High-Performance Multidimensional Chromatography MALDI-QFTICR MS for Bottom Up Proteomics
|
|
- Stephanie Stevens
- 8 years ago
- Views:
Transcription
1 High-Performance Multidimensional Chromatography MALDI-QFTICR MS for Bottom Up Proteomics Ansgar Brock, David M. Horn, Eric C. Peters, Christopher M. Shaw, Christer Ericson,, Qui Phung,, Art Salomon Genomics Institute of the Novartis Research Foundation, San Diego, CA Beyond Genome, San Diego, June 19th, 2003
2 Overview Introduction Bottom Up and Top Down approaches Off-line Proteomics Platform Scheme and Design Concepts System Automation 1D-LC Yeast Shotgun experiment Identification of a Proteins Using Accurate Mass Measurement of a Single Peptide AMT experiment on TM protein mixture
3 The Systems Biology Paradigm R. Aebersold & M. Mann, Mass Spectrometry based proteomics, Nature 422, (2003)
4 Bottom Up and Top Down Approach to Proteomics Reduce Data and Compile Information Analyse the Fragmented and Fractionated Mixtures by MS/MS Fractionate Protein Mixture by 1Dor Multidimensional Separations Digestion of Proteins Protein Mixture Purified Protein Optional Liquid-phase Fragmentation to Produce Large Fragments Gas-phase Purification Fragment Protein / Sequence Fragments Reduce Data and Compile Information
5 Bottom Up and Top Down Instrumentation QIT, Q-TOF, TOF-TOF, (Q-FTICR) Key Concept: use MS/MS of partial protein to ID Instrumentation FTICR, (Q-TOF) Key Concept: use full protein to ID and characterize protein + automated implementations available - poor fragmentation of some peptides prevents characterization + comprehensive protein characterization - lack of automation, still in development stage
6 Off-Line Shotgun Proteomics MALDI-FTICR MS Scheme Sample Processing Code S Mix Code R Processing Reference LC/LC Sample Deposition Peak capacity multiplication, flexibility, automation Protein ID by MS accurate mass methods Remaining ID through tandem MS data MALDI FTICR Data Reduction ID MALDI-FTICR MS/MS Data Reduction DB Search Decision Differential quantitation Highest possible characterization power Iterative analysis without sample reruns
7 Potential Benefits of an Off-Line Approach Decoupling of LC from time scale allows more comprehensive analysis without sample reruns Optimizations of separations independent from mass spectrometer data acquisition Re-addressable, permanent record of separation allows for non- sequential and partial sample scanning in regions of interest (throughput, biomarkers) Sample storage Intelligent decisions can be made during analysis allowing results driven analysis
8 Benefits of High Mass Accuracy, High Resolution, and Large Dynamic range Many component to be observed in a single spectrum More confident identifications in database searching increase with mass Less time spent on data validation New schemes of sample analysis become possible
9 The Recognized LC-MALDI Challenge However, if MALDI-MS/MS MS/MS is to be used with peptide chromatography, the effluent of a liquid chromatography run must be deposited on a sample plate and mixed with the MALDI matrix, a process that has thus far proven difficult to automate. In general, it can be expected that the trend towards the combination of liquid chromatography with ESI- or MALDIMS/ MS (Fig. 1) will continue. R. Aebersold & M. Mann, Mass Spectrometry based proteomics Nature 422, (2003)
