Mass spectrometry of proteins, peptides and other analytes: principles and principal methods. Matt Renfrow January 11, 2008

Transcription

1 Mass spectrometry of proteins, peptides and other analytes: principles and principal methods Matt Renfrow January 11, 2008

2 Objectives of the Lecture 1. Make ions 2. Separate/Analyze/Detect ions 3. What is mass resolution and mass accuracy?

3 What does a mass spectrometer do? 1. It measures mass better than any other technique. 2. It can give information about chemical structures. What are mass measurements good for? To identify, verify, and quantitate: metabolites, recombinant proteins, proteins isolated from natural sources, oligonucleotides, drug candidates, peptides, synthetic organic chemicals, polymers

4 Applications of Mass Spectrometry Pharmaceutical analysis Bioavailability studies Drug metabolism studies, pharmacokinetics Characterization of potential drugs Drug degradation product analysis Screening of drug candidates Identifying drug targets Biomolecule characterization Proteins and peptides Oligonucleotides Environmental analysis Pesticides on foods Soil and groundwater contamination Forensic analysis/clinical

5 QuickTime and a decompressor are needed to see this picture. MS of Proteins and Peptides 1D gel 2D gel Protein mixture or Complex mixture

6 QuickTime and a decompressor are needed to see this picture. Put it in your machine and tell 1D gel me the RIGHT answer 2D gel Protein mixture or Complex mixture

7 Put it in - We need Ions ( or - ) - In the gas phase Your machine - Tof, Tof Tof - Quadrupole, Ion trap - FT-ICR, Orbitrap (high resolution) - Hybrids Tell me the RIGHT answer - How right is it? mass resolution and accuracy

8 How does a mass spectrometer work? Sample Ion source: makes ions Mass analyzer: separates ions Mass spectrum: presents information

9 Mass Spectrometer Block Diagram High Vacuum System Inlet Ion source Mass Analyzer Detector Data System

10 Mass Spectrometer Block Diagram High Vacuum System Turbo molecular pumps Inlet Ion source Mass Analyzer Detector Data System

11 Sample Introduction High Vacuum System Inlet Ion Source Mass Analyzer Detector Data System HPLC Flow injection Sample plate

12 Ion Source High Vacuum System Inlet Ion Source Mass Analyzer Detector Data System MALDI ESI FAB LSIMS EI CI

13 Nobel Prize in Chemistry For getting proteins and peptides into the gas phase John Fenn Koichi Tanaka "for the the development of of methods for for identification and structure analyses of of biological macromolecules" and "for their development of of soft desorption ionisation methods for for mass spectrometric analyses of of biological macromolecules"

14 Ion Sources make ions from sample molecules (Ions are easier to detect than neutral molecules.) Electrospray ionization: Pressure = 1 atm Inner tube diam. = 100 um Sample Inlet Nozzle (Lower Voltage) Partial vacuum N 2 MH Sample in solution N 2 gas MH 2 MH 3 High voltage applied to metal sheath (~4 kv) Charged droplets

15 Electrospray Ionization (ESI) nebulizing gas sample solution HV N 2 curtain gas Mass Analyzer Atmospheric pressure 1. Solvent evaporation 2. Coulombic repulsion Vacuum [M nh] n

16 Electrospray Ionization (ESI) 5 μm

17 Electrospray Ionization (ESI) Process (Positive Mode) Ions Needle Taylor cone Site of Spray oxidation current ( i) ESI droplets Mass spectrometer Site of reduction 1-5 kv power supply Solvent and neutralized ions Adapted from Kebarle, P and Tang, L, Anal. Chem., 1993, 65(22), 972A

18 MALDI: Matrix Assisted Laser Desorption Ionization Sample plate hν Laser MH 1. Sample is mixed with matrix (X) and dried on plate. 2. Laser flash ionizes matrix molecules. 3. Sample molecules (M) are ionized by proton transfer: XH M MH X. /- 20 kv Grid (0 V)

19 MALDI generation of ions (Matrix-assisted laser desorption ionization) Laser pulse (337 nm) [MH] [M-H] - matrix ions Peptide/protein deposited on crystal surface Sample mixed with a UV-absorbing matrix and is allowed to co-crystallize on the metal target.

