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Transcript of Mass Spectrometry - Instruments - public.iastate.eduduahn/teaching/Neobiomaterials and... · Tandem...
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Mass Spectrometry - Instruments
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Genomic and Proteomic Research
• Genomic research: – Research on genomes.
– Defines potential contributors to cellular functions
• Proteomic Research: – Research on the comprehensive group of proteins
expressed by a given cell or tissue.
– Expressed genome defines actual contributors.
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Central tools in proteome research
• SDS‐
PAGE– 1D and 2D gel electrophoresis
• Protein sequencing– Edman degradation
– Mass Spectrometric technique (Tandemm and Maldi
• Identification techniques– Immunologic technique (Western blotting)
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Western blotting
• Identifies a protein based on pattern of antibody recognition.
• Presumptive and require the availability of a suitable antibody
• The confidence of the identification is limited by problems with the specificity of the
antibody
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Tandem Mass‐Spectrometry
• Cut bands of interest directly from the gel, digest, analyze and identify
• Advantages: – High sensitivity: femtomole level
– Rapid speed of analysis– Large amounts of information generated in each
experiment
– Ability to characterize post‐transitional modifications
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Mass Spectrometer Schematic
Inlet Ion Source
MassFilter Detector Data
System
High Vacuum System Turbo pumpsDiffusion pumpsRough pumpsRotary pumps
Sample PlateTargetHPLCGCSolid probe
MALDIESIIonSprayFABEI/CI
TOFQuadrupoleIon TrapMag. SectorFTMS
Microch plateElectron Mult.Hybrid Detec.
PC’sUNIXMac
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HPLC/MSD Unit
11/15/2010 Iowa State University - Dong Ahn 7
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LC/ESI‐Ion Trap MSD
11/15/2010 Iowa State University - Dong Ahn 8
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A simple definition of a Mass Spectrometer
• A Mass Spectrometer is an analytical instrument that can separate charged molecules according to their
mass–to–charge ratio.
• The mass spectrometer can answer the questions
– “what is in the sample”
(qualitative
structural information)
– “how much is present”
(quantitative
determination) for a very wide range of samples at high sensitivity
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10
MS Principles
• Different elements can be uniquely identified by their mass
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MS Principles
• Different compounds can be uniquely identified by their mass
CH3 CH2 OH
NOH
HO
-CH2 -
-CH2 CH-NH2
COOHHO
HO
Butorphanol L-dopa Ethanol
MW = 327.1 MW = 197.2 MW = 46.1
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How are mass spectra produced ?
• Ions are produced in the source and are transferred into the mass analyser
• They are separated according to their mass/charge ratio in the mass analyser (e.g.
Quadrupole, Ion Trap)
• Ions of the various m/z values exit the analyser and are ‘counted’
by the detector
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What is a Mass Spectrum?
• A mass spectrum is the relative abundance of ions of different m/z produced in an ion
source – A “chemical fingerprint”
• It contains – Molecular weight information (generally) – Structural Information (mostly) – Quantitative information
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What does a mass spectrum look like ?
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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
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Mass Spectrometry
• For small organic molecules the MW can be determined to within 5 ppm or 0.0005% which is
sufficiently accurate to confirm the molecular formula from mass alone
• For large biomolecules the MW can be determined within an accuracy of 0.01% (i.e. within 5 Da for a
50 kD protein)
• Recall 1 dalton = 1 atomic mass unit (1 amu)
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MS History
• 1948‐52 ‐
Time of Flight (TOF) mass analyzers introduced
• 1955 ‐
Quadrupole ion filters introduced by W. Paul, also invents the ion trap in 1983 (wins 1989 Nobel
Prize)
• 1968 ‐
Tandem mass spectrometer appears
• Mass spectrometers are now one of the MOST POWERFUL ANALYTIC TOOLS IN CHEMISTRY
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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?
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• Assigning numerical value to the intrinsic property of “mass” is based on using carbon-12, 12C, 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 12C atom has a mass of 12.0000 Da.
How is mass defined?
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Lecture 2.1 20
Resolution & Resolving Power
• Width of peak indicates the resolution of the MS instrument
• The better the resolution or resolving power, the better the instrument and the better the mass
accuracy
• Resolving power is defined as: M/ΔM– M is the mass number of the observed
– ΔM is the difference between two masses that can be separated
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Monoisotopic mass
Monoisotopic masscorresponds tolowest mass peak
When the isotopes are clearly resolved the monoisotopic mass
is used as it is the most accurate measurement.
