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The impact of high-resolution mass spectrometry in shotgun proteomics : two case studies Maarten Aerts Promotor : Prof. Dr. B. Devreese Co-Promotor : Prof. Dr. Em. J. Van Beeumen PhD. defense : Maarten Aerts, May 6 th 2010

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Presentation Outline Proteomics : an introduction Definitions Mass Spectrometry Protein/Peptide Identification Impact of High-Resolution MS Shotgun Approach OutlinePhD. defense : Maarten Aerts, May 6 th 2010

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Presentation Outline Proteomics : an introduction Case study 1 : N. vitripennis venomics Biological objectives Experimental set-up Results OutlinePhD. defense : Maarten Aerts, May 6 th 2010

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PhD. defense : Maarten Aerts, 6 th may 2010 Presentation Outline Proteomics : an introduction Case study 1 : N. vitripennis venomics Case study 2 : Comparative proteomics on ciprofloxacin resistance Comparative proteomics Medicinal objectives Experimental set-up Results Outline

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Presentation Outline Proteomics : an introduction Case study 1 : N. vitripennis venomics Case study 2 : Comparative proteomics on ciprofloxacin resistance Conclusions and future perspectives OutlinePhD. defense : Maarten Aerts, May 6 th 2010

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Central Dogma DNA mRNA Protein Proteomics : Introduction Introduction P Transcription Translation Duplication PhD. defense : Maarten Aerts, May 6 th 2010

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Proteins : - amino acid polymer structure and function - define a cells phenotype - molecular active molecules Structural proteins Transport proteins Enzymes Proteomics : Introduction IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Proteins : Proteome : total complement of all proteins present in a particular cell at a given time in a given environment Dynamic : alteration due to intra- and extracellular signals Genome : total complement of all the genes present in an organism Static : identical in all cells Gene expression (mRNA or proteins) = Gene function prediction Proteomics : Introduction IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Proteomics : Introduction Introduction Genomics Proteomics Transcriptomics Gene function Gene prediction Gene function PhD. defense : Maarten Aerts, May 6 th 2010

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Proteomics : Introduction Introduction Genomics Proteomics Transcriptomics Gene function Gene prediction Gene function micro array : fast and complete slow and incomplete coverage ? PhD. defense : Maarten Aerts, May 6 th 2010

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Central Dogma DNA mRNA Protein Proteomics : Introduction Introduction P Transcription Translation Duplication R R R PTM Localization PhD. defense : Maarten Aerts, May 6 th 2010

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Proteomics : Introduction Introduction Genomics Proteomics Transcriptomics Gene function Gene prediction Gene function micro array : fast and complete slow and incomplete coverage PhD. defense : Maarten Aerts, May 6 th 2010

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High-throughput analyses on proteomes, sub-proteomes or protein complexes based on mass spectrometry to identify, quantify and/or characterize proteins. analytical technique to determine the molecular weight of molecules, including peptides or proteins Proteomics : mass spectrometry IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Sample Peptides Proteins Proteomics : mass spectrometry PhD. defense : Maarten Aerts, May 6 th 2010Introduction

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Sample Peptides Proteins Ionization ESI MALDI Proteomics : mass spectrometry PhD. defense : Maarten Aerts, May 6 th 2010Introduction

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Sample Peptides Proteins Ionization ESI MALDI Detector Mass analyzer Quadrupole Ion Trap TOF FT-ICR Orbitrap Ion Mobility Proteomics : mass spectrometry PhD. defense : Maarten Aerts, May 6 th 2010Introduction

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Sample Peptides Proteins Ionization ESI MALDI Detector Mass analyzer Quadrupole Ion Trap TOF FT-ICR Orbitrap Ion Mobility Proteomics : mass spectrometry PhD. defense : Maarten Aerts, May 6 th 2010Introduction

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Proteomics : mass spectrometry PhD. defense : Maarten Aerts, May 6 th 2010Introduction

