Master course KEMM03 Principles of Mass Spectrometric Protein Characterization. Exam

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "Master course KEMM03 Principles of Mass Spectrometric Protein Characterization. Exam"

Transcription

1 Exam Master course KEMM03 Principles of Mass Spectrometric Protein Characterization kl Use a new paper for answering each question! Write your name on each paper! Aids: Mini calculator, table with amino acids (one letter codes and residue masses). Maximum number of points is 60. Pass (Godkänd) corresponds to >50% (30) and Well pass (Väl godkänt) corresponds to >75% (45). Results are announced on course webpage and at Student expedition within one week. 1. MS basics and MS-instrumentation. (10 p) a. Explain why a laser is used in MALDI-MS, and explain why it is not needed in so called electrospray instruments. b. When a MALDI-TOF MS-spectrum is aquired the m/z-values are determined for the ions. Which is the physical parameter that is actually measured, and how is it converted into m/z? c. At atmospheric pressure the mean free path of a typical ion is around 52 nm. How come that the ions can travel several meters in the drift tube? d. What is the reflector used for in MALDI-TOF/TOF? e. What is the time-gated ion selector used for in MALDI-TOF/TOF? f. In a typical mass spectrum, each peak appears as a couple of peaks in magnification, why? And what is the monoisotopic and average mass of the peak below? 3 p Reflector Spec #1[BP = , 6938] Mass (m/z) % Intensity Mass (m/z)

2 2. Terms and expressions (10 p) a. Connect the terms 1-8 related to protein mass spectrometry with the correctly corresponding terms a - h. 4 p 1. Internal calibration 2. MH + 3. O-methylisourea 4. UniProt KB 5. PMF 6. Lectin column 7. MS/MS 8. Mascot a. Single charging b. MS c. Glycopeptides d. Search engine e. Lysine-terminated peptides f. mgf-file g Da h. Database b. Below are some structural formulas which illustrate various phenomena in protein mass spectrometry that you have worked with in this course. Give a short comment to each of A, B and C and explain what it shows. Your answers should include the following words: primary and tertiary amine, digestion, polypeptide backbone. 6 p. A. B. C.

3 3. Protein and peptide separation (10 p) Because the complexity of a proteome is large there is often a need to start a proteomic investigation by reducing the sample complexity. a. Which physical property of the proteins, or peptides, are the following separation techniques based on? 1. Gel filtration 2. Reversed phase chromatography 3. Isoelectric focusing 4. SDS-PAGE b. What charge does a protein have below and above its isoelectric point? c. In MALDI mass spectrometry the mass spectrum quality of a certain sample can often be improved by treatment with so called C18 microcolumns. Why? d. Describe a typical solvent suitable for loading the tryptic digest onto the microcolumn, and a typical solvent used for eluation. 2p e. Describe two types of peptides that could be lost from the sample in spite of the general improvement that is often obtained. f. The dynamic range in protein concentration in a human plasma sample is what does that mean?

4 4. Protein identification using Mascot (10 p) a. Mascot was used to search the Swiss-Prot database with a peak list derived from an MSspectrum obtained by tryptic digestion of a protein spot obtained from 2DE-separation of a soluble extract from E. coli with the output below. How can you tell whether a protein has been reliably identified, or not? b. In the Mascot output table below, two peptides contain missed cleavage sites. Which peptides and what cleavage sites? Answer with peptide masses, and indicate where in each peptide the missed cleavage site is. Use one-letter code and amino acid number in sequence. c. In the table above, calculate the mass difference between the values in the column named Observed and column named Mr (expt). What is this mass difference due to? d. For two of the peptides the mass error in ppm is now hidden. Calculate the mass error in ppm for these two peptides (show your calculation). e. If one would have used 25 ppm as the peptide mass tolerance setting when submitting the search, which peptides in the above table would not have been matched? f. Assuming the protein identified based on the peptides above is 331 amino acids long, what is the sequence coverage?

