 7 The transcriptome 7

More information

ProteinPilot Software Overview

ProteinPilot Software Overview ProteinPilot Software Overview High Quality, In-Depth Protein Identification and Protein Expression Analysis Sean L. Seymour and Christie L. Hunter SCIEX, USA As mass spectrometers for quantitative proteomics

More information

QSTAR XL Hybrid LC/MS/MS System. Extended Performance Plus Exceptional Flexibility. QSTAR XL. Hybrid LC/MS/MS System

QSTAR XL Hybrid LC/MS/MS System. Extended Performance Plus Exceptional Flexibility. QSTAR XL. Hybrid LC/MS/MS System QSTAR XL Hybrid LC/MS/MS System Extended Performance Plus Exceptional Flexibility. QSTAR XL Hybrid LC/MS/MS System Extended performance and flexibility for your most challenging analyses. Applied Biosystems/MDS

More information

rapiflex Innovation with Integrity Designed for Molecules that Matter. MALDI TOF/TOF

rapiflex Innovation with Integrity Designed for Molecules that Matter. MALDI TOF/TOF rapiflex Designed for Molecules that Matter. Innovation with Integrity MALDI TOF/TOF rapiflex TM The first MALDI-TOF/TOF that adapts to your needs. The rapiflex is the most advanced MALDI TOF/TOF system

More information

A Software Suite for the Generation and Comparison of Peptide Arrays from Sets of Data Collected by Liquid Chromatography-Mass Spectrometry* S

A Software Suite for the Generation and Comparison of Peptide Arrays from Sets of Data Collected by Liquid Chromatography-Mass Spectrometry* S Research A Software Suite for the Generation and Comparison of Peptide Arrays from Sets of Data Collected by Liquid Chromatography-Mass Spectrometry* S Xiao-jun Li, Eugene C. Yi, Christopher J. Kemp, Hui

More information

Expand Your Research with Metabolomics and Proteomics. Christine Miller Omics Market Manager ASMS 2017

Expand Your Research with Metabolomics and Proteomics. Christine Miller Omics Market Manager ASMS 2017 Expand Your Research with Metabolomics and Proteomics Christine Miller Omics Market Manager ASMS 2017 New Additions to Agilent Omics Workflows Acquisition Ion Mobility Q-TOF IM All Ions MS/MS Find Features

More information

ProteinPilot Software for Protein Identification and Expression Analysis

ProteinPilot Software for Protein Identification and Expression Analysis ProteinPilot Software for Protein Identification and Expression Analysis Providing expert results for non-experts and experts alike ProteinPilot Software Overview New ProteinPilot Software transforms protein

More information

Combination of Isobaric Tagging Reagents and Cysteinyl Peptide Enrichment for In-Depth Quantification

Combination of Isobaric Tagging Reagents and Cysteinyl Peptide Enrichment for In-Depth Quantification Combination of Isobaric Tagging Reagents and Cysteinyl Peptide Enrichment for In-Depth Quantification Protein Expression Analysis using the TripleTOF 5600 System and itraq Reagents Vojtech Tambor 1, Christie

More information

Application Note # ET-20 BioPharma Compass: A fully Automated Solution for Characterization and QC of Intact and Digested Proteins

Application Note # ET-20 BioPharma Compass: A fully Automated Solution for Characterization and QC of Intact and Digested Proteins Application Note # ET-20 BioPharma Compass: A fully Automated Solution for Characterization and QC of Intact and Digested Proteins BioPharma Compass TM is a fully automated solution for the rapid characterization

More information

ProMass HR Applications!