10 m/z MALDI Signals 50:1 50: m/z m/z 1: : m/z m/z 10:1 35:1
11 Technical Challenges of an MALDI Off-Line Approach Eluent collection mechanism that minimizes sample loss Develop methods for optimal sample conditioning for analysis Automation of the analysis of a large number of samples (expert systems vs. brute force approach)
12 Off-Line Shotgun Proteomics MALDI-FTICR MS Scheme Sample Processing Code S Mix Code R Processing Reference LC/LC Sample Deposition O MALDI FTICR HN N Data Reduction ID MALDI-FTICR MS/MS Data Reduction DB Search Decision
13 Four Column Deposition System 1 st LC system with autosampler, UV cell, etc. Syringe pump for matrix addition Control box, power supply, etc. Four column RP-LC set-up 2nd LC system for RP-LC Motion table with 4 MALDI targets
14 LC Deposition Process
15 LC Deposition Process
16 Improved MALDI Ionization of Derivatized Peptides Native Labeled with O HN N Peters, et al. Rapid Commun. Mass Spectrom., 2001, 15,
17 Labeling of Myoglobin with Cyclic O-Methylisourea Analog O HN N X X X X X = H, D m = 4; 1 Label GLSDGEWQQVLNVWGK m = 8; 2 Labels GHHEAELKPLAQSHATK m m = 12; 3 Labels LFTGHPETLEKFDKFK Peters, et al. Rapid Commun. Mass Spectrom., 2001, 15,
18 MALDI-QFTICR System
19 Automated MALDI FT-ICR MS
20 Robust Automation 5:1 50:1 50: m/z m/z m/z 1: : m/z m/z 10: m/z m/z
21 BSA Peptide Map Summary Mass Peptide FTMS S286-K316 X X X X X X 2540 Q94-K114 X X X X 2491 G21-K41 X X X X 2457 D295-K316 X X X X X X 2246 E243-K261 X X X 2112 V240-R256 X 2044 R144-K159 X X X X 2018 L115-K131 X X X 1906 L505-K520 X X X X X X 1900 N99-K114 X X X X 1887 H145-K159 X 1879 R484-K499 X X X X X X X 1746 Y160-K173 X X X X 1723 M445-R458 X 1672 Q94-K106 X X X X 1638 K413-R427 X X X X X X 1575 L115-K127 X X X X 1566 D323-R335 X X X X X X X 1553 D363-K375 X X X X X X X 1531 L274-K285 X X X X 1501 E351-K362 X X X X X 1478 L397-R409 X X X X X X X 1462 T52-K64 X X X X X 1442 Y262-K273 X X X X 1438 R336-R347 X X X 1418 S65-K76 X X X X X X X 1398 T545-K556 X X X X X X X 1304 H378-K388 X X X X 1282 H337-R347 X 1248 F11-K20 X X X X X X 1162 L42-K51 X X X X X X 1141 K524-K533 X X 1137 C475-R483 X X X X 1106 E564-K573 X X X X 1067 Q389-K396 X X X 1000 A209-R217 X Isotopic clusters
22 Warning! Performance claims of MS manufacturer s are made mostly for very idealistic conditions that really hardly ever apply in proteomic analyses of even comparatively simple mixtures A typical analysis and automation require tradeoffs between sensitivity, dynamic range, mass accuracy, and speed.
23 RP-LC/MS of 200 fmol BSA Digest
24 Chromatographic Resolution
25 Automated LC/MALDI QFT-ICR MS/MS 1) Perform LC/MALDI FT-ICR MS and return a mass list 2) Select peptides based on criteria such as ion intensity, expression ratio, etc. for tandem MS 3) Submit selection list to customized software to perform automated LC/MALDI QFT-ICR MS/MS for peptides in list 4) Reduce data and submit to Mascot for protein identification
26 RP-LC/MS 10µg Yeast Cytosolic Protein Digest