5 g. A theoretical digest of the identified protein is shown below. What protease? Which is the C-terminal amino acid of this protein? h. Explain why the isoelectric point is below three for peptide with mass Da and above 12 for peptide with mass Da. MH + pi Sequence

6 5. Evaluation of mass spectra (10 p) a. An MS-spectrum was recorded for the WrbA protein from E. coli (A). Which of the four most abundant peaks belong to this E. coli protein? What are the other peaks? A. b. One of the peptides, with a peptide mass was selected for further analysis by MS/MS. How is such selection of only one peptide mass possible to obtain? Exain how you do it practically when you are setting up a job to acquire MS and MS/MS data at the ABI 4700 MALDI TOF/TOF instrument, and what principle and what device in the instrument that makes this possible. c. On next page the MS/MS spectrum (B) for this peptide is shown, and the output obtained when the MS/MS-data were matched into Mascot. Answer the following questions: 1. What is the mass of the y1-ion? 2. Is the peak with mass a b-ion or a y-ion? 3. Write the amino acid sequence of the b4 ion. 4. Are mostly b-ions or y-ions detected in this MS/MS spectrum? This is commonly occuring in a MALDI-TOF/TOF instrument. What does it tell about the fate of the single charge extra protonupon precursor ion fragmentation? 5. One amino acid in the peptide has been blanked out. What amino acid is this?

7 4700 MS/MS Precursor Spec #1[BP = 175.1, 287] B % Intensity Mass (m/z)

8 6. Protein quantification and modification specific proteomics (10 p) a. isotope labbeling is commonly used to make relative quantification of how much there is of a certain protein in different samples.shortly state three different aways to incorporate isotopes into a protein to allaw quantification. 3 p b. Explain what PTM means and state approximately how many PTMs are known. c. The picture below illustrates how phosphoproteins can be resolved by 2DE. What is the explanation to why phosphorylated and non-phoshorylated forms of a protein can be separated by 2DE? d. Explain how phosphopeptide peptides can be enriched if one wants to analyze phosphoprotein by mass spectrometry. e. Is the mass deviation of a phosphorylated peptide 80 Da or 16 Da? f. The picture below illustrates that the plasma membrane contains many glycoylated proteins. What does it mean that glycoproteins have N-glycosylation sites? g. Give one example of how glycopeptides can be enriched for MS-analysis..

Tutorial for Proteomics Data Submission. Katalin F. Medzihradszky Robert J. Chalkley UCSF

Tutorial 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 information

ProteinScape. Innovation with Integrity. Proteomics Data Analysis & Management. Mass Spectrometry

ProteinScape. 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 information

Workshop IIc. Manual interpretation of MS/MS spectra. Ebbing de Jong. Center for Mass Spectrometry and Proteomics Phone (612)625-2280 (612)625-2279

Workshop IIc. Manual interpretation of MS/MS spectra. Ebbing de Jong. Center for Mass Spectrometry and Proteomics Phone (612)625-2280 (612)625-2279 Workshop IIc Manual interpretation of MS/MS spectra Ebbing de Jong Why MS/MS spectra? The information contained in an MS spectrum (m/z, isotope spacing and therefore z ) is not enough to tell us the amino

More information

Laboration 1. Identifiering av proteiner med Mass Spektrometri. Klinisk Kemisk Diagnostik

Laboration 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 information

With data depth and quality

With data depth and quality With data depth and quality Analysis of a tryptic digest by peptide mass fingerprinting, MS/MS and MS/MS/MS MS was performed on the tryptic digest of horse myoglobin using DHBA on the target. The resulting

More information

Application Note # MT-90 MALDI-TDS: A Coherent MALDI Top-Down-Sequencing Approach Applied to the ABRF-Protein Research Group Study 2008

Application Note # MT-90 MALDI-TDS: A Coherent MALDI Top-Down-Sequencing Approach Applied to the ABRF-Protein Research Group Study 2008 Bruker Daltonics Application Note # MT-90 MALDI-TDS: A Coherent MALDI Top-Down-Sequencing Approach Applied to the ABRF-Protein Research Group Study 2008 In the ABRF-PRG study 2008 [*] the ability to characterize

More information

Peptide Sequencing by Mass Spectrometry. Alex Ramos 5 April 2005

Peptide Sequencing by Mass Spectrometry. Alex Ramos 5 April 2005 Peptide Sequencing by Mass Spectrometry Alex Ramos 5 April 2005 Edman degradation P he nyl iso thio c ya na te H O N C S H 2 N C C C H 3 A sp P he P he A rg C O O - L a be ling H N S C H N H O C C C H

More information

Proteomics in Practice

Proteomics 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 information

Effects 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 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 information