ProMass HR Applications! ProMass HR Applications! ProMass HR Features Ø ProMass HR includes features for high resolution data processing. Ø ProMass HR includes the standard ProMass deconvolution algorithm as well as the full Positive

More information

Protein Reports CPTAC Common Data Analysis Pipeline (CDAP)

Protein Reports CPTAC Common Data Analysis Pipeline (CDAP) Protein Reports CPTAC Common Data Analysis Pipeline (CDAP) v. 4/13/2015 Summary The purpose of this document is to describe the protein reports generated as part of the CPTAC Common Data Analysis Pipeline

More information

Overview. Tools for Protein Sample Preparation, 2-D Electrophoresis, and Imaging and Analysis

Overview. Tools for Protein Sample Preparation, 2-D Electrophoresis, and Imaging and Analysis Expression Proteomics // Tools for Protein Separation and Analysis www.expressionproteomics.com 1 2 3 4 Overview Tools for Protein Sample Preparation, 2-D Electrophoresis, and Imaging and Analysis overview

More information

How to view Results with Scaffold. Proteomics Shared Resource

How to view Results with Scaffold. Proteomics Shared Resource How to view Results with Scaffold Proteomics Shared Resource Starting out Download Scaffold from http://www.proteomes oftware.com/proteom e_software_prod_sca ffold_download.html Follow installation instructions

More information

Quantitative Analysis on the Public Protein Prospector Web Site. Introduction

Quantitative Analysis on the Public Protein Prospector Web Site. Introduction Quantitative Analysis on the Public Protein Prospector Web Site Peter R. Baker 1, Nicholas J. Agard 2, Alma L. Burlingame 1 and Robert J. Chalkley 1 1 Mass Spectrometry Facility, Dept. of Pharmaceutical

More information

Proteomics software at MSI. Pratik Jagtap Minnesota Supercomputing institute

Proteomics software at MSI. Pratik Jagtap Minnesota Supercomputing institute Proteomics software at MSI. Pratik Jagtap Minnesota Supercomputing institute http://www.mass.msi.umn.edu/ Proteomics software at MSI. proteomics : emerging technology proteomics workflow search algorithms

More information

27041, Week 02. Review of Week 01

27041, Week 02. Review of Week 01 27041, Week 02 Review of Week 01 The human genome sequencing project (HGP) 2 CBS, Department of Systems Biology Systems Biology and emergent properties 3 CBS, Department of Systems Biology Different model

More information

A Highly Accurate Mass Profiling Approach to Protein Biomarker Discovery Using HPLC-Chip/ MS-Enabled ESI-TOF MS

A Highly Accurate Mass Profiling Approach to Protein Biomarker Discovery Using HPLC-Chip/ MS-Enabled ESI-TOF MS Application Note PROTEOMICS METABOLOMICS GENOMICS INFORMATICS GLYILEVALCYSGLUGLNALASERLEUASPARG CYSVALLYSPROLYSPHETYRTHRLEUHISLYS A Highly Accurate Mass Profiling Approach to Protein Biomarker Discovery

More information

基于质谱的蛋白质药物定性定量分析技术及应用

基于质谱的蛋白质药物定性定量分析技术及应用 基于质谱的蛋白质药物定性定量分析技术及应用 蛋白质组学质谱数据分析 单抗全蛋白测序及鉴定 Bioinformatics Solutions Inc. Waterloo, ON, Canada 上海 中国 2017 1 3 PEAKS Studio GUI Introduction Overview of PEAKS Studio GUI Project View Tasks, running info,

More information

Informatics on MS-Based Proteomics

Informatics on MS-Based Proteomics Informatics on MS-Based Proteomics Yet-Ran Chen 陳逸然 Associate Research Fellow / Associate Professor Agricultural Biotech. Research Center / Institute of Biotechnology & Genomics and Systems Biology Academia

More information

Strategies in proteomics

Strategies in proteomics Strategies in proteomics Systems biology - understand cellpathways, network, and complex interacting (includes Genomics, Proteomics, Metabolomics..) Biological processes - characterize protein complexes,

More information

Spectronaut Pulsar X. Maximize proteome coverage and data completeness by utilizing the power of Hybrid Libraries

