Mass Analyzers Ion Movement

Home , Quadrupole ion trap

Mass Analyzers

Árpád Somogyi

CCIC MSP

OSU Summer Workshop

Ion movement

• Biased metal plates (electrodes, lenses) used to move ions between ion source and analyzers

• Electrodes and physical slits used to shape and restrict ion beam

• Good sensitivity is dependent on good ion transmittance efficiency in this area

Ionization Mass Detector source analyzer

inlet all ions sorted Data ions system

1 Ion detection

• Ions can be detected efficiently w/ high amplification by accelerating them into surfaces that eject electrons

Ionization Mass Detector source analyzer

inlet all ions sorted Data ions system

Detectors

TOF

2 Ion energy

• Kinetic energy of ions defined by

E = zeV = qV = ½ mv2

E = kinetic energy m = mass v = velocity e = electronic charge (1.60217e-19 C) z = nominal charge V = accelerating voltage

Learning Check Consider two electrodes,

one at 1000 V and one at ground (0 V)



1000 V0 V

+ ion will travel with kinetic energy of ______

3 Question: Consider an ion source block and an extraction lens. How would you bias the block and lens if you want the ions to be accelerated by a) 8000 eV (appropriate for magnetic sector)

b) 5 eV (appropriate for entering a quadrupole)

c) 20,000 eV (appropriate for entering a TOF)

Notice: accelerating voltages vary with analyzer (has consequences for MS/MS) • High voltage (keV energy range) – magnet (B) – electrostatic (E) – time-of-flight (TOF)

• Low voltage (eV energy range) – quadrupole (Q) – ion trap (IT, LT, OT) – ion cyclotron resonance (ICR)

4 Mass Resolution

• Mass spectrometers separate ions with a defined resolution/resolving power

• Resolving power- the ability of a mass spectrometer to separate ions with different mass to charge (m/z) ratios.

Example of ultrahigh resolution in an FTICR

J. Throck Watson “Introduction to Mass Spectrometry” p. 103

5 Resolution defined at 10% valley

R=M/∆M

∆M

General about mass spectrometers

• Common features – Accelerated charged species (ions) interact with/can be controlled by • Electrostatic field (ESA, OT) • Magnetic field (B, ICR) • Electromagnetic (rf) fields (Q, IT, LT) – Or ions just fly (TOF)

6 For each of the following applications, choose the most appropriate mass analyzer from the following list.

orbitrap (OT) quadrupole (Q) time-of-flight (TOF) FTICR

Analyzer Purpose

______synthetic organic chemist wants exact mass of compound ______biochemist wants protein molecular weight of relatively large protein (MW 300,000) ______EPA (Environmental Protection Agency) wants confirmation of benzene in extracts from 3000 soil samples ______Petroleum chemist wants to confirm the presence of 55 unique compounds at one nominal mass/charge value in a mass spectrum

Desirable mass spectrometer characteristics

7 Desirable mass spectrometer characteristics 1) They should sort ions by m/z

2) They should have good transmission (improves sensitivity)

3) They should have appropriate resolution (helps selectivity)

4) They should have appropriate upper m/z limit

5) They should be compatible with source output (pulsed or continuous)

Mass spectrometers record m/z values

m/z values are determined by actually measuring different physical parameters

Physical parameter used as Type of analyzer basis for separation • electric sector • kinetic energy/z • magnetic sector • momentum/z • quadrupole, ion trap •m/z • time-of-flight • flight time • FT-ion cyclotron resonance • m/z (resonance frequencies)

8 Types of Mass Analyzers • Magnetic (B) and/or Electrostatic (E) (HISTORIC/OLDEST)

• Time-of-flight (TOF)

• Quadrupole (Q)

• Quadrupole Ion Trap (IT)

• Linear Ion Trap (LT)

• Orbitrap

• Fourier Transform-Ion Cyclotron Resonance (ICR)

Performance Advantages / Disadvantages / $$$

Quadrupole TOF

Quadrupole Ion trap

FTICR

Orbitrap

9 MS and MS/MS

Ionization Analysis

MS:

Collide with target to produce fragments

MS/MS:

Ionization Selection Activation Analysis

http://www.iupac.org/goldbook/T06250.pdf

10 Tandem in Space

Triple quadrupole

Collisions with gas μsec dissociation

Tandem in Time MS/MS

T1 T2 T3

Collisions with gas msec dissociation

11 Current popular MS/MS arrangements (2012) Tandem in Space QqQ Q Trap Q TOF TOF TOF LTQ-Orbi (& QExactive) Tandem in Time Ion Trap (2 or 3 D) FT-ICR (FT)

Decision factors when choosing a mass spectrometer

• S p e e e e e e e e e e e e e d • R e s o l u t i o n • Sensitivity

•Dynamic range • Co$t

12 Quadrupole TOF

Quadrupole Ion trap

FTICR

Orbitrap

Time of Flight

m/z Detector

V KE = zeV = ½mv2 m = mass V = velocity v = D/t D = distance of flight t = time of flight ½m(D/t)2 = zeV KE = kinetic energy e = charge 1/ 2   t =  m  D  2zeV 

13 How does the ion generation step in TOF influence m/z analysis? Consider MALDI

h

Matrix Target + Analyte

Analyte ion may have (1) Kinetic Energy distribution or (2) Spatial distribution

How will KE spread influence the spectrum?

Ions of same m/z

Has slightly greater KE

Effect is broad peaks

c/o Cotter

14 How will KE spread influence the spectrum?

Solution to peak broadening caused by kinetic energy spread:

Reflectron (ion mirror)

Series of ring electrodes, typically with linear voltage gradient

Time-of-Flight Reflectron • Increased resolution by compensating for KE spread from the source

http://www.jic.bbsrc.ac.uk/services/proteomics/tof.htm

15 Reflectron TOF

Mass Analyzer Reflectron (TOF) Detector Ion Source (MALDI)

x x

x x x

High resolution

KE = ½ mv2

Reflectron TOF Mass Analyzer Reflectron (TOF) Detector Ion Source (MALDI)

High resolution

KE = ½ mv2

16 http://www.abrf.org/ABRFNews/1997/June1997/jun97lennon.html

We talked about how to deal with kinetic energy spread.

How do we deal with ions formed at different locations in the source (spatial distribution)?

17 Delayed Extraction

10 KV 10 KV

+ + + + + + + + + +

7 KV

Low mass (below 40 k Da) High resolution

Continuous vs. Delayed Extraction

Continuous TOF Resolution = 700 (FWHM)

Delayed Extraction Resolution = 6000 (FWHM)

18 Recent TOF designs: improved resolution, better sensitivity and mass accuracy (Ultraflex III MALDI TOF-TOF)

3145.708 * Pepmix\0_N6\1\1SRef 6000 Intens. [a.u.] 5000 Resolution: 25,000 S/N: 46 4000

3000

2000

3177.722 1000

0 3140 3145 3150 3155 3160 3165 3170 3175 3180 3185 m/z

Typical TOF Specs

• m/z Range: unlimited u • Quantification: low - • Resolution: ~20,000 medium (Reflectron) • Positive and • Mass Accuracy: ~ 3-10 Negative Ions ppm (300-4,000 u) • Scan Speed: 106 u/s • Variations: • Vacuum: 10-7 Torr Linear, Reflectron, • Tandem: w/ quads, TOFs and/or sectors

19 Linear TOF Quad 3D Trap FT‐ICR Orbitrap Trap mass range Resolution exact m/z sensitivity all ion detection ion storage speed dynamic range quantification MS/MS types sample introduction simplicity cost/performance

Can an MS/MS instrument be constructed if the only analyzer type available is TOF?