27 Automated LC/MALDI QFT-ICR MS/MS Yeast 10 µg, 1D RPLC-MALDI MALDI-FTMS/MS: 799 attempts (SNR >30), 226 peptide ID s, 111 proteins Ribosomal (40 total): Rpl10[5], Rpl11b[1], Rpl13ap[2], Rpl14bp[1], Rpl16ap[1], Rpl16bp[1], Rpl17ap[6], Rpl19ap[1], Rpl20ap[1], Rpl26bp[4], Rpl27bp[2], Rpl2ap[1], Rpl30p[1], Rpl4ap[1], Rpl5p[1], Rpl9ap[1], Rpm1p[1], Rpp0p[5], Rpp2bp[1], Rps10bp[1], Rps11bp[2], Rps12p[1], Rps13p[2], Rps14ap[1], Rps16bp[2], Rps17bp[1], Rps19bp[2], Rps1ap[1], Rps21bp[1], Rps24ap[1], Rps25ap[2], Rps29bp[1], Rps3p[2], Rps4bp[1], Rps5p[1], Rps6bp[1], Rps7ap[1], Rps7bp[1], Rps8ap[6], Rps9bp[1], Rsp14ap[1] Others (71 total): Others (71 total): Act1p[1], Adh1p[5], Adk1p[1], Ahp1p[1], Arg1p[1], Asc1p[2], Asn2p[1], Bmh2p[1], Cat8p[1], Cdc19p[10], Cof1p[1], Cph1p[2], Cys3p[1], Cys4p[1], Dal7p[1], Ded1p[1], Ded81p[1], Efb1p[1], Eft2p[5], Eno2p[9], Fas2p[2], Fba1p[5], Gdh3p[1], Glk1p[1], Gnd1p[1], Gpm1p[3], Gsp1p[1], Hom2p[1], Hsc82p[4], Hxk1p[2], Hyp2p[1], Leu1p[1], Lys1p[1], Lys9p[2], Met17p[2], Met6p[2], Msd1p[1], Oye2p[1], Pab1p[1], Pdc1p[11], Pdr13p[1], Pfk1p[3], Pgi1p[1], Pgk1p[11], Rnr4p[1], Sah1p[1], Ssa1p[1], Ssa2p[7], Ssb1p[1], Ssb2p[1], Sse1p[1], Tdh1p[3], Tdh3p[8], Tef2p[2], Tef4p[2], Tfp1p[1], Thr4p[1], Tif2p[1], Tkl1p[1], Tpi1p[4], Trp5p[1], Tsa1p[1], Uba1p[1], Ugp1p[2], Ura2p[1], Vma2p[1], Yef3p[3], Ykl056cp[1], Zuo1p[2]
28 LC/MALDI QFT-ICR MS/MS Results 799 attempts (S/N >30), 226 peptide ID s, 111 proteins For 799 submissions Mascot returned 257 possible assignments of which 31 were rejected in validation Unambiguous identification in the majority of cases despite Mascot scores below 95% confidence threshold (30-40), only 5 peptides with scores below 6 were rejected in validation 182 out of 226 identifications were assignable to only one peptide in the whole yeast proteome High mass accuracy data allows data validation to be performed in i less than 30 minutes and removes the data validation bottleneck without the need for additional score analysis software.
29 Automated LC/MALDI QFT-ICR MS/MS Parent ion mass: Identified by Mascot: O-acetylhomoserine-O-acetylserine acetylserine sulfhydralase Sequence: HGSQLFGLEVPGYVYSR No other suggested candidates by Mascot! Score: 48 y 1+ 8 Mass accuracy for fragments: y 1+ 5 y 1+ 6 y 1+ 7 b y y y y H 2 O m/z
30 Auto MS/MS of Yeast (spot 157; mass 1753) Significant hits: gi glyceraldehyde 3-phosphate dehydrogenase; Tdh2p Mass Top scoring peptide matches to query 1. Score greater than 11 indicates identity Score Delta Hit Protein Peptide gi LVSWYDNEYGYSTR RMS error of fragments 2ppm (Search Limits: MI ±10ppm; Frag. ±20mmu) 1 MVRVAINGFG RIGRLVMRIA LQRKNVEVVA LNDPFISNDY SAYMFKYDST 51 HGRYAGEVSH DDKHIIVDGH KIATFQERDP ANLPWASLNI DIAIDSTGVF 101 KELDTAQKHI DAGAKKVVIT APSSTAPMFV MGVNEEKYTS DLKIVSNASC 151 TTNCLAPLAK VINDAFGIEE GLMTTVHSMT ATQKTVDGPS HKDWRGGRTA 201 SGNIIPSSTG AAKAVGKVLP ELQGKLTGMA FRVPTVDVSV VDLTVKLNKE 251 TTYDEIKKVV KAAAEGKLKG VLGYTEDAVV SSDFLGDSNS SIFDAAAGIQ 301 LSPKFVKLVS WYDNEYGYST RVVDLVEHVA KA y y y MI
31 2D-LC MS of Yeast Cytosolic Protein Digest Fraction 24: masses Fraction 26: 7713 masses Fraction 34: 2486 masses SCX UV Trace minutes
32 SCX of Yeast Cytosolic Protein Digest Fraction # masses Fraction # masses Fraction # masses Total # of masses: ~76000
33 Assignment of Peptides Using Accurate Mass Introduced for use in FT-ICR MS in Conrads et al. 1 High throughput No extra tandem MS experiments required Improved dynamic range Can identify peptides that are not intense enough to perform tandem MS 1 Conrads, T. P., et al, Anal. Chem., 72, (2000).