Spectronaut Pulsar X. Maximize proteome coverage and data completeness by utilizing the power of Hybrid Libraries Spectronaut Pulsar X Maximize proteome coverage and data completeness by utilizing the power of Hybrid Libraries More versatility in proteomics research Spectronaut has delivered highest performance in

More information

Center for Mass Spectrometry and Proteomics Phone (612) (612)

Center for Mass Spectrometry and Proteomics Phone (612) (612) Outline Database search types Peptide Mass Fingerprint (PMF) Precursor mass-based Sequence tag Results comparison across programs Manual inspection of results Terminology Mass tolerance MS/MS search FASTA

More information

Appendix. Table of contents

Appendix. Table of contents Appendix Table of contents 1. Appendix figures 2. Legends of Appendix figures 3. References Appendix Figure S1 -Tub STIL (41) DVFFYQADDEHYIPR (55) (64) AVLLDLEPR (72) 1 451aa (1071) YLNENQLSQLSVTR (1084)

More information

AGILENT S BIOINFORMATICS ANALYSIS SOFTWARE

AGILENT 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 information

Liver Mitochondria Proteomics Employing High-Resolution MS Technology

Liver Mitochondria Proteomics Employing High-Resolution MS Technology Liver Mitochondria Proteomics Employing High-Resolution MS Technology Jenny Ho, 1 Loïc Dayon, 2 John Corthésy, 2 Umberto De Marchi, 2 Antonio Núñez, 2 Andreas Wiederkehr, 2 Rosa Viner, 3 Michael Blank,

More information

Highly Confident Peptide Mapping of Protein Digests Using Agilent LC/Q TOFs

Highly Confident Peptide Mapping of Protein Digests Using Agilent LC/Q TOFs Technical Overview Highly Confident Peptide Mapping of Protein Digests Using Agilent LC/Q TOFs Authors Stephen Madden, Crystal Cody, and Jungkap Park Agilent Technologies, Inc. Santa Clara, California,

More information

MetaboScape 2.0. Innovation with Integrity. Quickly Discover Metabolite Biomarkers and Use Pathway Mapping to Set them in a Biological Context

MetaboScape 2.0. Innovation with Integrity. Quickly Discover Metabolite Biomarkers and Use Pathway Mapping to Set them in a Biological Context M MetaboScape 2.0 Quickly Discover Metabolite Biomarkers and Use Pathway Mapping to Set them in a Biological Context Innovation with Integrity Metabolomics Providing a New Layer of Insight to Metabolomics

More information

Detecting Challenging Post Translational Modifications (PTMs) using CESI-MS

Detecting Challenging Post Translational Modifications (PTMs) using CESI-MS Detecting Challenging Post Translational Modifications (PTMs) using CESI-MS Sensitive workflow for the detection of PTMs in biological samples from small sample volumes Klaus Faserl, 1 Bettina Sarg, 1

More information

Automation of MALDI-TOF Analysis for Proteomics

Automation of MALDI-TOF Analysis for Proteomics Application Note #MT-50 BIFLEX III / REFLEX III Automation of MALDI-TOF Analysis for Proteomics D. Suckau, C. Köster, P.Hufnagel, K.-O. Kräuter and U. Rapp, Bruker Daltonik GmbH, Bremen, Germany Introduction

More information

Capabilities & Services

Capabilities & Services Capabilities & Services Accelerating Research & Development Table of Contents Introduction to DHMRI 3 Services and Capabilites: Genomics 4 Proteomics & Protein Characterization 5 Metabolomics 6 In Vitro

More information

Faster, easier, flexible proteomics solutions

Faster, easier, flexible proteomics solutions Agilent HPLC-Chip LC/MS Faster, easier, flexible proteomics solutions Our measure is your success. products applications soft ware services Phospho- Anaysis Intact Glycan & Glycoprotein Agilent s HPLC-Chip