Mass Spectrometry for Chemists and Biochemists

Mass Spectrometry for Chemists and Biochemists Erasmus Intensive Program SYNAPS Univ. of Crete - Summer 2007 Mass Spectrometry for Chemists and Biochemists Spiros A. Pergantis Assistant Professor of Analytical Chemistry Department of Chemistry University

More information

Advantages of the LTQ Orbitrap for Protein Identification in Complex Digests

Advantages 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 information

LABORATÓRIUMI GYAKORLAT SILLABUSZ SYLLABUS OF A PRACTICAL DEMONSTRATION. financed by the program

LABORATÓRIUMI GYAKORLAT SILLABUSZ SYLLABUS OF A PRACTICAL DEMONSTRATION. financed by the program TÁMOP-4.1.1.C-13/1/KONV-2014-0001 projekt Az élettudományi-klinikai felsőoktatás gyakorlatorientált és hallgatóbarát korszerűsítése a vidéki képzőhelyek nemzetközi versenyképességének erősítésére program

More information

Session 1. Course Presentation: Mass spectrometry-based proteomics for molecular and cellular biologists

Session 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 information

Mass Spectrometry Based Proteomics

Mass 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 information

Aiping Lu. Key Laboratory of System Biology Chinese Academic Society APLV@sibs.ac.cn

Aiping Lu. Key Laboratory of System Biology Chinese Academic Society APLV@sibs.ac.cn Aiping Lu Key Laboratory of System Biology Chinese Academic Society APLV@sibs.ac.cn Proteome and Proteomics PROTEin complement expressed by genome Marc Wilkins Electrophoresis. 1995. 16(7):1090-4. proteomics

More information

MALDI-TOF/TOF MS Protocols

MALDI-TOF/TOF MS Protocols MALDI-TOF/TOF MS Protocols Objectives: 1. To be familiar with the basic operation of the MALDI-TOF-TOF mass spectrometer. 2. To use MALDI-TOF-TOF mass spectrometer for peptide mass fingerprinting, peptide

More information

Introduction to Proteomics

Introduction 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 information

Mass Spectra Alignments and their Significance

Mass 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 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 Pow erful mass spectrometers like

More information

Introduction to Proteomics 1.0

Introduction 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 information

ProSightPC 3.0 Quick Start Guide

ProSightPC 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 information

Protein Sequencing and Identification With Mass Spectrometry

Protein Sequencing and Identification With Mass Spectrometry Protein Sequencing and Identification With Mass Spectrometry Tandem Mass Spectrometry De Novo Peptide Sequencing Spectrum Graph Protein Identification via Database Search Identifying Post Translationally

More information

Protein Hit1, a novel box C/D snornp assembly factor, controls cellular concentration of protein Rsa1p by direct interaction

Protein 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 information

AB 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 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 information

Choices, choices, choices... Which sequence database? Which modifications? What mass tolerance?

Choices, 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 information

In-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 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 information

Pinpointing phosphorylation sites using Selected Reaction Monitoring and Skyline

Pinpointing phosphorylation sites using Selected Reaction Monitoring and Skyline Pinpointing phosphorylation sites using Selected Reaction Monitoring and Skyline Christina Ludwig group of Ruedi Aebersold, ETH Zürich The challenge of phosphosite assignment Peptides Phosphopeptides MS/MS

More information

Principles and Applications of Proteomics

Principles 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 information

Electrospray Ion Trap Mass Spectrometry. Introduction

Electrospray Ion Trap Mass Spectrometry. Introduction Electrospray Ion Source Electrospray Ion Trap Mass Spectrometry Introduction The key to using MS for solutions is the ability to transfer your analytes into the vacuum of the mass spectrometer as ionic

More information

Proteome Discoverer 1.3 Software: Enhanced Tools For Protein Identification

Proteome Discoverer 1.3 Software: Enhanced Tools For Protein Identification Proteome Discoverer 1.3 Software: Enhanced Tools For Protein Identification David Horn Proteomics Software Strategic Marketing Manager September 22, 2011 Hybrid Orbitrap Mass Spectrometers CID HCD ETD

More information

TECHNICAL BULLETIN. ProteoMass Peptide & Protein MALDI-MS Calibration Kit. Catalog Number MSCAL1 Store at Room Temperature

