FOURIER TRANSFORM MASS SPECTROMETRY

Transcription

1 FOURIER TRANSFORM MASS SPECTROMETRY FT-ICR Theory Ion Cyclotron Motion Inward directed Lorentz force causes ions to move in circular orbits about the magnetic field axis Alan G. Marshall, Christopher L. Hendrickson, and George S. Jackson Encyclopedia of Analytical Chemistry, R.A. Meyers (Ed.), John Wiley & Sons Ltd, Chichester, 2, pp

2 FT-ICR Theory Ion Cyclotron Motion Ion cyclotron motion. Ions rotate in a plane perpendicular to the direction of a spatially uniform magnetic field, Note that positive and negative ions orbit in opposite senses. FT-ICR Theory Ion Cyclotron Motion X Y ω c = qb m Z 2

3 Once we make an ion, we move it into the center of the Magnet. Then, we trap it before it can escape. Electrostatic Barrier Ion is now trapped in the magnet. ION + Ion sees barrier and is turned back Gate shut before the ion escapes From Primer 1998 Marshall. FT-ICR Theory - Ion Trapping X Z T T Magnetic Field (B) Y E Axial Position 3

4 FT-ICR Theory - Ion Trapping X Y Z T T Magnetic Field (B) E Axial Position FT-ICR Theory - Ion Trapping X Y Z T T Magnetic Field (B) E Axial Position 4

5 FT-ICR Theory Combined Ion Motion v m = magnetron motion v c = cyclotron motion v t = trapping oscillations Alan G. Marshall, Christopher L. Hendrickson, and George S. Jackson Encyclopedia of Analytical Chemistry, R.A. Meyers (Ed.), John Wiley & Sons Ltd, Chichester, 2, pp FT-ICR Theory - Excitation Image Time (ms) 5

6 FT-ICR Theory - Excitation X Z or B o Y Amplitude Excitation Electrodes Time FT-ICR Theory Excitation Alan G. Marshall, Christopher L. Hendrickson, and George S. Jackson Encyclopedia of Analytical Chemistry, R.A. Meyers (Ed.), John Wiley & Sons Ltd, Chichester, 2, pp

7 SWIFT Excitation Single Notch SWIFT Event (MS/MS) Data Count Affects Resolution (Limited to < 512K) Freq Cutoff Bandwidth 1% Start Frequency End Frequency Power % Frequency SWIFT Excitation 1% Power % Frequency IFT 7

8 FT-ICR Theory - Excitation X Z or B o Y Amplitude Time Excitation Electrodes SWIFT Excitation On -the -fly SWIFT isolation of a single Isotope of Bovine Ubiquitin M+4 Isotope

9 FT-ICR Theory - Detection X Z or B o Y Multiplex Detection in FT-ICR.5 Time Domain Transient.4.3 Differential Amplifier Image Current Time (ms) 9

10 Multiplex Detection in FT-ICR.5.4 Time Domain Transient.3 Differential Amplifier Image Current Time (ms) Fourier Transforms in FT-ICR Differential Amplifier Image Current Time Domain Transient Time (ms) Fourier Transform Frequency Spectrum Frequency (khz)

11 Mass Calibration in FT-ICR Frequency Spectrum Mass Spectrum m z A = + BV t f f Frequency (khz) Space Charge and Resolution in FT-ICR T T LOW ION DENSITY FT Detection Time (msec) FT T T Detection Time (msec) 8 HIGH ION DENSITY

12 Effect of Magnetic Field Strength Resolving Power Highest Non-Coalesced Mass Scan Speed (LC/MS) Axialization Efficiency Number of Ions Tr apped I on Upper Mass Li mi t 2D-FT Resolving Power Ion Trapping Time Ion Energy Field Strength (Tesla) FT-ICR Experiment - Event Sequences - Use a single mass analyzer but separate the mass analysis and ion isolation events in time - Can perform many successive stages of MS (MS n ) Event Sequence Ion Transfer / Ion Trapping Parent Ion Fragmentation Ionization Parent Ion Isolation Daughter Ion Detection 12

13 Ultra-high Resolving Power Peak Capacity = () max - () min Δm 5% Δm 5% () min () max Separation Method Maximum # of Components Maximum Peak Capacity Theoretical Plates HP-TLC , Isocratic LC , Gradient LC , HPLC 37 1, 1,5, CE 37 1, 1,5, Open Tubular GC 37 1, 1,5, ESI FT-ICR MS 525 2, 6,,, m/δm 5% > 2, 2 < < 1, m average +/-.25 Da Skip Prior Chemical Separation and Identify Components by MS! 13