34 Assignment of Peptides Using Accurate Mass Thermotoga maritima sequences % Thermotoga proteome coverage 100.0% 80.0% 60.0% 40.0% 20.0% 0.0% Mass only # K known Mass Accuracy (PPM)
35 Assignment of Peptides Using Accurate Mass Thermotoga maritima sequences tryptic peptides peptide % Thermotoga coverage 100.0% 80.0% 60.0% 40.0% 20.0% 0.0% ~50 identifiable peptides/protein Mass only # K known PPM Error
36 Assignment of Peptides Using Accurate Mass Human sequences % human proteome coverage 100.0% 80.0% 60.0% 40.0% 20.0% 0.0% identifiable tryptic peptides identifiable tryptic peptides PPM Error Mass only # K known
37 Identification of Proteins from Thermotoga maritima by Accurate Mass 1) Combine 85 previously identified TM proteins 2) Digest the TM protein mixture 3) Split the TM digest into two aliquots and label with D4 and H4 labels 4) Combine the labeled materials and perform LC separation 5) Analyze by LC/MS only of MALDI FTICR 6) Assign uniquely identifiable peptides based on mass (5 ppm) ) and number of lysine
38 Identification of Proteins from Thermotoga maritima by Accurate Mass Accurate mass + #K identified 65 of the proteins This is approximately the same number of identifications that resulted from an analysis by data dependent LC/MS/MS on a QTOF
39 Conclusions Multidimensional LC MALDI FT-ICR MS has been demonstrated for a complex proteome Protein Identification by accurate mass and number of lysine constraints possible for smaller organism Protein profiling by LC MALDI FTICR takes full advantage of the benefits of an off-line approach to capitalize optimally from the high mass accuracy capabilities of FTICR The technology seems to be uniquely suited for intelligent data driven proteomic bootstrapping approaches
40 Acknowledgments GNF Larry Brill Heath Klock Scott Lesley Matrix Science John Cottrell
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 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 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 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 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 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 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 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 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 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 2014 Training Course Wei-Hung Chang ( 張 瑋 宏 ) ABRC, Academia
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 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 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 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 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 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 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 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 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 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 informationAbsolute 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 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 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 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 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 informationMascot Integra: Data management for Proteomics ASMS 2004
Mascot Integra: Data management for Proteomics 1 Mascot Integra: Data management for proteomics What is Mascot Integra? What Mascot Integra isn t Instrument integration in Mascot Integra Designing and
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 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 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 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 informationApplication 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 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 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 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 informationA Quadrupole-Orbitrap Hybrid Mass Spectrometer Offers Highest Benchtop Performance for In-Depth Analysis of Complex Proteomes
A Quadrupole-Orbitrap Hybrid Mass Spectrometer Offers Highest Benchtop Performance for In-Depth Analysis of Complex Proteomes Zhiqi Hao 1, Yi Zhang 1, Shannon Eliuk 1, Justin Blethrow 1, Dave Horn 1, Vlad
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 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 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 informationTECHNICAL 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 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 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 informationPinpointing 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 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 informationThermo Scientific Prelude SPLC System FPO. Making LC/MS accessible. to clinical research and toxicology labs
Thermo Scientific Prelude SPLC System FPO Making LC/MS accessible to clinical research and toxicology labs Specifically designed to make the power of LC/MS accessible Analysis of target compounds in complex
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 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 informationApplication Note # LCMS-62 Walk-Up Ion Trap Mass Spectrometer System in a Multi-User Environment Using Compass OpenAccess Software
Application Note # LCMS-62 Walk-Up Ion Trap Mass Spectrometer System in a Multi-User Environment Using Compass OpenAccess Software Abstract Presented here is a case study of a walk-up liquid chromatography
More informationSeparation of Peptides from Enzymatic Digestion on Different Acclaim Columns: A Comparative Study
Application Update Now sold under the Thermo Scientific brand Separation of Peptides from Enzymatic Digestion on Different claim Columns: A Comparative Study INTRODUCTION Separation of peptides which can
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 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 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 informationElectrospray 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 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 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 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 informationWATERS QUANTITATIVE ANALYSIS solutions
More sensitivity. More speed. What more can you ask for in a complete quantitative analysis solution? WATERS QUANTITATIVE ANALYSIS solutions THE CHALLENGE OF QUANTITATIVE ANALYSIS Tandem mass spectrometry,