TECHNICAL BULLETIN. ProteoMass Peptide & Protein MALDI-MS Calibration Kit. Catalog Number MSCAL1 Store at Room Temperature ProteoMass Peptide & Protein MALDI-MS Calibration Kit Catalog Number MSCAL1 Store at Room Temperature TECHNICAL BULLETIN Description This kit provides a range of standard peptides and proteins for the

More information

Application Note # LCMS-66 Straightforward N-glycopeptide analysis combining fast ion trap data acquisition with new ProteinScape functionalities

Application Note # LCMS-66 Straightforward N-glycopeptide analysis combining fast ion trap data acquisition with new ProteinScape functionalities Application Note # LCMS-66 Straightforward N-glycopeptide analysis combining fast ion trap data acquisition with new ProteinScape functionalities Introduction Glycosylation is one of the most common and

More information

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 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 information

Post-translational Modification. Post-translational Modification. Learning Objective. Proteomics

Post-translational Modification. Post-translational Modification. Learning Objective. Proteomics Many proteins undergo chemical modifications at certain amino acid residues following translation. These modifications are essential for normal functioning of the protein and are carried out by one or

More information

Polyacrylamide gel formation

Polyacrylamide gel formation Part II- Protein Identification PolyAcrylamide Gel Electrophoresis (PAGE) is the best method in protein identification, MW determination, DNA sequencing, protein-protein or protein-dna interaction etc

More information

Global and Discovery Proteomics Lecture Agenda

Global 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 information

Analysis of proteins

Analysis of proteins Analysis of proteins Western blot Protein seperation (liqiuid chromatography) Mass spectrometry Assaying of protein in... Blood (e.g. viral infections, pregnancy test) Cells Tissue Urin (bladder infection)

More information

Introduction to Proteomics

Introduction 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 information

Labeling Technologies for Quantitative Protein Expression Analysis

Labeling Technologies for Quantitative Protein Expression Analysis Innovative Solutions for Quantitative Protein and Biomarker Research Labeling Technologies for Quantitative Protein Expression Analysis Understanding Disease States via Quantitative Protein Expression

More information

MS Amanda Standalone User Manual

MS Amanda Standalone User Manual MS Amanda Standalone User Manual February 2014 Viktoria Dorfer, Peter Pichler, Stephan Winkler, and Karl Mechtler 1. Installation of MS Amanda Standalone In order to install MS Amanda Standalone please

More information

Guest Lecture Protein and Peptide Mass Spectrometry CU- Boulder CHEM 5181 Mass Spectrometry & Chromatography

Guest Lecture Protein and Peptide Mass Spectrometry CU- Boulder CHEM 5181 Mass Spectrometry & Chromatography Guest Lecture Protein and Peptide Mass Spectrometry CU- Boulder CHEM 5181 Mass Spectrometry & Chromatography Prof. William ld Fall 2011 2002 Nobel Prize in Chemistry for developing electrospray ionization

More information

Q-TOF User s Booklet. Enter your username and password to login. After you login, the data acquisition program will automatically start.

Q-TOF User s Booklet. Enter your username and password to login. After you login, the data acquisition program will automatically start. Q-TOF User s Booklet Enter your username and password to login. After you login, the data acquisition program will automatically start. ~ 1 ~ This data acquisition window will come up after the program

More information

Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics

Challenges 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 information

Mascot Search Parameters

Mascot Search Parameters Mascot Search Parameters 1 Search Parameters for Peptide mass fingerprint Sequence Query MS-MS searches Generating ideal peak lists for Peptide mass fingerprints LC ms-ms runs 2 Three ways to use mass

More information

PROTEIN SEQUENCING. First Sequence

PROTEIN SEQUENCING. First Sequence PROTEIN SEQUENCING First Sequence The first protein sequencing was achieved by Frederic Sanger in 1953. He determined the amino acid sequence of bovine insulin Sanger was awarded the Nobel Prize in 1958

More information

Interpretation of MS-Based Proteomics Data

Interpretation 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 information

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometer

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometer Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometer Serving Advanced Technology Unrivaled SpiralTOF Technology The JMS-S3000 is a MALDI-TOFMS* incorporating an innovative SpiralTOF

More information

New PhosphoPep help page and tutorial for users

New PhosphoPep help page and tutorial for users New PhosphoPep help page and tutorial for users Buttons used in PhosphoPep View available KEGG pathways for this protein (http://www.genome.jp/kegg/) 1 Start cytoscape network with this protein (http://www.cytoscape.org/)