20 TOF-TOF

http://docs.appliedbiosystems.com/pebiodocs/00106293.pdf

High-energy (keV) Collisions with Gas in a TOF-TOF

21 16O/18O-labeled DLEEGIQTLMGR

*Resolution

Medzihradszky, KF et al. Anal Chem. 2000, 72: 552-558 High (keV) collisions allow for w peptide ions and immonium ions

4 x10 328.574 6 Intens. [a.u.] 492.623 981.346 5

4 186.600 656.765 146.669

821.038 2

120.694 1 284.552 90.771 941.468 443.572 612.695 721.026 776.938 0 200 400 600 800 1000 m/z

MALDI TOF-TOF fragmentation spectrum of a sodiated polymer

O CH CH * 2 2 m O n O 3-OEB, m=1-3 (164, 44) Copolymer of 2-hydroxybenzoic acid and ethylene carbonate

22 Advantages and Disadvantages

Mass Spectrometer Advantages Disadvantages TOF-TOF high resolution, high Large size m/z fragment ions Not ideal for keV CID continuous ionization source

easier de novo $$$ peptide sequencing

dn and wn to MALDI source distinguish Ile/Leu

Analyzers Quadrupole TOF

Quadrupole Ion trap

FTICR

Orbitrap

23 Quadrupole (Q)

http://www.files.chem.vt.edu/chem-ed/ms/quadrupo.html

Quadrupole (Q) • four parallel rods or poles • fixed DC and alternating RF voltages

rf voltage +dc voltage rf voltage 180° out of phase -dc voltage • only particular m/z will be focused on the detector, all the other ions will be deflected into the rods • scan by varying the amplitude of the voltages – (AC/DC constant).

24 Quadrupole Field Animation

Positive rod

Negative rod

Negative rod Positive rod

http://www.kettering.edu/~drussell/Demos/MembraneCircle/Circle.html

negative DC offset

-DC

- positive DC offset -

+ +DC

25 Ion Motion in Quadrupoles - a qualitative understanding

• + DC, ions focused to center

• - DC, ions defocused

• +DC w/ rf, light ions respond to rf, eliminated (high mass filter)

• -DC w/ rf, light ions respond to rf, focused to center (low mass filter)

26 Quadrupole animation

http://www.youtube.com/watch?v=8AQaFdI1Yow&feature=related

http://www.youtube.com/watch?v=pjCun7QF19U

Initial kinetic energy affects ion motion in quad

27 Figure 9. The a-q stability diagram: a) The shaded area represents those areas in a-q space which correspond to stable solutions of Mathieu’s differential equation. B) The one amu bandpass mass filter: Notice that only ions of m/e m+1 fall within the stability diagram.

Miller, P., Denton, M.B., J.Chem Ed., 63:7, pg 617, 1986.

Quadrupole Typical Specs

• Quantification: good • m/z Range: 2-4000 u choice • Resolution: Unit • Positive and Negative • Mass Accuracy: ca +/- Ions 0.1 u • Variations: SingleQ, • Scan Speed: 4000 u/s TripleQ, Hybrids • Vacuum: 10-4 –10-5 Torr • Low Voltages: RF ~6000 –10000 V DC ~500V-840V Source near ground

28 Linear TOF Quad 3D Trap FT‐ICR Orbitrap Trap mass range Resolution exact m/z sensitivity all ion detection ion storage speed dynamic range quantification MS/MS types sample introduction simplicity cost/performance

What MS/MS instruments can be produced from Q?

What MS/MS instruments can be produced from Q and TOF?

29 Triple Quadrupole - since 1970’s and still going strong!

Q1 Q2 Q3

S D

Attractive Features:

• Source near ground and operates at relatively high pressure

Couples well to source and to chromatography

•Multiple scan modes easy to implement

Triple Quadrupole (QQQ)

Detection System Dynode Turbo Q3 Q3 Source Q0 Q1

Q2 Q2

Heated Q1 Q0 Q00 Capillary c/o Thermo Finnigan Corp.

c/o Agilent Corp.

