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Chap 7 Mass Spectrometry

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Chap 7 Mass Spectrometry Chap 7 Mass Spectrometry Biochemistry and Molecular Biology 9.1 Introduction 9.2 Ionization 9.3 Mass Analysis 9,5 Structural Information by Tandem Mass Spectrometry 9.7 Computing and Database Analysis 1 Biological Mass Spectrometry A key tool for Protein. Peptides. Carbohydrate. DNA………and more 2 Back to the history……… The first mass spectrometer - parabola spectrograph 1912 J. J. Thomson 3 Back to the history……… J.J. Thomson • J.J. Thomson observes a line at mass 22 in the spectrum of neon. • J.J. Thomson delivers his Bakerian Lecture, “Rays of Positive Electricity” to the Royal Society of London. 4 • Francis Aston is awarded the Nobel Prize in chemistry for his discovery of isotopes of “inactive elements.” Francis Aston 5 Advances in Modern Mass Spectrometry Limitations of traditional MS on biological applications ♦ High molecular weight >50,000 ♦ Amount of Sample < 10-12 -10-15 mole ElectroSpray Ionization MS Matrix Assisted Laser Desorption Ionization MS John B. Fenn Koichi Tanaka ESI MALDI 6 Evolution of Mass Spectrometry-1 Francis Aston is awarded the Nobel Prize in chemistry for his discovery of isotopes of “inactive The double-foucsing elements.” mass spectrograph is developed J.J. Thomson Rays of Positive Electricity 1913 1922 1934 1946 7 Evolution of Mass Spectrometry-2 Biomolecules Ion-molecule reaction, unimolecular dissociation Volatile organic molecules 1960 1970 1980 1990 2000 8 Human Genome Project 2003, 4, 14 35000-40000 Genes 9 Genomics (基因體學) 1953: Watson and Crick: DNA double helix Danio rerio C. Elegans (1998) Rattus norvegicus Anopheles gambiae (2002 Homo sapiens (2001) Fugu rubripes (2002) Mus musculus10(2002) Drosophila melanogaster (2000) From Genomics to Proteomics Genome Transcriptome Proteome DNA RNA Proteins Modified Biological Proteins Function Y Y Transcription Translation Post-Translation Modification PROTEin complement to a genOME Entire protein complement in a given cell, tissue or organism 11 PR TE MICS 蛋白質體學 Protein activity, modifications, localizations, amd interactions of proteins in complexes Proteomics can be defined as the qualitative and quantitative comparison of proteomes under different conditions to further unravel biological processes 12 Protein chemistry and proteomics Protein Identification ( 蛋白質鑑定) Protein chemistry Proteomics Individual proteins Complex mixtures Complete sequence analysis Partial sequence analysis Emphasis on structure and function Emphasis on identification by database matching Structual biology Systems biology 13 Disease Proteomics 一滴血可以診斷出疾病嗎? 14 Protein Chips 蛋白質晶片 15 找尋腫瘤標記蛋白質 正常人 良性攝護 腺腫瘤 攝護腺癌 16 17 Wide Applications of Mass Spectrometry Jennings et al , Int. J. Freiser et al , Morris et al, Rapid Mass Spectrom. Ion. Anal. Chem. 54, commun. Mass Phys. 1, 227 (1968) 1431 (1982) Spectrom. 10, 889 (1996) COLLISIONAL- Derrick et al, Org. FOURIER TRANSFORM Mass Spectrom. 27, ORTHOGONAL INDUCED ION CYCLOTRON 1077 (1992) QUADRUPOLE- DISSOCIATION TIME-OF-FLIGHT RESONANCE MS TIME-OF-FLIGHT /TIME-OF-FLIGHT MS MS Futrell et al Yost et al, J. Am. Cooks et al, (1964) Chem. Soc. 100, Anal. Chem. 2274 (1978) 59, 1677 (1987) FIVE TRIPLE QUADRUPOLE Hager et al , Rapid Commun. SECTOR QUADRUPOLE ION TRAP MS Mass Spectrom. 