More information

Identification and Distribution of a Reserpine Metabolite in Whole-Body Rat Tissue using MS and MS/MS Mass Spectrometric Imaging

Identification and Distribution of a Reserpine Metabolite in Whole-Body Rat Tissue using MS and MS/MS Mass Spectrometric Imaging Identification and Distribution of a Reserpine Metabolite in Whole-ody Rat Tissue using MS and MS/MS Mass Spectrometric Imaging High Confidence Imaging using the A SCIEX TOF/TOF 5800 System Patrick Pribil

More information

Pep-Miner: A Novel Technology for Mass Spectrometry-Based Proteomics

Pep-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 information

Standard Mixture. TOF/TOF Calibration Mixture. Calibration Mixture 1 (Cal Mix 1, 1:10) Calibration Mixture 1 (Cal Mix 1, 1:100)

Standard Mixture. TOF/TOF Calibration Mixture. Calibration Mixture 1 (Cal Mix 1, 1:10) Calibration Mixture 1 (Cal Mix 1, 1:100) Mass Standards Kit for Calibration of AB SCIEX TOF/TOF Instruments Protocol 1 Product Description The Mass Standards Kit includes reagents needed to test instrument function, optimize instrument parameters,

More information

SimGlycan Software*: A New Predictive Carbohydrate Analysis Tool for MS/MS Data

SimGlycan 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 information

MULTIFACTORIAL MODELING OF ION ABUNDANCE IN TANDEM MASS SPECTROMETRY EXPERIMENTS ZEESHAN FAZAL THESIS

MULTIFACTORIAL MODELING OF ION ABUNDANCE IN TANDEM MASS SPECTROMETRY EXPERIMENTS ZEESHAN FAZAL THESIS MULTIFACTORIAL MODELING OF ION ABUNDANCE IN TANDEM MASS SPECTROMETRY EXPERIMENTS BY ZEESHAN FAZAL THESIS Submitted in partial fulfillment of the requirements for the degree of Master of Science in Bioinformatics

More information

Fast and Automatic Mapping of Disulfide Bonds in a Monoclonal Antibody using SYNAPT G2 HDMS and BiopharmaLynx 1.3

Fast and Automatic Mapping of Disulfide Bonds in a Monoclonal Antibody using SYNAPT G2 HDMS and BiopharmaLynx 1.3 Fast and Automatic Mapping of Disulfide Bonds in a Monoclonal Antibody using SYNAPT G2 HDMS and BiopharmaLynx 1.3 Hongwei Xie and Weibin Chen Waters Corporation, Milford, MA, U.S. A P P L I C AT ION B

More information

Protein Prospector and Ways of Calculating Expectation Values

Protein 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 information

Spectrum Quality Assessment in Mass Spectrometry Proteomics

Spectrum Quality Assessment in Mass Spectrometry Proteomics Spectrum Quality Assessment in Mass Spectrometry Proteomics 1. Background Rheanna Mainzer Supervised by Dr. Luke Prendergast La Trobe University An important research problem in mass spectrometry is in

More information

How Mascot Integra helps run a Core Lab

How Mascot Integra helps run a Core Lab How Mascot Integra helps run a Core Lab 1 Areas where a database can help a core lab Project, experiment and sample tracking Flexibility in experiment design Role based security Automation Custom results

More information

MASCOT Search Results Interpretation

MASCOT 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 information

Guide to Quantitative Proteomics using Tandem Mass Tags (TMT)

Guide to Quantitative Proteomics using Tandem Mass Tags (TMT) Guide to Quantitative Proteomics using Tandem Mass Tags (TMT) SIMULTANEOUSLY IDENTIFY AND QUANTITATE PROTEINS WITH TMT This guide begins with an introduction to the basics of protein identification using

More information

Error Tolerant Searching of Uninterpreted MS/MS Data

Error 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 information

Application 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 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 information

Evaluation 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 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 information

Identification of Serum Protein Biomarkers for Autistic Spectrum Disorder. Melissa Butkiewicz

Identification 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

Introduction to Database Searching using MASCOT

Introduction to Database Searching using MASCOT Introduction to Database Searching using MASCOT 1 Three ways to use mass spectrometry data for protein identification 1.Peptide Mass Fingerprint A set of peptide molecular masses from an enzyme digest

More information

Statistics and Algorithms for Peptide Mass Fingerprinting

Statistics and Algorithms for Peptide Mass Fingerprinting Statistics and Algorithms for Peptide Mass Fingerprinting Dipl.-Math. Hans-Michael Kaltenbach Thesis submitted to the Faculty of Technology, Bielefeld University, Germany for the degree of Dr. rer. nat.