More information

Využití cílené proteomiky pro kontrolu falšování potravin: identifikace peptidových markerů v mase pomocí LC- Q Exactive MS/MS

Využití cílené proteomiky pro kontrolu falšování potravin: identifikace peptidových markerů v mase pomocí LC- Q Exactive MS/MS Využití cílené proteomiky pro kontrolu falšování potravin: identifikace peptidových markerů v mase pomocí LC- Q Exactive MS/MS Michal Godula Ph.D. Thermo Fisher Scientific The world leader in serving science

More information

Exam MOL3007 Functional Genomics

Exam MOL3007 Functional Genomics Faculty of Medicine Department of Cancer Research and Molecular Medicine Exam MOL3007 Functional Genomics Thursday December 20 th 9.00-13.00 ECTS credits: 7.5 Number of pages (included front-page): 5 Supporting

More information

Supplementary Figure 1. Utilization of publicly available antibodies in different applications.

Supplementary Figure 1. Utilization of publicly available antibodies in different applications. Supplementary Figure 1 Utilization of publicly available antibodies in different applications. The fraction of publicly available antibodies toward human protein targets is shown with data for the following

More information

Spectral Counting Approaches and PEAKS

Spectral Counting Approaches and PEAKS Spectral Counting Approaches and PEAKS INBRE Proteomics Workshop, April 5, 2017 Boris Zybailov Department of Biochemistry and Molecular Biology University of Arkansas for Medical Sciences 1. Introduction

More information

Biology 644: Bioinformatics

Biology 644: Bioinformatics Processes Activation Repression Initiation Elongation.... Processes Splicing Editing Degradation Translation.... Transcription Translation DNA Regulators DNA-Binding Transcription Factors Chromatin Remodelers....

More information

AB SCIEX TripleTOF 5600 SYSTEM. High-resolution quant and qual

AB SCIEX TripleTOF 5600 SYSTEM. High-resolution quant and qual AB SCIEX TripleTOF 5600 SYSTEM High-resolution quant and qual AB SCIEX TripleTOF 5600 SYSTEM AB SCIEX is a global leader in the development of life science analytical technologies that help answer complex

More information

Protein Grouping, FDR Analysis and Databases.

Protein Grouping, FDR Analysis and Databases. Protein Grouping, FDR Analysis and Databases. March 15th 2012 Pratik Jagtap The Minnesota http://www.mass.msi.umn.edu/ Protein Grouping, FDR Analysis and Databases Overview. Protein Grouping : Concept

More information

Thermo Scientific Q Exactive HF Orbitrap LC-MS/MS System. Higher-Quality Data, Faster Than Ever. Speed Productivity Confidence

Thermo Scientific Q Exactive HF Orbitrap LC-MS/MS System. Higher-Quality Data, Faster Than Ever. Speed Productivity Confidence Thermo Scientific Q Exactive HF Orbitrap LC-MS/MS System Higher-Quality Data, Faster Than Ever Speed Productivity Confidence Transforming discovery quantitation The Thermo Scientific Q Exactive HF hybrid

More information

Filter-based Protein Digestion (FPD): A Detergent-free and Scaffold-based Strategy for TMT workflows

Filter-based Protein Digestion (FPD): A Detergent-free and Scaffold-based Strategy for TMT workflows Supporting Information Filter-based Protein Digestion (FPD): A Detergent-free and Scaffold-based Strategy for TMT workflows Ekaterina Stepanova 1, Steven P. Gygi 1, *, Joao A. Paulo 1, * 1 Department of

More information

The Agilent Metabolomics Dynamic MRM Database and Method

The Agilent Metabolomics Dynamic MRM Database and Method The Agilent Metabolomics Dynamic MRM Database and Method White Paper Author Mark Sartain Agilent Technologies, Inc. Santa Clara, California, USA Introduction A major challenge in metabolomics is achieving

More information

Supplementary Figure 1. Processing and quality control for recombinant proteins.

