Mass Spectrometry and Proteomics - Lecture 1 - Matthias Trost Newcastle University [email protected] Content Lectures 1-3 • The basics of mass measurement Lecture 1 • Ionisation techniques • Mass analysers • Detectors Lecture 2 • Tandem mass spectrometry • Fragmentation techniques Lecture 3 • Peptide fragmentation • Hybrid instruments 2 Content Lectures 4-6 • What is proteomics? • Sample Preparation Lecture 4 • Experimental Design • Quantification techniques • Search engines, Databases, FDR Lecture 5 • Data analysis & Data inspection • Fractionation techniques Lecture 6 • Phosphoproteomics and other PTMs • Proteomics experiments 3 Lecture 1 • Basics – Components of a mass spectrometer – Isotopes and isotopic profiles – Resolution – Accuracy vs. Precision • Ionisation techniques – Electrospray Ionisation – Matrix-assisted Laser Desorption/Ionisation 4 The basics of mass measurements The zeroth law of mass spectrometry: Never ever say mass spectroscopy! Spectroscopy involves the measurement of electromagnetic waves and we look at “particles”. 5 History of mass spectrometry 1886 E. Goldstein discovers anode rays in a gas discharge tube. 1897 J.J. Thomson discovers the electron and determines its m/z (Nobel Prize in 1906) 1912 J.J. Thomson constructs the first mass spectrometer and sees spectra of O2, N2, CO, CO2 and COCl2. He observes negative ions, multiply charged ions and identifies isotopes of 20Ne and 22Ne. 1918 A.J. Demster develops the electron impact ion source and constructs the first mass spectrometer that allows focusing of ions in direction. 1919 F.W. Aston constructs the first mass spectrometer that allows focusing of ions by velocity (Nobel Prize 1922). 1931 E. O. Lawrence invents the cyclotron (Nobel Prize in 1939). 1934 J. Mattauch and R. Herzog develop the first mass spectrometer that allows focusing of ions in direction and momentum with an electrostatic sector and a magnetic sector. 1934 W.R. Smythe, L.H. Rumbaug and S.S. West perform the first preparative separation of isotopes. 1940 A.O. Nier et al isolate the isotope 235U. 6 History of mass spectrometry 1942 First commercial sector mass spectrometer by CEC. 1948 A.E. Cameron et D.F. Eggers elaborate the plan for a Time-of-Flight mass spectrometer after a principle proposed by W. Stephens in 1946. 1952 Quasi-equilibrium theorie (QET) and Rice–Ramsperger–Kassel–Marcus (RRKM) theory explain the molecular fragmentation of ions. Marcus receives Nobel Prize in 1992 1952 W. Paul and H.S. Steinwedel describe the first ion trap mass spectrometer. W. Paul, H.S Reinhard and U. von Zahn publish the first quadrupol mass spectrometer. Paul and Dehmelt (“Penning trap”) receive Nobel Prize in 1989. 1956 J. Beynon show the first identification of the empirical formula through measurement of exact mass. First GC-MS by F.W. McLafferty and R.S. Gohlke. 1966 M.S.B. Munson et F.H. Field introduce the chemical ionisation. K. Biemann et al determine first peptide sequence by mass spectrometry. 1967 F.W. McLafferty and K.R. Jennings introduce collision-induced dissociation (CID). 1968 Finnigan commercialises the first quadrupol mass spectrometer. 7 History of mass spectrometry 1972 V.I. Karataev, B.A. Mamyrim et D.V. Smikk introduce the first Time-of-Flight mass spectrometer with reflectron. 1974 M.D. Comisarov and A.G. Marshall apply the Fourier transformation to analyse ion cyclotron resonance mass spectra. P.J. Arpino, M.A. Bladwin and F.W. McLafferty present the first mass spectrometer coupled to a liquid chromatography system. 1978 R.A. Yost and C.G. Enke construct the first triple quadrupol mass spectrometer. 1981 M. Barber, R.S. Bordoli, R.D. Sedgwick and A.H. Tyler describe the atom bombardment ion source and publish the first spectrum of Insulin in 1982. 1982 Sciex and Finnigan commercialise the first triple quadrupol mass spectrometer 1987 M. Karas and F. Hillenkamp develop matrix-assisted laser desorption/ionisation (MALDI), K. Tanaka laser desorption. Tanaka receives Nobel Prize in 2002. 1988 J. Fenn develops electrospray ionisation after a concept proposed by M.Dole in 1968. Fenn receives Nobel Prize in 2002. 1999 A.A. Makarov presents a new type of mass analyser – the Orbitrap. 2004 D.F. Hunt lab develops electron-transfer dissociation (ETD) mass spectrometry. 8 The basics of mass measurements Sample IonisationMass analyser Detector Data introduction Acquisition and Analysis Electron ESI Quadrupol multiplier Computer MALDI Ion trap Microchannel Chromatography plate (GC, HPLC) FAB TOF Ion-to-photon Direct injection CI FT-ICR detectors Capillary FD/FI Sectors (B, E) FT-ICR electrophoresis II Orbitrap Orbitrap Vacuum 9 The basics of mass measurements: vacuum Vacuum technology Pressure (mbar) Pressure (mtorr) Vacuum 1000 - 1 750 torr-750 mtorr Primary Vacuum 100-10-3 750-0.75 Intermediate Vacuum 10-3-10-7 0.75-7.5 * 10-5 High Vacuum <10-7 <7.5 * 10-5 Ultra-high vacuum • Rotation pumps (backing/roughing pumps): 4-16 m3/h for the primary vacuum necessary for turbomolecular pumps (turbo pumps). • Ultra-high vacuum almost entirely achieved by turbo pumps (200-500 L/sec) (20- 90,000 rpm!, up to several thousand km/h!). Less used are diffusion pumps (600- 2000 L/sec) and cryo-pumps. 