More information

Increasing the Multiplexing of High Resolution Targeted Peptide Quantification Assays

Increasing 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 information

Product Information Sheet

Product Information Sheet Product Information Sheet Safety This peptide is for use as a research tool only it must not be used in humans. Standard laboratory practices should be followed when handling this material. The toxicological

More information

Thermo Scientific PepFinder Software A New Paradigm for Peptide Mapping

Thermo 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 information

CARE. Price List for CARE Products. Version CARE in JPY as of Jan, 2015 Prices are subject to change without prior notice. Innovation with Integrity

CARE. Price List for CARE Products. Version CARE in JPY as of Jan, 2015 Prices are subject to change without prior notice. Innovation with Integrity Price List for CARE Products Version CARE in JPY as of Jan, 2015 Innovation with Integrity Bruker Daltonics Price List 1 Bruker Matrix Selection Guide oligonucleotide mass < 6.5kDa 1kDa

More information

Proteomics Workflows & Technologies

Proteomics Workflows & Technologies Proteomics Workflows & Technologies Proteomics "The analysis of the entire PROTEin complement expressed by a genome, or by a cell or tissue type." Wasinger VC et al, Electrophoresis 16 (1995) Proteomics

More information

High-resolution MALDI-FT-ICR MS Imaging for the in-situ Analysis of Metabolites from Intact Tissues. Axel Walch. Research Unit Analytical Pathology

High-resolution MALDI-FT-ICR MS Imaging for the in-situ Analysis of Metabolites from Intact Tissues. Axel Walch. Research Unit Analytical Pathology High-resolution MALDI-FT-ICR MS Imaging for the in-situ Analysis of Metabolites from Intact Tissues Axel Walch Research Unit Analytical Pathology Neuherberg, 2016-10-12 Molecular Tissue Analysis by MALDI

More information

Relative Quantitation of Human Polymorphonuclear Leukocyte Cell Membrane GPEtn Lipids

Relative Quantitation of Human Polymorphonuclear Leukocyte Cell Membrane GPEtn Lipids For Research Use Only. Not For Use In Diagnostic Procedures. Relative Quantitation of Human Polymorphonuclear Leukocyte Cell Membrane GPEtn Lipids Using the QTRAP System with mtraq Reagents Karin A. Zemski-Berry,

More information

Agilent G2721AA/G2733AA Spectrum Mill MS Proteomics Workbench

Agilent 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 information

MRMPilot Software: Accelerating MRM Assay Development for Targeted Quantitative Proteomics

MRMPilot 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 information

A Strategy for the Efficient Identification of Modified Peptides

A Strategy for the Efficient Identification of Modified Peptides A Strategy for the Efficient Identification of Modified Peptides 1 Aim To get matches to additional modified peptides Unsuspected chemical or post-translational modifications Minor sequence variants, such

More information

Protein Purification and Analysis

Protein Purification and Analysis Protein Purification and Analysis Numbers of genes: Humans ~40,000 genes Yeast ~6000 genes Bacteria ~3000 genes Solubility of proteins important for purification: 60-80% soluble, 20-40% membrane Some proteins

More information

Teaching notes: Time of flight mass spectrometry

Teaching notes: Time of flight mass spectrometry Teaching notes: Time of flight mass spectrometry These teaching notes relate to section 3.1.1.2 Mass numbers and isotopes of our AS and A-level Chemistry specifications (7404, 7405). This resource aims

More information

Introduction to mass spectrometry (MS) based proteomics and metabolomics

Introduction 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 information

# LCMS-35 esquire series. Application of LC/APCI Ion Trap Tandem Mass Spectrometry for the Multiresidue Analysis of Pesticides in Water

# 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 information

Shop! VWRBiosciences,more than just a helping hand

Shop! VWRBiosciences,more than just a helping hand section line 2 BioSciences section line 1 VWRBiosciences,more than just a helping hand Proteomics round-up What can we offer? In today s world of discovery, technology is critical to a better understanding