20 Matrices for MALDI analysis Peptides/proteins -- 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid) -- α-cyano-4-hydroxycinnamic acid (CHCA) -- 2,5-dihydroxybenzoic acid (DHB) -- 2-(4-hydroxyphenylazo)-benzoic acid (HABA) Oligonucleotides -- 2-aminobenzoic acid -- 3-hydroxypicolinic acid (3-HPA) -- 2,4,6-trihydroxyacetophenone (THAP) The choice of of matrix depends greatly on on the the solute to to be be analyzed.

21 Put it in - We need Ions ( or - ) - In the gas phase Your machine - Tof, Tof / Tof - Quadrupole, Ion trap - FT-ICR, Orbitrap (high resolution) - Hybrids Tell me the RIGHT answer - How right is it? mass resolution and accuracy

22 Mass Analyzer High Vacuum System Inlet Ion source Mass Analyzer Detector Data System Time of flight (TOF) Quadrupole Ion Trap Magnetic Sector FT-ICR MS Orbitrap MS

23 Mass analyzers separate ions based on their mass-to-charge ratio (m/z) Operate under high vacuum (keeps ions from bumping into gas molecules) Actually measure mass-to-charge ratio of ions (m/z) The importance of the mass-to-charge ratio is that according to classical electrodynamics two particles with the same mass-to-charge ratio move in the same path in a vacuum when subjected to the same electric and magnetic fields. F=ma (Newton s second law of motion) F=q(E v B) (Lorentz force Law) (m/q)a = E v B Key specifications are resolution, mass measurement accuracy, and sensitivity.

24 Time-of-flight (Tof) analyzer MALDI Laser; High Energy Monochromatic Light Source time-of-flight (Tof) tube detector Accelerating pulse

25 Time-of-flight (TOF) Mass Analyzer Source Drift region (flight tube) detector V Ions are formed in pulses. The drift region is field free. Measures the time for ions to reach the detector. Small ions reach the detector before large ones.

26 Time-of-flight (Tof) analyzer Source Accelerating pulse Detector Tof tube ( m) Effective flight tube (3.0 m) Detector Reflector Resolution 2 x 10 4 No upper limit of mass Scan times ~ 1 μsec, good for LC-MSMS Ions Ions are are accelerated so so that that they they have have equal equal kinetic kinetic energy. The The ions ions drift drift down down a meter meter tube tube before before striking a photomultiplier detector. time time of of flight flight (t) (t) depends on on the the mass mass of of the the ion ion (m), (m), where where t t = (m/2ev) 1/2 1/2 *D *D V is is the the applied potential and and D is is the the flight flight tube tube distance. For For a given given instrument, the the flight flight time time varies varies as as the the square square root root of of the the mass mass of of the the ion. ion.

27 Principals of the MALDI-Tof/Tof 4700

28 QSTAR TM ESI QQ TOF or MALDI QQ TOF Sample Q0 Q1 Q2 Effective Flight Path = 2.5 m Ion Mirror (reflector)

29 Quadrupole Mass Analyzer Uses a combination of RF and DC voltages to operate as a mass filter. Has four parallel metal rods. Lets one mass pass through at a time. Can scan through all masses or sit at one fixed mass.

30 Quadrupoles have variable ion transmission modes m2 m4 m1 m3 m4 m3 m2 m1 mass scanning mode m2 m4 m1 m3 m2 m2 m2 m2 single mass transmission mode

31 Quadrupole mass filter / ion guide Octapole

32 Quadrupole analyzer Mass resolution 2 x 10 3 Tolerant of relatively high pressure (10-4 torr) Upper limit for m/z is 3,000-4,000 Ions Ions are are accelerated electrically (5-15V) and and passed along along the the long long central central axis axis of of four four rods rods arranged symmetrically. By By applying combined DC DC and and oscillating RF RF potentials, the the ions ions drift drift along along irregular flight flight paths paths along along the the rod rod axis. axis. The The DC/RF DC/RF ratio ratio is is held held constant and and the the absolute values values of of DC DC and and RF RF are are varied. varied. Only Only ions ions with with a particular m/z m/zvalue have have stable stable trajectories for for a given given value value of of DC DC and and RF. RF. If If DC DC is is set set to to 0, 0, then then all all ions ions have have stable stable trajectories. A scan scan can can be be accomplished over over a period period of of msec. msec.