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Proteomics : Protein/Peptide Identification Trypsin : K/R m/z MS Unique Peptide Mass Fingerprint Protein database prediction PMF IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Proteomics : Protein/Peptide Identification Trypsin : K/L m/z MS Unique Peptide Mass Fingerprint MS/MS m/z Unique Peptide Fragment Fingerprint m/z IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Sample Peptides Proteins Ionization ESI MALDI Detector Mass analyzer Quadrupole Ion Trap TOF FT-ICR Orbitrap Ion Mobility Tandem MS CID ECD ETD Proteomics : Protein/Peptide Identification IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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PMF Peptide Mass Fingerprint Single protein Database searching Unique MS fingerprint PFF Peptide Fragment Fingerprint Peptide selection Database searching Amino acid sequence (MS/MS) m/z Proteomics : Protein/Peptide Identification IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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High-throughput analyses on proteomes, sub-proteomes or protein complexes based on mass spectrometry to identify, quantify and/or characterize proteins. analytical technique to determine the molecular masses of molecules, including peptides or proteins High-Resolution MS High-Resolution Mass Spectrometry IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Rs : peak width at half peak intensity Sharp peaks Peak capacity Peak detection Peak selection Charge state determination Mass accuracy High-Resolution Mass Spectrometry IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Rs : peak width at half peak intensity Sharp peaks Peak capacity : isobaric peptides Peak detection Peak selection Charge state determination Mass accuracy High-Resolution Mass Spectrometry IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Rs : peak width at half peak intensity Sharp peaks Peak capacity Peak detection Peak selection Charge state determination Mass accuracy High-Resolution Mass Spectrometry IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Rs : peak width at half peak intensity Sharp peaks Peak capacity Peak detection Peak selection Charge state determination : zm Mass accuracy High-Resolution Mass Spectrometry IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Rs : peak width at half peak intensity Sharp peaks Peak capacity Peak detection Peak selection Charge state determination Mass accuracy : database searching High-Resolution Mass Spectrometry IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Rs : peak width at half peak intensity Sharp peaks Peak capacity Peak detection Peak selection Charge state determination Mass accuracy : database searching peptide identification peptide quantification High-Resolution Mass Spectrometry IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Rs : peak width at half peak intensity FT-ICR : Fourier Transformation Ion Cyclotron Resonance High-Resolution Mass Spectrometry Cyclotron frequency, Magnetic field, B IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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High-Resolution Mass Spectrometry IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Rs : peak width at half peak intensity FT-ICR : Fourier Transformation Ion Cyclotron Resonance High-Resolution Mass Spectrometry Cyclotron frequency, Magnetic field, B Introduction ~ m/z PhD. defense : Maarten Aerts, May 6 th 2010

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Rs : peak width at half peak intensity FT-ICR : Fourier Transformation Ion Cyclotron Resonance High-Resolution Mass Spectrometry Cyclotron frequency, Magnetic field, B Multiple m/zcomplex waveform FT m/z Introduction ~ m/z PhD. defense : Maarten Aerts, May 6 th 2010

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Rs : peak width at half peak intensity FT-ICR : Fourier Transformation Ion Cyclotron Resonance High-Resolution Mass Spectrometry Cyclotron frequency, Magnetic field, B Multiple m/zcomplex waveform Slow IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Rs : peak width at half peak intensity FT-ICR : Fourier Transformation Ion Cyclotron Resonance LTQ-FTUltra MS High-Resolution Mass Spectrometry LTQ FT-MS PhD. defense : Maarten Aerts, May 6 th 2010Introduction

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Rs : peak width at half peak intensity FT-ICR : Fourier Transformation Ion Cyclotron Resonance LTQ-FTUltra MS High-Resolution Mass Spectrometry PhD. defense : Maarten Aerts, May 6 th 2010Introduction

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Rs : peak width at half peak intensity FT-ICR : Fourier Transformation Ion Cyclotron Resonance LTQ-FTUltra MS Data-Dependent Acquisition Ideal LC-MS platform high quality MS high quantity MS/MS High-Resolution Mass Spectrometry PhD. defense : Maarten Aerts, May 6 th 2010Introduction