14 17,+ Compositionally Distinct Components Resolved by High Resolution 9.4 Tesla Electrospray FT-ICR MS Negative Ion ESI Mass Spectrum Positive Ion ESI Mass Spectrum 6,118 resolved components 11,127 resolved components ~ )Ryan P. Rodgers, Alan G. Marshall, Petroleomics: Advanced Characterization of Petroleum-Derived Materials by Fourier Transform Ion Cyc lotron Resonanc e Mass Spectrometry (FT-ICRMS, As phaltenes, Heavy Oils, and Petroleomic s 27, pp Ryan P. Rodgers and Alan G. Marshall Figure Negative-ion ESI selective ion accumulation 9.4-T FT-ICR mass spectrum of acidic asphaltenes. Note the resolution of 55 peaks at a single nominal mass. )Ryan P. Rodgers, Alan G. Marshall, Petroleomics: Advanced Characterization of Petroleum-Derived Materials by Fourier Transform Ion Cyc lotron Resonanc e Mass Spectrometry (FT-ICRMS, As phaltenes, Heavy Oils, and Petroleomic s 27, pp more complex petroleum fractions such as asphaltenes. For example, Figure 3.11 shows an ESI FT-ICR mass spectrum of acidic asphaltenes with 55 peaks resolved at a single nominal mass. Currently, detailed chemical composition (class, type, and carbon number) of samples of such complexity is accessible only by FT-ICR MS. 14

15 Isotopic Fine Structure Resolving power M ΔM 5% = 8,, S. D.-H. Shi, C. L. Hendrickson, and A. G. Marshall Proc. Natl. Acad. Sci. USA, 1998, 95, Unit Mass Baseline Resolution for an Intact 148 kda Therapeutic Monoclonal Antibody by FT-ICR Mass Spectrometry Anal Chem. 211 November 15; 83(22): d oi: /ac c. 15

16 Unit Mass Baseline Resolution for an Intact 148 kda Therapeutic Monoclonal Antibody by FT-ICR Mass Spectrometry Valeja et al. Page 9 NIH-PA Author Manuscript NIH-PA Author Manuscript Figure 2. Anal Chem. 211 November 15; 83(22): doi:1.121/ac22429c. Broadband positive ESI 9.4 T FT-ICR MS mass spectrum for an IgG1k antibody protein. The characteristic charge state distribution envelope from 47+ to 67+ ( 2,2 3,2) is achieved by front-end skimmer dissociation of non-covalent adducts. NIH-PA Author Manuscript NIH-PA Author Manuscript Unit Mass Baseline Resolution for an Intact 148 kda Therapeutic Monoclonal Antibody by FT-ICR Mass Spectrometry Valeja et al. Page 1 Anal Chem. Author manuscript; available in PMC 212 November 15. NIH-PA Author Manuscript Figure 3. Anal Chem. 211 November 15; 83(22): doi:1.121/ac22429c. NIH-PA Author Manu Top: Positive ESI 9.4 T magnitude-mode FT-ICR mass spectrum for quadrupole-selected IgG1k showing 57+ charge state molecular ions along with various adducts, based on an 11.6 s transient with 5 isotopic beats (inset). Bottom: Mass scale-expanded segment, demonstrating unit mass baseline resolution of the isotopic distribution at ~29, average resolving power. 16

17 Single-scan electrosprayft-icr mass spectrum of the isolated 48+ charge state of bovine serum albumin Bovine Serum Albumin 66,433 Da [M+48H] 48+ m = 2,, m 5% Figure 3. J. Am. Soc. Mass Spectrom. (215) 26:1626Y1632 Single-scan electrospray FT-ICR mass spectrum of Principle of Trapping in the Orbitrap The Orbitrap is an ion trap but there are no RF or magnet fields! Moving ions are trapped around an electrode - Electrostatic attraction is compensated by centrifugal force arising from the initial tangential velocity Potential barriers created by end-electrodes confine the ions axially One can control the frequencies of oscillations (especially the axial ones) by shaping the electrodes appropriately Thus we arrive at Orbital traps Kingdon (1923) 17