33 QTRAP: Linear Ion Trap on a Triple Quadrupole Q0 Q1 Q2 Q3 Exit linear ion trap

34 Ion Traps The The ion ion trap trap is is an an energy energy well well --ions ions with with sufficient energy energy to to enter enter the the trap trap are are retained by by an an energy energy barrier barrier on on the the exit exit side side of of the the trap. trap. The The advantage of of the the ion ion trap trap is is that that it it accumulates selected ions ions prior prior to to their their analysis giving giving it it high high initial initial sensitivity (detection limit limit of of approx fmol). fmol). Ions Ions are are fragmented by by collision with with helium helium gas gas and and their their daughter ions ions analyzed within within the the trap. trap. Selected daughter ions ions can can undergo further further fragmentation, thus thus allowing MS MS n n.. The The ion ion trap trap has has a high high efficiency of of transfer of of fragment ions ions to to the the next next stage stage of of fragmentation (unlike (unlike the the triple triple quadrupole instrument).

35 Expanded view of 3D ion trap

36 3D ion trap and 2D ion trap

37 2D ion trap detection Conversion dynodes

38 Penning Trap (ICR cell)

39 Penning Trap (ICR cell) magnetic field

40 Put the trap in a high magnetic field Ion cyclotron resonance 7 Tesla magnet, or 9.4 T or 12 T or 14.5 T

41 Detector High Vacuum System Inlet Ion source Mass Analyzer Detector Data System Microchannel Plate Electron Multiplier Mass analyzer/ion trap AC image

42 3D ion trap and 2D ion trap

43 2D ion trap detection Conversion dynodes

44 2D ion trap detection Conversion dynodes (electron multipliers)

45

46 Detecting in the ion trap Ion cyclotron resonance (ICR) 7 Tesla magnet, or 9.4 T or 12 T or 14.5 T

47 Fourier transform- Ion cyclotron resonance FT-ICR MS m/z = k * B / f Frequencies are converted to masses.

48 ThermoFinnigan LTQ-FT

49 LTQ Orbitrap Hybrid Mass Spectrometer Finnigan LTQ Linear Ion Trap API Ion source Linear Ion Trap C-Trap Differential pumping Orbitrap Differential pumping Inventor: Dr. Alexander Makarov, Thermo Electron (Bremen)

50 Orbitrap Mass Analyzer ω = k m / z

51 Data System High Vacuum System Inlet Ion source Mass Analyzer Detector Data System PC

52 The mass spectrum shows the results MALDI TOF spectrum of IgG Relative Abundance (M2H) 2 MH (M3H) Mass (m/z)

53 ESI Spectrum of Trypsinogen (MW 23983) M 15 H M 16 H M 14 H M 13 H m/z Mass-to-charge ratio

54 How do mass spectrometers get their names? Types of ion sources: Electrospray (ESI) Matrix Assisted Laser Desorption Ionization (MALDI) Types of mass analyzers: Quadrupole (Quad, Q) Ion Trap Time-of-Flight (TOF) -Either source type can work with either analyzer type: MALDI- TOF, ESI-Quad. -Analyzers can be combined to create hybrid instruments. ESI-QQQ, MALDI QQ TOF, Q Trap

55 Summary: acquiring a mass spectrum Ionization Mass Sorting (filtering) Detection Ion Source Form ions (charged molecules) Mass Analyzer Sort Ions by Mass (m/z) Ion Detector Detect ions Inlet Solid Liquid Vapor Mass Spectrum

56 Put it in - We need Ions ( or - ) - In the gas phase Your machine - Tof, Tof / Tof - Quadrupole, Ion trap - FT-ICR, Orbitrap (high resolution) - Hybrids Tell me the RIGHT answer - How right is it? mass resolution and accuracy

57 How is mass defined? Assigning numerical value to the intrinsic property of mass is based on using carbon-12, 12 C, as a reference point. One unit of mass is defined as a Dalton (Da). One Dalton is defined as 1/12 the mass of a single carbon-12 atom. Thus, one 12 C atom has a mass of Da.