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High-throughput analyses on proteomes, sub-proteomes or protein complexes based on mass spectrometry to identify, quantify and/or characterize proteins. analytical technique to determine the molecular masses of molecules, including peptides or proteins High-Resolution MS Sample complexity fractionation strategies Protein/Peptide separation PhD. defense : Maarten Aerts, May 6 th 2010Introduction

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Protein mixture 2D-PAGE Digest on single spot containing one protein MS and MS/MS PMF or PFF pI / MW

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Protein mixture 2D-PAGE Digest on single spot containing one protein MS and MS/MS PMF or PFF

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Protein mixture 2D-PAGE Digest on single spot containing one protein MS and MS/MS PMF or PFF n x Dim-LC - SEC - SCX - RP - CF Digest on single protein MS and MS/MS on intact protein (Top-Down) MS and MS/MS PMF or PFF

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Protein mixture 2D-PAGE Digest on single spot containing one protein MS and MS/MS PMF or PFF n x Dim-LC - SEC - SCX - RP - CF Digest on single protein MS and MS/MS on intact protein (Top-Down) MS and MS/MS PMF or PFF Limitations : Dynamic range : low abundant Range physicochemical properties pI, MW and hydrophobicity

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n x Dim-LC - SEC - SCX - RP - CF Digest on single protein MS and MS/MS on intact protein (Top-Down) MS and MS/MS PMF or PFF GeLC Digest on gel band containing few proteins LC-MS/MS PFF 2D-PAGE Digest on single spot containing one protein MS and MS/MS PMF or PFF Protein mixture

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GeLC Digest on gel band containing few proteins LC-MS/MS PFF n x Dim-LC - SEC - SCX - RP - CF Digest on single protein MS and MS/MS on intact protein (Top-Down) MS and MS/MS PMF or PFF 2D-PAGE Digest on single spot containing one protein MS and MS/MS PMF or PFF Shotgun proteomics Digest on complete protein mixture Enrichment of targeted peptides 2D LC-MS/MS - SCX - RP PFF

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Protein mixture Shotgun proteomics Digest on complete protein mixture Enrichment of targeted peptides 2D LC-MS/MS - SCX - RP PFF Shotgun proteomics Tryptic digest : complexity multidimensional LC Peptide sequencing : MS/MS Analyzable peptides represent proteins Proteome coverage GeLC Digest on gel band containing few proteins LC-MS/MS PFF

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Shotgun Proteomics Shotgun proteomics Tryptic digest : complexity Bottom-up proteomics Analyzable peptides represent proteins Peptide sequencing : MS/MS Sensitivity Dynamic range Top-down proteomics Intact proteins : Limited proteome coverage Protein sequencing : MS/MS IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Shotgun Proteomics LC-MS platform : - Multi-dimensional LC - High-Resolution MS - MS/MS database searching Application : 1.Venom proteins of Nasonia vitripennis (parasitoid wasp) 2.Drug resistance mechanism on mouse macrophages IntroductionPhD. defense : Maarten Aerts, May 6 th 2010

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Nasonia vitripennis Ectoparasitoid wasp Nasonia Venomics : Introduction Nasonia VenomicsPhD. defense : Maarten Aerts, May 6 th 2010

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Nasonia vitripennis Ectoparasitoid wasp Nasonia Venomics : Introduction Nasonia VenomicsPhD. defense : Maarten Aerts, May 6 th 2010

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Nasonia vitripennis Ectoparasitoid wasp Nasonia Venomics : Introduction Nasonia VenomicsPhD. defense : Maarten Aerts, May 6 th 2010

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Nasonia vitripennis Ectoparasitoid wasp Nasonia Venomics : Introduction Nasonia VenomicsPhD. defense : Maarten Aerts, May 6 th 2010

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Nasonia vitripennis Ectoparasitoid wasp Nasonia Venomics : Introduction Nasonia Venomics Venom proteins : - Host behavior - Growth alteration - Immune suppression - Nutrient metabolism PhD. defense : Maarten Aerts, May 6 th 2010

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Nasonia vitripennis Ectoparasitoid wasp 50 years scientific history Biological model organism : parasitoids - controller of insect populations crop pests disease vectors - commercialized Nasonia Venomics : Introduction Nasonia VenomicsPhD. defense : Maarten Aerts, May 6 th 2010