30 MS/MS Scan Modes

Product Ion Scan Select Dissociate Scan

Precursor Ion Scan Scan Dissociate Select

Neutral Loss Scan  ScanDissociate Scan

Selected Reaction Monitoring (SRM) SelectDissociate Select

Scan RF 300 Voltage 200 100 DC Analyte Mixture

100

200 300

Vm1 Vm2 Vm3

m/zm1 m/zm2 m/zm3 mass spectrum

31 Scan RF 300 Voltage 200 100 DC Analyte Mixture

100

200 300

Vm1 Vm2 Vm3

100 100 100300 200200 300 100300 200 300200

Scan RF 300 Voltage 200 100 DC Analyte Mixture

100

200 300

Vm1 Vm2 Vm3

100 100 100300 200200 300 100300 200 300200

32 Scan RF 300 Voltage 200 100 DC Analyte Mixture

100

200 300

Vm1 Vm2 Vm3

100 100 100300 200200 300 100300 200 300200

Select

Voltage 200 Analyte Mixture RF DC 100

200 300

Vm2

Desired Analyte m/zm2 mass spectrum

33 Modes of scanning in a Triple Quadrupole (QQQ)

Q1 q2 (gas) Q3 scan or rf only scan or select select

• Quadrupole is a mass filter • QQQ used in this tutorial to describe scan modes – Q1 and Q3 = analyzers – q2 (middle quadrupole) used for CID (dissociation) • Ways to set quadrupoles: Scan, Select & rf only • Other instruments are used: Q-tof, Q-trap, Linear Trap- Orbitrap, Trapping instruments

Quadrupole Time of Flight (Q-TOF)

http://www.waters.com/WatersDivision/waters_website/products/micromass/ms_top.asp (outdated)

34 Low-energy (eV) Collisions with Gas

Q-TOF

80 fmol BSA digest

QQQ

Shevchenko, A., et al., Rapid. Commum. Mass Spectrom., 1997, 11: 1015-1024

35 QTOF with Ion Mobility

Analyzers Quadrupole TOF

Quadrupole Ion trap

FTICR

Orbitrap

36 What is small, inexpensive and still gives great MSMS ?????

Quadrupole Ion Traps Miniature IT: Cooks, R. G. and coworkers Anal. Chem. 2002, 74, 6145-6153; 2000, 72, 3291-3297.

http://www.chem.wm.edu/dept/faculty/jcpout/faculty.html

Ion path in a trap

37 Quadrupole Ion Trap (QIT)

http://www-methods.ch.cam.ac.uk/meth/ms/theory/iontrap.html

Quadrupole Ion Trap (QIT)

• Quadrupole ion trap mass analyzer consists of three hyperbolic electrodes: the ring electrode, the entrance end cap electrode and the exit endcap electrode. • Ions enter trap through inlet focusing system and entrance endcap electrode. • An AC potential of constant frequency and variable amplitude is applied to the ring electrode to produce a 3D quadrupolar potential field within the trapping cavity which traps ions in a stable oscillating trajectory confined within the trapping cell. • The oscillating trajectory is dependent on the trapping potential and the mass-to-charge ratio of the ions. • During ion detection, the electrode system potentials are altered to produce instabilities in the ion trajectories and thus eject the ions.

38 Quadrupole Ion Trap (QIT)

3D - Quadrupole Ion Trap (Demo)

39 Activation: Low-energy (eV) Collisions with Gas

IRMPD (Infrared Multiphoton Dissoc)

Research: Micro CIT Array

Matt Blain, Sandia Cooks, Purdue

1.8 µm

2.4 µm

Top End Cap Array

Ring Electrode Array Bottom End Cap Array Collector Array

40 QIT Typical Specs

• m/z Range: 20-6000 u • Quantification: • Resolution: Unit possible, not accurate • Mass Accuracy: ca +/- • Positive and 0.1 u Negative Ions • Scan Speed: 4000 u/s • Vacuum: 10-3 Torr

Advantages and Disadvantages

Mass Spectrometer Advantages Disadvantages QIT Compact Limited storage of ions limits the dynamic range of the ion trap (space charge effect) MSn 1/3 of low mass range lost in MS/MS mode, typical operation Data dependent scanning Relatively Low E collisions inexpensive