Supplementary Figure 1. Processing and quality control for recombinant proteins. Supplementary Figure 1 Processing and quality control for recombinant proteins. (a) Schematic representation of processing of a recombinant protein library. Recombinant proteins were generated individually.

More information

Proteomics and Mass Spectrometry

Proteomics and Mass Spectrometry Molecular Cell Biology Lecture. Oct. 18, 2018 Proteomics and Mass Spectrometry Ron Bose, MD PhD Biochemistry and Molecular Cell Biology Programs Lab: Couch Research Building (4515 McKinley), 3 rd floor

More information

Introduction to Proteomics

Introduction to Proteomics Introduction to Proteomics Tasso Miliotis, PhD AstraZeneca R&D Gothenburg Translational Sciences tasso.miliotis@astrazeneca.com 1 Site Management Mölndal May 2008 Outline Drug Discovery AZ R&D Sample Preparation

More information

N- The rank of the specified protein relative to all other proteins in the list of detected proteins.

N- The rank of the specified protein relative to all other proteins in the list of detected proteins. PROTEIN SUMMARY file N- The rank of the specified protein relative to all other proteins in the list of detected proteins. Unused (ProtScore) - A measure of the protein confidence for a detected protein,

More information

timstof Pro with PASEF and Evosep One: Maximizing throughput, robustness and analytical depth for shotgun proteomics

timstof Pro with PASEF and Evosep One: Maximizing throughput, robustness and analytical depth for shotgun proteomics timstof Pro with PASEF and Evosep One: Maximizing throughput, robustness and analytical depth for shotgun proteomics The timstof Pro powered by PASEF enables sequencing speed of > 2 Hz, high sensitivity

More information

Public sharing of complex MS- based qualita:ve and quan:ta:ve proteomic data analysis workflows: adding value to big data repositories

Public sharing of complex MS- based qualita:ve and quan:ta:ve proteomic data analysis workflows: adding value to big data repositories Public sharing of complex MS- based qualita:ve and quan:ta:ve proteomic data analysis workflows: adding value to big data repositories ASMS annual conference June 16, 2014 Tim Griffin tgriffin@umn.edu

More information

INTEGRATED DATA MODELING IN HIGH-THROUGHPUT PROTEOMICES

INTEGRATED DATA MODELING IN HIGH-THROUGHPUT PROTEOMICES INTEGRATED DATA MODELING IN HIGH-THROUGHPUT PROTEOMICES By SHUANGSHUANG JIN A dissertation submitted in partial fulfillment of The requirements for the degree of DOCTOR OF PHILOSOPHY IN COMPUTER SCIENCE

More information

NPTEL

NPTEL NPTEL Syllabus Proteomics: Principles and Techniques - Video course COURSE OUTLINE An introduction to proteomics: Basics of protein structure and function, An overview of systems biology, Evolution from

More information

Enabling Systems Biology Driven Proteome Wide Quantitation of Mycobacterium Tuberculosis

Enabling Systems Biology Driven Proteome Wide Quantitation of Mycobacterium Tuberculosis Enabling Systems Biology Driven Proteome Wide Quantitation of Mycobacterium Tuberculosis SWATH Acquisition on the TripleTOF 5600+ System Samuel L. Bader, Robert L. Moritz Institute of Systems Biology,

More information

Xevo G2-S QTof and TransOmics: A Multi-Omics System for the Differential LC/MS Analysis of Proteins, Metabolites, and Lipids

Xevo G2-S QTof and TransOmics: A Multi-Omics System for the Differential LC/MS Analysis of Proteins, Metabolites, and Lipids Xevo G2-S QTof and TransOmics: A Multi-Omics System for the Differential LC/MS Analysis of Proteins, Metabolites, and Lipids Ian Edwards, Jayne Kirk, and Joanne Williams Waters Corporation, Manchester,