More information

MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification

MultiQuant 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 information

Quan%ta%ve proteomics. Maarten Altelaar, 2014

Quan%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 information

High-Throughput 3-D Chromatography Through Ion Exchange SPE

High-Throughput 3-D Chromatography Through Ion Exchange SPE High-Throughput 3-D Chromatography Through Ion Exchange SPE Application Note 205 Luke Roenneburg and Alan Hamstra (Gilson, Inc.) Introduction 2-dimensional (2-D) separation is the separation of a sample

More information

SimGlycan Software*: A New Predictive Carbohydrate Analysis Tool for MS/MS Data

SimGlycan 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 information

Absolute quantification of low abundance proteins by shotgun proteomics

Absolute quantification of low abundance proteins by shotgun proteomics Absolute quantification of low abundance proteins by shotgun proteomics Dr. Stefanie Wienkoop www.proteomefactory.com In cooperation with: Max-Planck-Institut für Molekulare Pflanzenphysiologie Stable

More information

Methods for Protein Analysis

Methods for Protein Analysis Methods for Protein Analysis 1. Protein Separation Methods The following is a quick review of some common methods used for protein separation: SDS-PAGE (SDS-polyacrylamide gel electrophoresis) separates

More information

THE ABC S (AND XYZ S) OF PEPTIDE SEQUENCING

THE ABC S (AND XYZ S) OF PEPTIDE SEQUENCING TE ABC S (AD XYZ S) F PEPTIDE SEQUECIG anno Steen* and Matthias Mann Abstract Proteomics is an increasingly powerful and indispensable technology in molecular cell biology. It can be used to identify the

More information

Definition of the Measurand: CRP

Definition 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 information

Chapter 3. Protein Structure and Function

Chapter 3. Protein Structure and Function Chapter 3 Protein Structure and Function Broad functional classes So Proteins have structure and function... Fine! -Why do we care to know more???? Understanding functional architechture gives us POWER

More information

The Proteome. Protein Mass and Concentration

The Proteome. Protein Mass and Concentration The Proteome Proteome is the protein equivalent of the genome The proteome consist of all of the proteins expressed by a cell under specific conditions The proteome of a cell depends on the cell type,

More information

Experimental workflow

Experimental workflow Experimental workflow Pg. 3 Lysis Protein quant Protein precipitation Pg. 4 Digest Pgs. 5&6 Label Peptides Peptide quant Ratio check Search, filter & compile data Pgs. 9-12 Combine Samples LC-MS3 Pg. 8

More information

Introduction to Mass Spectrometry. W.M. Keck Biomedical Mass Spectrometry Lab

Introduction to Mass Spectrometry. W.M. Keck Biomedical Mass Spectrometry Lab Introduction to Mass Spectrometry W.M. Keck Biomedical Mass Spectrometry Lab Moore Health Sciences Library Rooms 1335 & 1337 May 18, 2010 The Keck Mass Spectrometry Lab of the Biomolecular Resource Facility

More information

Mass Spectrometry Signal Calibration for Protein Quantitation

Mass 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 information

JEOL Mass Spectrometers

JEOL Mass Spectrometers JEOL Mass Spectrometers MS: Elemental Composition Calculations and their Interpretation Introduction Accurate mass measurements are frequently used to determine the elemental composition for molecular

More information

for mass spectrometry calibration tools Thermo Scientific Pierce Controls and Standards for Mass Spectrometry

for mass spectrometry calibration tools Thermo Scientific Pierce Controls and Standards for Mass Spectrometry Thermo Scientific Pierce Controls and Standards for Mass Spectrometry calibration tools for mass spectrometry Ensure confidence in instrument performance with Thermo Scientific Pierce Calibration Solutions

More information

Mass spectrometry based proteomics

Mass 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 information

Protein Separation and Purification

Protein Separation and Purification Protein Separation and Purification Methods rely on specific properties of protein Why purify a protein? Isolate Allows: Analysis of the biological properties Understand its structure Study interactions

More information

Appendix 5 Overview of requirements in English

Appendix 5 Overview of requirements in English Appendix 5 Overview of requirements in English This document is a translation of Appendix 4 (Bilag 4) section 2. This translation is meant as a service for the bidder and in case of any differences between

More information

Quantitative proteomics background

Quantitative 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 information

La Protéomique : Etat de l art et perspectives

La 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 information