10 The basics of mass measurements: vacuum Why is a vacuum necessary? The mean free path, , is the average distance traveled by an ion before it collides with an air molecule, and is given by: = 1/N where N is the gas number density, and is the collision cross section between the ion and the molecule (typically ~50 Å2 for a small peptide ion). Using a collision cross section of 50 Å2, the following table may be constructed: 11 The basics of mass measurements Positive-ion mode: the molecule with an additional proton Negative-ion mode: the molecule with a proton less. The calculated mass can be obtained from the empirical formula: C11H10N3Cl In the literature, the molecular mass can be shown as: Average mass: 219.67 Da Normalised on the most abundant peak Nominal mass: 219 u Monoisotopic mass: 219.0563 u m/z: 220.06 Th 12 The basics of mass measurements: isotopes Isotopes • A molecule is defined by its empiric formula • Each atom has a natural isotopic ratio due to difference in the number of neutrons. E.g. carbon and chlorine: 12C: 12.0000u <-> 13C: 13.0034u 35Cl: 34.9689u <-> 37Cl: 36.9659u 1u=1 Da=1/12 of 12C ~ mass of the H-atom (1.00794u) • Each isotope has a natural abundance: E.g. 12C: 100% <-> 13C: 1.08% 13 The basics of mass measurements: isotopes Symbol #atomic Nominal mass Isotopic Composition Isotopic mass Average Mass H 1 1 100 1.007825 1.00795 2 0.0115 2.014101 Na 11 23 100 22.989769 22.989769 P 15 31 100 30.973762 30.973762 C 6 12 100 12.000000 12.0108 13 1.08 13.003355 N 7 14 100 14.003070 14.00675 15 0.369 15.000109 O 8 16 100 15.994915 15.9994 17 0.038 16.999132 18 0.205 17.999116 S 16 32 100 31.972071 32.067 33 0.8 32.971459 34 4.52 33.967867 36 0.02 35.967081 Cl 17 35 100 34.968853 35.4528 37 31.96 36.965903 Br 35 79 100 78.918338 79.904 81 97.28 80.916291 14 Mass Defect • The mass of an atom is less than the sum of the individual parts (protons, neutrons and electrons). This difference is called mass defect. • The mass defect originates from the binding energy of protons and neutrons in the nucleus. • The energy can be calculated by E=mc2. http://pprco.tripod.com/SIMS/Theory.htm http://nsb.wikidot.com/pl-9-8-3-9 15 The basics of mass measurements: isotopes Isotope pattern is dependent on the composition and the number of atoms. In larger biomolecules, the 13C-peak becomes the main peak. ~75 C-Atoms ~100 C-Atoms ~125 C-Atoms 16 The distances between isotopic peaks reveal charge state mix of 6 proteins LCT protein_modeling prot_mix_0724a 651 (10.856) Sm (SG, 2x6.00); Cm (648:651) 505.3506 TOF MS ES+ 505.3506 783 100 +1 % 1.00 mix of 6 proteins LCT protein_modeling rot_mix_0724a 350 (5.837) Sm (SG, 2x6.00); Cm (343:374) 915.7363 TOF MS ES+ 506.3584 915.4818 915.7363 1.86e3 506.3584 00 915.4818 507.3566 915.9765 507.3566 915.9765 +4 0 m/z 500 501 502 503 504 505 506 507 508 509 510 511 512 915.2247 % 915.2274 916.2311 916.2311 mix of 6 proteins LCT protein_modeling prot_mix_0724a 655 (10.923) Sm (SG, 2x6.00); Cm (645:675) 1086.5515 TOF MS ES+ 916.4857 1086.5515 454 0.25 916.4857 100 1086.0433 916.7402 1086.0433 0 m/z 915 916 917 918 0.5 1086.0444 1087.0444 +2 % 1087.5529 1087.5529 1088.0460 1088.0460 0 m/z 1084 1085 1086 1087 1088 1089 1090 17 The basics of mass measurements: resolution Resolution 18 The basics of mass measurements: resolution Resolution How does the isotopic pattern vary with resolution for a peptide of 2000 Da? 19 The basics of mass measurements: resolution Resolution Impact on the identification of an ion species: + C20H9 + R>10000 R=1000 C19H7N C H N O + + + + 13 19 3 2 C19H7N C20H9 C13H19N3O2 249 249.0580 249.0700 249.1479 Typical resolution of mass spectrometers: • Quadrupol, Ion trap: <10,000 • Orbitrap: up to 500,000-1,000,000 • Time-of-Flight: 10-30,000 • FT-ICR >1,000,000 20 The basics of mass measurements: Accuracy and Precision 21 Ionisation techniques • Electrospray ionisation (ESI) • Matrix-assisted laser desorption/ionisation (MALDI) • Not covered: Electron Ionisation (EI), Chemical Ionisation (CI), Fast-Atom Bombardment (FAB) 22 Electrospray 23 Electrospray 24 Electrospray Ionisation (ESI) • Ionisation of molecules from solution • “Soft” ionisation technique • Ease of coupling with separation techniques such as nano-LC • Production of multiply charged ions ( MS/MS) 25 Electrospray • ESI of large peptides and proteins: Production of multiply charged species: [M+zH]z+ • Space between two ions corresponds to the difference of one charge.