2002, 16, MS MS 512 (2002) LINEAR ION TRAP 1960 1970 1980 1990 2000 ¾ FTICR- TRAP 1943 ¾ ION- TRAP ¾Triple Q ¾Q-TOF ¾Q-FTICR 1943 ¾ ION- TRAP ¾¾EBE-TOFTriple Q ¾Q-TOF ¾Q-FTICR 1st COMMERICAL ¾EBE-TOF ¾TOF-TOF 18 MASS1st COMMERICAL SPECTROMETER ¾LINEAR¾TOF-TOF TRAP MASS SPECTROMETER ¾LINEAR TRAP What is mass spectrometry? 1619.28 100 968.64 1251.93 1252.97 2313.69 969.70 2312.76 1621.14 2314.75 1670.25 Ionization 1671.24 + - % 2315.80 M or M 970.69 1254.00 1672.14 M 1013.80 2366.83 836.58 1060.23 1570.17 2367.90 893.67 1873.46 1061.26 2271.83 2368.85 1448.14 1853.38 2019.57 1876.41 2036.57 2369.91 2718.09 0 m/z 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 Mass-to-charge Ratio ( m/z ) MS is an analytical tool that measure the molecular weight of molecules based on the motion of charged particle in an electrical or magnetic field. 19 Two different ways of measurement • Composition of analyte (MS) e.g. Peptide mass fingerprinting • Structure of analyte (MS/MS, tandem MS) Dissociation 20 Turbo pumps High Vacuum System Diffusion Pumps Rough pumps Rotary pumps Detector Data Inlet Ion source Mass Filter System •Microchannel Plate •PC’s •Sample plate •MALDI •TOF •Electron Multiplier •SunSPARK •“Hybrid” •DECStation •Target •Electrospray •Quadrupole •Macs •HPLC •FAB •Ion Trap •GC •LSIMS •Magnetic Sector •CE •EI •FTMS •CI 21 Ionization Methods • Electron Impact (EI) • Fast Atom Bombardment (FAB) • Electrospray Ionization (ESI) • Matrix-Assisted Laser Desorption Ionization (MALDI) 22 Advances in Modern Mass Spectrometry Limitations of traditional MS on biological applications ♦ High molecular weight >50,000 ♦ Amount of Sample < 10-12 -10-15 mole ElectroSpray Ionization MS Matrix Assisted Laser Desorption Ionization MS 2002 Nobel Prize in Chemistry 23 Matrix-Assisted Laser Desorption Ionization (MALDI) 24 Matrix-Assisted Laser Desorption Ionization (MALDI) Analyte Metal Ion Matrix http://www.ionsource.com 25 Matrix selection CH O CH CHCOOH 3 α-Cyano-4-hydroxy- Peptides<10kDa cinnamic acid (CHCA) HO CH O Sinapinic Acid Proteins >10kDa 3 Sinapinic acid (3,5-Dimethoxy- 2,5-Dihydroxybenzoic Neutral Carbohydrates, 4-hydroxy cinnamic acid) acid (DHB) Synthetic Polymers COOH “Super DHB” Proteins, OH Glycosylated proteins N 3-Hydroxypicolinic acid Oligonucleotides 3-hydroxypicolinic acid (3-HPA) HABA Proteins, Oligosaccharides CH C(CN)COOH COOH NN HO OH α-cyano-4-hydroxycinnamic acid 2-(4-hydroxyphenylazo)-benzoic acid (HABA) 26 A typical mass spectra [M+H]+ [M+2H]2+ 27 Electrospray: Generation of aerosols and droplets 28 ElectroSpray Ionization (ESI) 29 Charge Residue Model Coulomb repulsion : Charge repulsion > surface tension Ion Desorption Model Ion desorption from the droplet surface 30 Multiple-charged ESI spectra Deconvolution 31 32 Deconvolution Step 1: assume 190.1 = mass/charge 379.2 = mass/charge Step 2: assume the two peaks are related 190.1 = m/(z+1) 379.2=m/z Step 3: solve m and z m=378.2, z=1 Charge state Calculation Unprotonated mass +1 (379.2-1)*1 378.2 +2 (190.1-1)*2 378.2 average 378.2 33 34 Molecular Weight of Proteins 35 Mass Analysis Ions are separated