18 Orbitrap - Electrostatic Field Based Mass Analyser U( r, z) = k { z r / 2 + R ln( r / )} r m R m z φ Korsunskii M.I., Basakutsa V.A. Sov. Physics-Tech. Phys. 1958; 3: Knight R.D. Appl.Phys.Lett. 1981, 38: 221. Gall L.N.,Golikov Y.K.,Aleksandrov M.L.,Pechalina Y.E.,Holin N.A. SU Pat , Ion Motion in Orbitrap Only an axial frequency does not depend on initial energy, angle, and position of ions, so it can be used for mass analysis The axial oscillation frequency follows the formula ω = k m / z 18

19 Ions of Different in Orbitrap Analytical Chemistry Large ion capacity stacking the rings Fourier transform needed to obtain individual frequencies of ions of different FTICR, the use of ion trapping in precisely defined electrode structures from the radiofrequency ion trap, pulsed injection and the use of electrostatic fields from the TOF analyzers. Altogether, these features resulted in a powerful and unique combination of analytical features. At the same time, they allowed one to address some of the major limitations of the older relatives, such as necessity for a superconducting magnet in FTICR, severe limitations on space charge in the radiofrequency ion trap, or on dynamic range of detection in TOF analyzers. HOW DOES IT WORK? The Orbitrap mass analyzer consists essentially of three electrodes as shown in Figure 1. The cut-outs represent both How Big Is the Orbitrap? Figure 1. Cut-outs of a standard (top) and a high-field (bottom) Orbitrap analyzer. Reprinted with permission from Thermo Fisher Scientific. Copyright 212 Thermo Fisher Scientific. the standard trap as introduced commercially in 25 and the 3,4 Fourier-transformed into th way as in FTICR and then c HISTORY OF THE TEC The roots of the Orbitrap an when the principle of orbital by placing a charged wire in can. The ions formed by disc toward the wire but missed tangential velocity, starting prolonged periods of time. Experiments performed w subsequent half a century an efficiency of electrostatic trap to use this device for mass charged particle optics, new used, e.g., a quadro-logarit employed by Knight for o ions.7 Crude mass analysis w resonant excitation of trapped a detector placed near the a device was not capable of sep this attempt made it clear tha high-performance analyzer. C key areas were necessary, definition of the quadro-loga the analyzer from an extern matching the features of the These crucial issues have seminal work of Makarov.8 U central electrode was implem as a massive metal electrode machining at the limit of th electrodes followed the eq shape of the central electrode work as receiver plates for im of the trap was optimized to higher harmonics. 19 Following the first proof-o

20 Getting Ions into the Orbitrap The ideal Kingdon field has been known since 195 s, but not used in MS. Why? There is a catch how to get ions into it? Ions coming from the outside into a static electric field will zoom past, like a comet from the outer space flies through a solar system The catch: The field must not be static when ions come in! A potential barrier stopping the ions before they reach an electrode can be created by lowering the central electrode voltage while ions are still entering Thus we arrive at the principle of Electrodynamic Squeezing A.A. Makarov, Anal. Chem. 2, 72: A.A. Makarov, US Pat. 5,886,346, A.A. Makarov et al., US Pat. 6,872,938, 25. Curved Linear Trap (C-trap) for Fast Injection Gate Deflector Push Trap Pull Lenses Orbitrap Ions are stored and cooled in the RF-only C-trap After trapping the RF is ramped down and DC voltages are applied to the rods, creating a field across the trap that ejects along lines converging to the pole of curvature (which coincides with the orbitrap entrance). As ions enter the orbitrap, they are picked up and squeezed by its electric field As the result, ions stay concentrated (within 1 mm 3 ) only for a very short time, so space charge effects do not have time to develop Now we can interface the orbitrap to whatever we want! A.A. Makarov et al., US Pat. 6,872,938, 25. A. Kholomeev et al., WO5/124821, 25. 2

21 Comparison of Resolving Power as a function of mass for Orbitrap and ICR Dependence of resolving power on for the following analyzers (all data are shown for a.76 s scan): (i) standard trap (magnitude mode, 3.5 kv on central electrode), (ii) compact high-field trap (eft, 3.5 kv on central electrode), (iii) FTICR (magnitude mode, 15 T), (iv) FTICR (absorption mode, 15 T). Anal. Chem. 213, 85, Hybrid Orbitrap Elite 21