41 Advantages and Disadvantages

Mass Spectrometer Advantages Disadvantages QIT Poor quantification Sensitive Collision energy not well-defined in CID MS/MS

Mass Accuracy

To increase mass accuracy in a Trap  LT, orbitrap, FT-ICR

RF ION TRAP ELECTRODE STRUCTURES

LCQ-Type 3D LTQ-Type (2D) Quadrupole Trap Linear Quadrupole Trap

ASMS Fall Workshop 2006 JEPS

42 2D vs. 3D Ion Traps

Ion Transfer Tube

Skimmer

Tube Lens

Linear Trap Demo

Ion Transfer Tube

Skimmer

Tube Lens

43 Estimating Relative Ion Storage Capacity 3D Ion vs Linear (2D) Quadrupole Ion Traps

3D RF Quadrupole 2D RF Quadrupole Ion Trap Linear Ion Trap z z y

y L

x x

R3D R2D ~ Spherical Ion Cloud ~ Cylindrical Ion Cloud

ASMS Fall Workshop 2006 JEPS

Overall Performance Gains

LTQ 3D Traps Increase

•Trapping efficiency ~ 55-70% ~5% ~ 11-14x •Detection efficiency ~ 50-100% ~50% ~ 1-2x

•Trapping capacity ~ 20,000 ions ~500 ions ~ 40x

44 Motivating Factors Realized

• Increased Trapping Efficiency • Increased Trapping Capacity Which means....

• Increased Sensitivity • Increased Inherent Dynamic Range • Increased S/N for full Scan MS • Practical MSn •Faster Scan Times - no μscans (only one)

How are 3-D traps and linear ion traps used in MS/MS

Stand alone 3-D traps LTQ Front or back end of tandem-in-space LT-TOF LT-FT, LT-Orbitrap, QTrap

45 LIT and QTrap; Different ways of using Linear Traps

Linear Ion Trap ~ 100% of ions trapped are detected due to radial ejection

Skimmer

Axial ejection allows for hybridization – without compromise (FT)!

Hybrid Quadrupole Trap Majority of trapped ions cannot be scanned out ~ 15% detected*

Axial ejection depends on fringe fields generated by grid – this grid compromises triple quadrupole performance

*Hager, J., RCM., 2003, 17, 1389

9 Protein Mixture

9 Protein Mixture Peptide Identification

80 73

70 61 Number of PeptidesNumber of 60

50 42

35 Deca XP plus 40 31 LTQ 30 21 24

20 12

0 10min 20min 30min 60min Gradient (min)

46 Activation:

CID Low-energy (eV) Collisions with Gas

IRMPD (Infrared Multiphoton Dissoc)

ETD (electron transfer dissociation)

Linear TOF Quad 3D Trap FT‐ICR Orbitrap Trap mass range Resolution exact m/z sensitivity all ion detection ion storage speed dynamic range quantification MS/MS types sample introduction simplicity cost/performance

47 Analyzers Quadrupole TOF

Quadrupole Ion trap

FTICR

Orbitrap

For a charge q moving with a velocity of v in a magnetic field B there exists a force (F) which is perpendicular to the plane determined by v and B.

48 Analyzers based on magnetic fields: ICR

Magnetic forces move ions in a circular path

demo http://www.casetechnology.com/implanter/magnet.html

Cyclotron motion of an ion in a magnetic field (B). Note: ion motion is much more complex due to the presence of electrostatic field (magnetron/cyclotron motion, see below)

49 50 a

time (ms) C9H16N5 194.1405 b c

C11H20N3 194.1657 C7H12N7 194.1154

Modified van Krevelen diagram for LDI ions

51 11+

12+ 10+

Charge state/MW determination for proteins

∆m = z ∆(m/z)

Carbons isotopes so ∆m=1 Da

Calc ∆(m/z)

52 FTICR animation http://www.youtube.com/watch?v=a5aLlm9q-Xc&NR=1

New ICR cell design by E. Nikolaev et al.