according to their mss-to-charge (m/z) TRANSPORT of + / FULL + / - IONS AND -IONS TO SCAN NEUTRALS PARENT MASS ION SPECTRA TO FORMED IN ANALYZER THE DETECTOR ion SOURCE ION SOURCE Transport Mass analyzer DETECTOR optics 36 Ion Mass Data source Detector Inlet Filter System • •Sector Instruments Time-of-flight Analyzer Quadrupole Mass Filter Ion-Trap Instrument FT-ICR 37 Quadrupole Mass Filter (m/z -4000) M+ 2 2 au = ax = -ay = 4zU / mω ro a/q = 2U/V, others fixed 2 2 qu = qx = -qy = 2zV / mω ro 38 Length, diameter, kinetic energy -Æm/e range, resolution 39 Ion-Trap Instrument Cap electrode • Principle very similar to quadrupole • Ions stored by RF & DC fields • Scanning field can eject ions of Ring electrode specific m/z MSn 40 41 Multiple MS/MS (MSn) for Structural determination 42 Time-of-flight Mass Spectrometry 43 Laser 2500 Volt ＋ ＋ ＋ ＋ ＋ ＋ electric field drift region ~3.6cm ~1m 1 Mass spectrum m 2 ＋ t = D 2zeEs ＋ ＋ ＋ t= 100 µ second for mass 50 ( small moleculae) 1000 µ second for mass 5,000 (peptide, polymer…) 3000 µ second for mass 50,000 (protein, DNA….) m/z 44 Calibration of Mass Spectrum Flight time 1 D: drift length m 2 t = D 2zeEs 1 t = a()m 2 + b The mass is independent of any instrumental parameters [M+H]+ Internal calibration External calibration 45 m/z is a function of flight time Vacuum pump S D 10-5 ~10-8 torr E=V/s V In a electric field E = where V = accelerating voltage s 1 2 1 2 2zeEs In drift region mv = qV = zeEs v = 2 m 1 m 2 Flight time t = D 2zeEs m 2eEs Relation between m/z and t = t 2 z D2 46 FactorsFactors ofof PoorPoor ResolutionResolution inin TOFTOF MSMS Linear MALDI TOF Time-of-flight will be affected by: Linear MALDI TOF Temporal Distribution Large kinetic energy spread, broad peaks time of ion formation poor resolution Spatial Distribution (unresolved isotope) initial location in the extraction field m/z Kinetic Energy Distribution different initial kinetic energy 47 Ions of same mass, Delayed Extraction (DE) different velocities 1: No applied electric field. 0 V Ions spread out. Uslow > Umedium > Ufast V < V < V Potential +20 kV 2: Field applied. Gradient accelerates slow ions more than fast ones. +20 kV + 3: Slow ions catch up with faster ones at the detector 48 Fourier Transform Ion Cyclotron Resonance Analyzer, FTICR Z Comisarow, M. B.; Marshall, A. G. Fourier transform ion cyclotron resonance spectroscopy49 Chem. Phys. Lett. 1974, 25, 282-283. v F=z v x B F: Magnetic force on the ion z: Charge of the ion F v: Velocity of the ion X B: Magnetic Field Z A charged particle (ion) will rotate around the magnetic field line of a homogeneous magnetic field in a circular motion. 50 Large biological system Exact mass measurement LC-MS Comparison of Different Types of Mass Spectrometers Characteristic Magnetic Quadrupole QIT TOF FT-ICR Sector Mass Range 15,000 4,000 100,000 unlimited > 106 (Da) Resolution 200,000 Unit 30,000 15,000 > 106 Dynamic ++++ +++ +++ +++ ++ Range MS/MS ++++ +++ +++ +++ ++ LC or CE + ++++ +++ ++ ++ Cost $$$$ + + ++ ++++ 51 Tandem Mass Spectrometry PARENT MASS ANALYZER IS PRODUCT PARENT IONS PARKED, PASSING MASS ANALYZER ENTER ONLY PARENT IONS MS 2 IS SCANNED, TRANSPORT of + / COLLISION CELL +
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