More information

ENHANCED PROTEIN AND PEPTIDE CHARACTERIZATION

ENHANCED PROTEIN AND PEPTIDE CHARACTERIZATION Agilent MassHunter BioConfirm Software ENHANCED PROTEIN AND PEPTIDE CHARACTERIZATION Spectrum Algorithm Peak Modeling Deconvolution Mass 16951.778 Sequence Name Myoglobin (horse) Target mass 16951.673

More information

LECTURE-3. Protein Chemistry to proteomics HANDOUT. Proteins are the most dynamic and versatile macromolecules in a living cell, which

LECTURE-3. Protein Chemistry to proteomics HANDOUT. Proteins are the most dynamic and versatile macromolecules in a living cell, which LECTURE-3 Protein Chemistry to proteomics HANDOUT PREAMBLE Proteins are the most dynamic and versatile macromolecules in a living cell, which regulates essential activities of the cell. The classical protein

More information

LC/MS/MS Solutions for Biomarker Discovery QSTAR. Elite Hybrid LC/MS/MS System. More performance, more reliability, more answers

LC/MS/MS Solutions for Biomarker Discovery QSTAR. Elite Hybrid LC/MS/MS System. More performance, more reliability, more answers LC/MS/MS Solutions for Biomarker Discovery QSTAR Elite Hybrid LC/MS/MS System More performance, more reliability, more answers More is better and the QSTAR Elite LC/MS/MS system has more to offer. More

More information

Bioinformatic Tools. So you acquired data.. But you wanted knowledge. So Now What?

Bioinformatic Tools. So you acquired data.. But you wanted knowledge. So Now What? Bioinformatic Tools So you acquired data.. But you wanted knowledge So Now What? We have a series of questions What the Heck is That Ion? How come my MW does not match? How do I make a DB to search against?

More information

RockerBox. Filtering massive Mascot search results at the.dat level

RockerBox. Filtering massive Mascot search results at the.dat level RockerBox Filtering massive Mascot search results at the.dat level Challenges Big experiments High amount of data Large raw and.dat files (> 2GB) How to handle our results?? The 2.2 peptide summary could

More information

Mass Spectrometry-based Methods of Proteome Analysis

Mass Spectrometry-based Methods of Proteome Analysis 1 Mass Spectrometry-based Methods of Proteome Analysis Boris L. Zybailov and Michael P. Washburn Stowers Institute for Medical Research, Kansas City, MO, USA 1 Principles and Instrumentation 3 1.1 Proteome

More information

perspective Proteomics: a pragmatic perspective Parag Mallick 1,2 & Bernhard Kuster 3, Nature America, Inc. All rights reserved.

perspective Proteomics: a pragmatic perspective Parag Mallick 1,2 & Bernhard Kuster 3, Nature America, Inc. All rights reserved. Proteomics: a pragmatic perspective Parag Mallick 1,2 & Bernhard Kuster 3,4 The evolution of mass spectrometry based proteomic technologies has advanced our understanding of the complex and dynamic nature

More information

How to view Results with. Proteomics Shared Resource

How to view Results with. Proteomics Shared Resource How to view Results with Scaffold 3.0 Proteomics Shared Resource An overview This document is intended to walk you through Scaffold version 3.0. This is an introductory guide that goes over the basics

More information

Proteomics Technology Note

Proteomics Technology Note Targeted Proteomics for the Identification of Nucleic Acid Binding Proteins in E. coli: Finding more low abundant proteins using the QSTAR LC/MS/MS System, Multi- Dimensional Liquid Chromatography, Pro

More information

Accelerating Throughput for Targeted Quantitation of Proteins/Peptides in Biological Samples

Accelerating Throughput for Targeted Quantitation of Proteins/Peptides in Biological Samples Technical Note Accelerating Throughput for Targeted Quantitation of Proteins/Peptides in Biological Samples Biomarker Verification Studies using the QTRAP 5500 Systems and the Reagents Triplex Sahana Mollah,

More information