E. Nikolaev et al., Initial Characterization of a New Ultrahigh Resolution FTICR Cell with Dynamic Harmonization, JASMS, 2011, 22, 1125-1133.

E. Nikolaev and coworkers, Twelve Million Resolving Power on 4.7T FT-ICR Instrument with Dynamically Harmonized Cell – Observation of Fine Structure In Peptide Mass Spectra, JASMS, 2014, 25, 790-799.

53 Bruker 9.4 T FT-ICR Apex-Qh Tandem Mass Spectrometer

Dual source, MS only, no ion selection MALDI

ESI

QCID (eV) MS/MS

Ion selection and activation in the ICR IRMPD, SORI, ECD

HDX in the ICR cell

54 Activation: SORI CID Low-energy (eV) Collisions with Gas (off resonance) RE (resonance excitation) IRMPD (Infrared Multiphoton Dissoc) ECD (electron transfer dissociation)

Intens. YIGSR_QCID_22eV_000002.d: +MS2(595.0) x107 3.0 + MH 249.1593 595.3171 2.5 QCID 22 eV MS/MS spectra depend 2.0 on i) Charge state 1.5 302.1453 1.0 ii) Ion activation method 175.1186 560.2803 0.5 iii) Collision energy 408.1864 465.2077 90.2256 0.0 x108 YIGSR_doubly_QCID_6eV_000001.d: +MS2(298.0)

(more details in the 2+ 319.1718 1.5 [M+2H] Ion Activation QCID 6 eV Methods by Vicki Wysocki) 1.0 249.1593

0.5 y5 277.1541 432.2552 136.0756 0.0 x107 YIGSR_doubly_IRMPD_40P_0_30s_000001.d: +MS2(298.0)

2+ 298.2804 2.0 [M+2H] IRMPD 30s, 30% 1.5

1.0

249.1644

0.5

102.7325 595.3466 0.0 100 200 300 400 500 600 m/z

55 FTICR Typical Specs

• m/z Range: > 15000 u • Quantification: • Resolution: High, 106 possible, not accurate • Mass Accuracy: 100 • Positive and ppb Negative Ions • Scan Speed: slow • Vacuum: 10-9-10-11Torr

Advantages and Disadvantages

Mass Spectrometer Advantages Disadvantages FTICR Highest recorded Limited Dynamic mass resolution of all Range mass spectrometers MSn Low E collisions Non-destructive ion High vacuum detection Low presure (difficult GC/LC coupling) Accurate mass Big size measurement Powerful capabilities Not a high for ion chemistry throughput technique experiments (ion- molecule rxns)

56 Linear TOF Quad 3D Trap FT‐ICR Orbitrap Trap

mass range Resolution exact m/z sensitivity all ion detection ion storage speed dynamic range quantification MS/MS types sample introduction simplicity cost/performance

Analyzers Quadrupole TOF

Quadrupole Ion trap

FTICR

Orbitrap

57 Orbitrap Readings

Pictured: August 2009 cover of J. Am. Soc. Mass Spectrom.

A New Kind of FTMS: The Orbitrap

58 How does it trap ions? • Quadro-electrostatic field (Orbital trapping of ions) – Electrostatic field with potential distribution • Field is the sum of the quadrupole field of the ion trap and the logarithmic field of the cylindrical capacitor (center electrode)

2 2 2 U(r/z) = k/2(z –r/2) + k/2(Rm) ln[r/Rm] + C

– Electrodynamic squeezing • Ions entering with a tangential velocity (acceleration voltage) are pulled into orbit around center electrode due to a voltage drop on the center electrode

Orbitrap

59 LTQ Orbitrap™ Hybrid MS

Finnigan LTQ™ Linear Ion Trap

API Ion source Linear Ion Trap C-Trap

Orbitrap Differential pumping

Differential pumping

LTQ Orbitrap Hybrid MS System Integration

Finnigan LTQ™ Linear Ion Trap

Gas <1 mtorr V

-2 k V

Central Electrode Voltage

-3.5 k V

60 Lord of the ion rings: Retainment of the rings

Image current detection on split outer electrodes

k   m / z

1. Frequencies are determined using a Fourier Transformation 2. For higher sensitivity AND resolution, transients should not decay too fast