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Nasonia vitripennis Ectoparasitoid wasp 50 years scientific history Biological model organism : parasitoids Genetic model organism - Ease of breeding - Haplodiploidy (recessive vs. dominance) - Inter-fertility : N. giraulti, N. longcornis (Complex trait analyses) Genome sequence Nasonia Venomics : Introduction Nasonia VenomicsPhD. defense : Maarten Aerts, May 6 th 2010

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Genome sequence Characterization of Venom - Venom experience (bee) - Function during reproduction : - Host behavior - Growth alteration - Immune suppression - Nutrient metabolism - Bioinformatic approach : venom protein prediction candidate gene list confirmation at mRNA - Proteomic approach Nasonia Venomics : Introduction Nasonia Venomics Bee venom : defensive PhD. defense : Maarten Aerts, May 6 th 2010

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Nasonia Venomics : Proteomic analysis Nasonia Venomics 10 venom reservoirs Trypsin Shotgun proteomic approach via LC-MS platform - 2D-LC : first dimension SCX (charge) second dimension RP (hydrophobicity) PhD. defense : Maarten Aerts, May 6 th 2010

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Nasonia Venomics : Proteomic analysis Nasonia Venomics 10 venom reservoirs Trypsin Shotgun proteomic approach via LC-MS platform - 2D-LC : first dimension SCX (charge) second dimension RP (hydrophobicity) - MALDI TOF-TOF29 peptides 14 proteins - ESI FT-MS258 peptides 76 proteins PhD. defense : Maarten Aerts, May 6 th 2010

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76 proteins :61 secretion signal limited overlap with bioinformatic approach complexity venom reservoir venom gland 23 unknown function Nasonia Venomics : Results Nasonia VenomicsPhD. defense : Maarten Aerts, May 6 th 2010

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First identification of venom proteins Characterization of the molecular mechanism behind venom activity : efficiency as pest controller : agriculture and human health pharmaceutical applications transgenic plants or viruses Nasonia Venomics : Future directions Nasonia VenomicsPhD. defense : Maarten Aerts, May 6 th 2010

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Case Study 2 : Ciprofloxacin resistance PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Intracellular accumulating antibiotic intracellular infections e.g. Listeria monocytogenes Ciprofloxacin resistance PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Intracellular accumulating antibiotic intracellular infections e.g. Listeria monocytogenes Ciprofloxacin resistance PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Intracellular accumulating antibiotic intracellular infections e.g. Listeria monocytogenes Ciprofloxacin resistance PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Intracellular accumulating antibiotic Long-term exposure to ciprofloxacin eukaryotic resistance Ciprofloxacin resistance PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Intracellular accumulating antibiotic Long-term exposure to ciprofloxacin eukaryotic resistance Ciprofloxacin resistance PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Intracellular accumulating antibiotic Long-term exposure to ciprofloxacin eukaryotic resistance Ciprofloxacin resistance PhD. defense : Maarten Aerts, May 6 th 2010

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Intracellular accumulating antibiotic Long-term exposure to ciprofloxacin eukaryotic resistance Ciprofloxacin resistance PhD. defense : Maarten Aerts, May 6 th 2010

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Intracellular accumulating antibiotic Long-term exposure to ciprofloxacin eukaryotic resistance Ciprofloxacin resistance PhD. defense : Maarten Aerts, May 6 th 2010

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Intracellular accumulating antibiotic Long-term exposure to ciprofloxacin eukaryotic resistance Ciprofloxacin resistance PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Intracellular accumulating antibiotic Long-term exposure to ciprofloxacin eukaryotic resistance Ciprofloxacin resistance ATP PhD. defense : Maarten Aerts, May 6 th 2010

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Intracellular accumulating antibiotic Long-term exposure to ciprofloxacin eukaryotic resistance Ciprofloxacin resistance ATP PhD. defense : Maarten Aerts, May 6 th 2010

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Intracellular accumulating antibiotic Long-term exposure to ciprofloxacin eukaryotic resistance Ciprofloxacin resistance MK571 PhD. defense : Maarten Aerts, May 6 th 2010