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 informationIndustry Perspective: Advantages of Open Access and Walkup LC/ MS Supporting Protein Drug Discovery and Development
Industry Perspective: Advantages of Open Access and Walkup LC/ MS Supporting Protein Drug Discovery and Development Dawn Stickle, Agilent Technologies Originally presented by Eric Fang, Novartis Overview
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 informationMarkerView Software 1.2.1 for Metabolomic and Biomarker Profiling Analysis
MarkerView Software 1.2.1 for Metabolomic and Biomarker Profiling Analysis Overview MarkerView software is a novel program designed for metabolomics applications and biomarker profiling workflows 1. Using
More informationA Navigation through the Tracefinder Software Structure and Workflow Options. Frans Schoutsen Pesticide Symposium Prague 27 April 2015
A Navigation through the Tracefinder Software Structure and Workflow Options Frans Schoutsen Pesticide Symposium Prague 27 April 2015 Kings day in The Netherlands 1 Index Introduction Acquisition, Method
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 informationHigh-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 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 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 informationMultiQuant Software Version 3.0 for Accurate Quantification of Clinical Research and Forensic Samples
MultiQuant Software Version 3.0 for Accurate Quantification of Clinical Research and Forensic Samples Fast and Efficient Data Review, with Automatic Flagging of Outlier Results Adrian M. Taylor and Michael
More informationLearning Objectives:
Proteomics Methodology for LC-MS/MS Data Analysis Methodology for LC-MS/MS Data Analysis Peptide mass spectrum data of individual protein obtained from LC-MS/MS has to be analyzed for identification of
More informationAppendix 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 informationDesign considerations for proteomic reference materials
4220 DOI 10.1002/pmic.201000242 Proteomics 2010, 10, 4220 4225 Design considerations for proteomic reference materials David M. Bunk Analytical Chemistry Division, National Institute of Standards and Technology,
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 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 informationA Hybrid Microchip/Capillary Electrophoresis Mass Spectrometry Platform for Rapid and Ultrasensitive Bioanalysis
A Hybrid Microchip/Capillary Electrophoresis Mass Spectrometry Platform for Rapid and Ultrasensitive Bioanalysis Ryan Kelly 1, Chenchen Wang, Cheng S. Lee, Richard D. Smith, Keqi Tang 1 Environmental Molecular
More informationfor 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 informationSpikeTides TM Peptides for relative and absolute quantification in SRM and MRM Assays
Protocol SpikeTides TM Peptides for relative and absolute quantification in SRM and MRM Assays Contact us: InfoLine: +49-30-6392-7878 Order per fax: +49-30-6392-7888 or e-mail: www: peptide@jpt.com www.jpt.com
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 informationDRUG METABOLISM. Drug discovery & development solutions FOR DRUG METABOLISM
DRUG METABLISM Drug discovery & development solutions FR DRUG METABLISM Fast and efficient metabolite identification is critical in today s drug discovery pipeline. The goal is to achieve rapid structural
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 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 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 informationHenry Shion, Robert Birdsall, Steve Cubbedge, and Weibin Chen Waters Corporation, Milford, MA, USA APPLICATION BENEFITS INTRODUCTION WATERS SOLUTIONS
Development of Integrated Informatics Workflows for the Automated Assessment of Comparability for Antibody Drug Conjugates (ADCs) Using LC-UV and LC-UV/MS Henry Shion, Robert Birdsall, Steve Cubbedge,
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 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 informationEKSIGENT EKSPERT NANOLC 400. Unmatched flexibility for low flow LC/MS
EKSIGENT EKSPERT NANOLC 4 Unmatched flexibility for low flow LC/MS EKSIGENT EKSPERT NANOLC 4 Focused ekspertise In 23, Eksigent changed the way scientists looked at nanoscale chromatography with the introduction
More informationMascot Search Results FAQ
Mascot Search Results FAQ 1 We had a presentation with this same title at our 2005 user meeting. So much has changed in the last 6 years that it seemed like a good idea to re-visit the topic. Just about
More informationProteomic Technologies
Review Multidimensional Separations for Protein/ Peptide Analysis in the Post-Genomic Era BioTechniques 32:898-911 (April 2002) Hongbin Liu, Dayin Lin, and John R. Yates III The Scripps Research Institute,
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 informationamazon SL Innovation with Integrity Setting New Standards in Performance, Simplicity and Value Ion Trap MS
amazon SL Setting New Standards in Performance, Simplicity and Value Innovation with Integrity Ion Trap Best-In-Class Ion Trap Mass Spectrometer for Routine Analysis The amazon SL entry-level system is
More informationUnique Software Tools to Enable Quick Screening and Identification of Residues and Contaminants in Food Samples using Accurate Mass LC-MS/MS
Unique Software Tools to Enable Quick Screening and Identification of Residues and Contaminants in Food Samples using Accurate Mass LC-MS/MS Using PeakView Software with the XIC Manager to Get the Answers
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 informationIntroduction 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 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 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 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 informationThermo Scientific SIEVE Software for Differential Expression Analysis
m a s s s p e c t r o m e t r y Thermo Scientific SIEVE Software for Differential Expression Analysis Automated, label-free, semi-quantitative analysis of proteins, peptides, and metabolites based on comparisons
More informationWeek 9: MS in Space and Proteomics
Week 9: MS in Space and Proteomics 1 Last Time Detectors Small Molecule Applications, Environmental: (e.g. TWQC) 2 Mass Spectrometry in Space Possibly the coolest application of small molecule MS is in
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 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 informationHow 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 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 information