Ultra-high vacuum Ultra-high precision http://apps.thermoscientific.com/media/SID/LSMS/Video/webinar/orbitrap_elite/animation/ http://www.youtube.com/watch?v=KjUQYuy3msA

Ion Motion in the Orbitrap

Simulation of ion trajectory with SIMION

Characteristic frequencies 2  z  Rm      1 – Frequency of rotation ωφ 2  R 

2  Rm  r   z    2 – Frequency of radial oscillations ωr  R  k – Frequency of axial oscillations ωz   z m / q

61 Orbitrap --Resolving Power

Insulin: m/z = 5733 +5 Charge state: +5, +4 and +3

+3 +5

m/m = 70,000 +4

1,200 1,400 1,600 1,800 2,000 m/z +4 1,147 1,148 1,149 m/z m/m = 45,000 +3

m/m = 40,000

1,434 1,435 1,436 m/z R. Noll, H. Li, 2002 1,911 1,912 1,913 1,914 m/z

Orbitrap LTQ Velos: Analysis time High resolution acquisition R = 7,500

R = 15,000 R = Time R = 30,000 R = 60,000 R = 100,000

Low resolution acquisition R = unit Figure adapted from Olsen J V et al. Mol Cell Proteomics 2009;8:2759-2769

62 http://fscimage.thermoscientific.com/images/D13092~.pdf

63 translation inhibitor endoribonuclease [Clostridium difficile BI1] High Resolution Fragments Charge: +3, Monoisotopic m/z: 744.71710 Da (-1.83 ppm), MH+: 2232.13675 Da, RT: 67.42 min,

High Resolution Fragments

Fragment Errors (ppm, partial list)

64 Manual http://sjsupport.thermofinnigan.com/techpubs/manuals/LTQ-Orbitrap- Velos_Start_2_6_0.pdf

Video

http://www.youtube.com/watch?v=-u1keatKtMI

Application/Optimization

65 Instrument Performance for Proteomic Applications

Han et al., Curr. Opin. Chem. Biol. 2008; 12(5):483-490.

Learning Check Draw the appearance of the mass spectrum in which both singly and doubly charged YGGFLR (molecular weight 711.3782) are produced and analyzed with a quadrupole, TOF and orbitrap (Hint: peaks widths important)

66 712 in Quad, TOF, ICR

TOF

QUAD Intensity

m/z Intensity ICR

m/z Intensity

m/z

General Conclusions • Many instruments are complementary • More Activation methods, the better • Assess your needs • Assess your budget • @ Research level, may want to build your own

67 Suggested Reading List

GENERAL MS AND MS/MS

Kinter, M. and Sherman, N. E., Protein Sequencing and Identification Using Tandem Mass Spectrometry, Wiley and Sons, New York, NY, 2000.

De Hoffmann E., Mass Spectrometry – Principles and Applications (Second Edition), Wiley and Sons, New York, NY, 2002.

Busch, K.L., et al., Mass spectrometry/ mass spectrometry: techniques and applications of tandem mass spectrometry, VCH Publishing, New York, NY, 1988.

McLafferty, F.W. (Ed) Tandem Mass Spectrometry, Wiley and Sons, New York, NY, 1983.

McLafferty, F.W. and Turecek, F. Interpretation of Mass Spectra, University Science Books, New York, NY, 1993.

Siuzdak, G. Mass Spectrometry for Biotechnology, Academic Press, San Diego, CA, 1996.

Gygi, S.P. and Aebersold, R., Curr. Opin. Chem. Biol., 4 (5): 489, 2000.

Roepstorff, P., Curr. Opin. Biotech., 8: 6, 1997.

De Hoffmann, JMS, 31: 129, 1996.

Mann, M. et al., Annu. Rev. Biochem., 70: 437, 2001.

McLuckey, S and Wells, J.M., Chem. Rev., 101: 571, 2001.