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Intracellular accumulating antibiotic Long-term exposure to ciprofloxacin eukaryotic resistance life-threatening infections ATP-driven Inhibitors Multidrug Resistance Proteins Comparative proteomic analysis on membrane proteomes Ciprofloxacin resistance PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Comparative proteomics PhD. defense : Maarten Aerts, May 6 th 2010

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Comparative proteomics WT Heavy labeled CIP Light labeled Tryptic digest LC-MS PhD. defense : Maarten Aerts, May 6 th 2010

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Comparative proteomics WT Heavy labeled CIP Light labeled Tryptic digest LC-MS m/z PhD. defense : Maarten Aerts, May 6 th 2010

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Comparative proteomics PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Comparative proteomics PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Results LC-MS (FT-MS) 900 protein identified and (relatively) quantified 136 proteins with significant abundance difference between WT and CIP macrophages MRP4 (ABCC4) - Multidrug Resistance protein - ATP $ PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Discussion MRP4 Confirmed : - RT-PCR (mRNA) - Western blot (protein) PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Discussion MRP4 (ABCC4) p58 IPK : Negative regulator of UPR evoked by ER stress CIP resistance ~ Stress resistance PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Discussion MRP4 (ABCC4) p58 IPK : Negative regulator of UPR evoked by ER stress CIP resistance ~ Stress resistance PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Discussion MRP4 (ABCC4) p58 IPK : Negative regulator of UPR evoked by ER stress CIP resistance ~ Stress resistance ? MRP4 over-expression ER stress ? No other UPR proteins are differentially expressed ! Genome organization PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Discussion Chr. 14 mrp4 p58 IPK Gene duplication PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Discussion MRP4 (ABCC4) p58 IPK : Negative regulator of UPR evoked by ER stress Remaining proteins : related to drug resistance ? secondary effects ? MRP4 : cAMP, Leukotriens, etc. p58 IPK : regulator of Transcription Factors PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Conclusion Identified ciprofloxacin efflux pump : MRP4 mode of induction : gene duplication A model for in vivo drug resistance mechanism - MRP family : broad substrate specificity Antibiotics Anti-viral drug Chemotherapeutics - Secondary effects Stress resistance cell motility and adherence creating an environment for new resistance mechanism PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Conclusion PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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Conclusion PhD. defense : Maarten Aerts, May 6 th 2010Ciprofloxacin resistance

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General Conclusions PhD. defense : Maarten Aerts, May 6 th 2010Conclusions

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Shotgun proteomics : relevant biological and medicinal problems LC-MS platform : 2D-LC or GeLC Database searching Automated statistical validation software High-Resolution MS : FT-ICR mass accuracy peptide coverage protein coverage peak detection quantification General Conclusions PhD. defense : Maarten Aerts, May 6 th 2010Conclusions

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Shotgun proteomics : relevant biological and medicinal problems LC-MS platform : Nasonia venomics : new venom proteins Ciprofloxacin resistance mechanism : MRP4, gene duplication Start of new discovery phase General Conclusions PhD. defense : Maarten Aerts, May 6 th 2010Conclusions

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Holy grail : sensitivity Complete proteome coverage LC-MS platforms - Mass spectrometry : mass analyzers ionization - Peptide fractionation : chip-based LC - Data analysis : MS/MS homology Estimation of FPR MS/MS independent identification Future perspectives PhD. defense : Maarten Aerts, May 6 th 2010Future perspectives

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Promotor : Prof. Dr. B. Devreese Co-Promotor : Prof. Dr. J. Van Beeumen Friends and Family L-ProBE colleagues Acknowledgement Laboratory of Zoophysiology : prof. Dr. D. de Graaf Marleen Brunain Ellen Danneels Ellen Formesyn Unit de Pharamcologie Cellulaire et Molculaire (UCL) : prof. Dr. P. Tulkens prof. Dr. F. Van Bambeke Nancy Caceres Beatrice Marquez PhD. defense : Maarten Aerts, May 6 th 2010Acknowlegment

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PhD. defense : Maarten Aerts, May 6 th 2010 ? Questions