22 Hybrid Orbitrap Elite Hybrid Orbitrap Fusion 22

23 ControlB3a #487 RT: AV: 1 NL: 7.16E3 T: ITMS + c NSI d Full ms @cid3. [ ] ControlB3a #4871 RT: AV: 1 NL: 4.17E3 T: ITMS + c NSI d Full ms @cid3. [ ] ControlB3a #4872 RT: AV: 1 NL: 3.27E3 T: ITMS + c NSI d Full ms @cid3. [2.-79.] ControlB3a #4873 RT: AV: 1 NL: 1.54E3 T: ITMS + c NSI d Full ms @cid3. [ ] ControlB3a #4873 RT: AV: 1 NL: 1.54E3 T: ITMS + c NSI d Full ms @cid3. [ ] ControlB3a #4869 RT: AV: 1 NL: 7.39E6 T: FTMS + p NSI Full ms [ ] Highly Parallel Data Acquisition Parallel Detection in Orbitrap and Linear Ion Trap RT: MS/MS of Sc an # 487 RT: High resolution Full scan # 4869 Relative Abundance Relative Abundance RT: MS/MS of Sc an # 4871 RT: MS/MS of Sc an # 4872 Relative Abundance RT: 41.6 MS/MS of Sc an # 4874 RT: MS/MS of Sc an # 4873 Total cycle is 2.4 seconds 1 High resolution scan 5 ion trap MS/MS in parallel 23

24 The One Hour Yeast Proteome* S Alexander S. Hebert **, Alicia L. Richards **, Derek J. Bailey, Arne Ulbrich, Emma E. Coughlin, Michael S. Westphall, and Joshua J. Coon We describe the comprehensive analysis of the yeast proteome in just over one hour of optimized analysis. We achieve this expedited proteome characterization with improved sample preparation, chromatographic separations, and by using a new Orbitrap hybrid mass spectrometer equipped with a mass filter, a collision cell, a highfield Orbitrap analyzer, and, finally, a dual cell linear ion trap analyzer (Q-OT-qIT, Orbitrap Fusion). This system offers high MS 2 acquisition speed of 2 Hz and detects up to 19 peptide sequences within a single second of operation. Over a 1.3 h chromatographic method, the Q-OTqIT hybrid collected an average of 13,447 MS 1 and 8,46 MS 2 scans (per run) to produce 43,4 (x ) peptide spectral matches and 34,255 (x ) peptides with unique amino acid sequences (1% false discovery rate (FDR)). On average, each one hour analysis achieved detection of 3,977 proteins (1% FDR). We conclude that further improvements in mass spectrometer scan rate could render comprehensive analysis of the human proteome within a few hours. Molecular & Cellular Proteomics 13: 1.174/ mcp.m , , 214. pression levels of each yeast gene using either GFP or TAP tags (9). This seminal work established that 45 proteins are expressed during log-phase yeast growth. Subsequent mass spectrometry-based studies have confirmed this early estimate (9 12). With this knowledge, we hereby define comprehensive proteome analysis as an experiment that detects 9% of the expressed proteome ( 4 proteins for yeast). Note others have used the term nearly complete for this purpose; we posit that comprehensive has identical meaning (i.e. including many, most, or all things) (13). Initial MS-based proteomic analyses of yeast, each identifying up to a few hundred proteins, were conducted using a variety of separation and MS technologies (14 16). Yates and co-workers reported the first large-scale yeast proteome study in 21 with the identification of 1483 proteins following 68 h of mass spectral analysis, i.e..4 proteins were identified per minute (17). Their method two dimensional chromatography coupled with tandem mass spectrometry has provided a template for large-scale protein analysis for the past decade (18 2). By incorporating an offline first dimension of separation with more extensive fractionation (8 versus 15) Gygi et al. expanded on this work in 23 (21). That January 1, 214 Molecular & Cellular Proteomics, 13, FIG. 2. Overview of Q-OT-qIT scan cycle. At a retention time of min scan #59,211, an MS 1, was acquired and presented several spectral features for MS 2 analysis. Triangles indicate the 22 precursors that were selected for subsequent MS 2 sampling all of which were acquired within 1 s of scan #59, of these 22 MS 2 spectra were subsequently mapped to sequence. TABLE I Summary of identification results for the quintuplicate one hour yeast proteome experiments using the Q-OT-qIT mass spectrometer. Note SGD stems from the Saccharomyces Genome Database ( Experiment PSMs Peptides Proteins SGD verified SGD un-characterized SGD dubious 1 43,423 34, ,622 34, ,339 33, ,326 34, ,343 34, Total 216,256 47, January 1, 214 Molecular & Cellular Proteomics, 13,

25 Rate of protein identifications as a function of mass spectrometer scan rate for selected large-scale yeast proteo me analyses over the past decade. Each data point is annotated with the year, corresponding author, type of MS system used, and reference number. January 1, 214 Molecular & Cellular Proteomics, 13,