58 Isotopes Most elements have more than one stable isotope. For example, most carbon atoms have a mass of 12 Da, but in nature, 1.1% of C atoms have an extra neutron, making their mass 13 Da. Why do we care? Mass spectrometers can see isotope peaks if their resolution is high enough. If an MS instrument has resolution high enough to resolve these isotopes, better mass accuracy is achieved.

59 Stable isotopes of most abundant elements of peptides Element Mass Abundance H % C N O

60 Mass spectrum of peptide with 94 C-atoms (19 amino acid residues) Monoisotopic mass No 13 C atoms (all 12 C) One 13 C atom Two 13 C atoms

61 Isotope pattern for a larger peptide (207 C-atoms) m/z

62 Mass spectrum of insulin 2 x 13 C 13 C 12 C : Insulin has 257 C-atoms. Above this mass, the monoisotopic peak is too small to be very useful, and the average mass is usually used.

63 Monoisotopic mass Monoisotopic mass corresponds to lowest mass peak When the isotopes are clearly resolved the monoisotopic mass is used as it is the most accurate measurement.

64 Average mass Average mass corresponds to the centroid of the unresolved peak cluster When the isotopes are not resolved, the centroid of the envelope corresponds to the weighted average of all the the isotope peaks in the cluster, which is the same as the average or chemical mass.

65 What if the resolution is not so good? At lower resolution, the mass measured is the average mass. Better resolution Poorer resolution Mass

66 100 How is mass resolution calculated? ISO:CH3 M R = M/ΔM % Intensity FWHM = ΔM Mass (m/z)

67 Mass measurement accuracy depends on resolution High resolution means better mass accuracy ppm error Resolution =18100 Counts ppm error Resolution = ppm error Resolution = Mass (m/z)

68 How do we achieve superior mass resolution? Reflector TOF Mass Analyzer Delayed Extraction on a MALDI source Measure frequency (FT-ICR MS, Orbitrap MS)

69 Important performance factors Mass accuracy: How accurate is the mass measurement? Resolution: How well separated are the peaks from each other? Sensitivity: How small an amount can be analyzed?

70 Two peptides - same nominal mass - simulation Peptide mixture: [Val 5 ]-Angiotensin II Lys-des-Arg 9 -Bradykinin Sequence: DRVYVHPF KRPPGFSPF Formula: C 49 H 69 N 13 O 12 C 50 H 73 N 13 O 11 Exact mass: [M2H] 2 = [M2H] 2 = Δm (mmu): 18.2 mmu RP = 18,000 RP = 56, (observed) Intensity (%) (correct) (correct) Intensity (%) m/z m/z

71 Is Mass Accuracy Important? Results for error limit up to 5 ppm Theoretical Delta Delta RDB Composition Mass [ppm] [mmu] 1 ppm (4) 2 ppm (10) 5 ppm (23) C 49 H 71 O 12 N C 49 H 79 O 11 N 9 S C 41 H 75 O 14 N 15 S C 43 H 77 O 15 N 12 S C 48 H 75 O 16 N C 51 H 73 O 13 N C 47 H 69 O 11 N C 47 H 77 O 10 N 12 S C 44 H 73 O 11 N 16 S C 45 H 79 O 16 N 9 S C 52 H 69 O 9 N C 46 H 73 O 15 N C 38 H 79 O 14 N 15 S C 46 H 81 O 14 N 8 S C 45 H 75 O 9 N 15 S C 46 H 75 O 12 N 13 S C 52 H 75 O 11 N 9 S C 54 H 71 O 10 N C 44 H 71 O 14 N C 40 H 81 O 15 N 12 S C 44 H 79 O 13 N 11 S C 40 H 73 O 16 N C 48 H 77 O 13 N 10 S 1

72 Mass Resulution = m / Δm 50% m/z RP = / amu = 89,319 FT-ICR MS RP = / 0.69 amu = 712 LTQ MS m/z m/z

73 Objectives of the Lecture 1. Make ions ESI, MALDI 2. Separate/Analyze/Detect ions Tof, ion trap, quadrupole, FT-ICR, Orbitrap Electron multipliers 3. What is mass resolution and mass accuracy?

74 Slide Acknowledgements Thermo Electron (Fisher) Bruker ABI Sandler Mass Spectrometry Group David Agard group (Univ. of Calif Sanfrancisco)