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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.
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15.01500 15.01820 15.02140 15.02460 15.02780 15.03100Mass (m/z)
100
0
10
20
30
40
50
60
70
80
90
100
% In
tens
ity
ISO:CH3
15.0229
M
FWHM = ΔM
R = M/ΔM
How is mass resolution calculated?
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Advantage of using high resolution mass spectrometry
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25
MS Principles
• Find a way to “charge”
an atom or molecule (ionization)– Generate gas‐phase ions derived from an analyte (protein)
– Measure the mass‐to‐charge (m/z) of those ions
• Place charged molecule in a electromagnetic field and measure its speed or radius of curvature relative to its mass‐to‐charge ratio (mass analyzer)
• Gas‐phase ion– can be precisely controlled in electromagnetic field that contain the
ions for study
– Can be manipulated to probe the movement of the ions in the field
• Detect ions using microchannel plate or photomultiplier tube
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Mass Spec Principles
Ionizer
Sample
+_
Mass Analyzer Detector
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Different Ionization Methods
• Electron Impact (EI
‐
Hard method)
– small molecules, 1‐1000 Daltons, structure
• Fast Atom Bombardment (FAB
– Semi‐hard)
– peptides, sugars, up to 6000 Daltons• Electrospray Ionization (ESI
‐
Soft), Atmospheric Pressure
Chemical and photoionization (APPI and APCI ‐
Soft)
– peptides, proteins, up to 200,000 Daltons• Matrix Assisted Laser Desorption (MALDI‐Soft)
– peptides, proteins, DNA, up to 500 kD
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Comparison of Ionisation Techniques
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Electron Impact Ionisation
• Widely used technique when coupled to GC
• Suitable for volatile organic compounds– e.g. hydrocarbons, oils, flavours, fragrances
• Energetic process – A heated filament emits electrons which are accelerated by a
potential difference of usually 70eV into the sample chamber
• Molecule is “shattered”
into fragments (70 eV >> 5 eV bonds)
• Ionisation of the sample occurs by removal of an electron from the molecule
• Produces M+.
radical cation giving molecular weight
• Produces abundant fragment ions
• Fragments sent to mass analyzer
• Library searchable spectra
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EI Fragmentation of CH3
OH
CH3 OH CH3 OH+
CH3 OH + CH2 O=H+ + H
CH3 OH +CH3 + OH-
CHO=H+ + H+CH2 O=H+
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Electron Ionisation
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Chemical Ionisation
• Similar ionisation technique to EI except that a reagent gas is introduced into the chamber in excess of the
sample• Positive CI uses methane, isobutane or ammonia as
reagent gases• Negative CI uses methane as a reagent gas in electron
capture mode• Ionised reagent gas protonate the sample molecules
leaving a neutral reagent gas species• Softer ionisation technique• Positive mode generates ions of M + H
• Negative mode generates ions of M ‐
H• Not reproducible from lab to lab.
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Chemical Ionisation
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Chemical Ionisation
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Why You Can’t Use EI For Analyzing Proteins
• EI shatters chemical bonds
• Any given protein contains 20 different amino acids
• EI would shatter the protein not only into amino acids but also amino acid sub‐fragments and even peptides of
2,3,4…
amino acids
• Result is 10,000’s of different signals from a single protein ‐ ‐
too complex to analyze
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Soft Ionization
• Soft ionization techniques keep the molecule of interest fully intact
• Electro‐spray ionization was first conceived in 1960’s by Dole but put into practice in 1981 by Barber (FAB) in 1985
by Fenn (ESI)
• MALDI first introduced in 1988 by Hillenkamp and Karas
• Made it possible to analyze large molecules via inexpensive mass analyzers such as quadrupole, ion trap
and TOF
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Lecture 2.1 37
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Fast Atom Bombardment
• Used for large compounds with low volatility (e.g., peptides, proteins, carbohydrates)
• Solid or liquid sample is mixed with a non‐volatile matrix (e.g., glycerol, crown ethers, nitrobenzyl
alcohol)
• Immobilised matrix is bombarded with a fast beam of Argon or Xenon atoms.
• Charged sample ions are ejected from the matrix and extracted into the mass analysers
• Gives (M+H)+, (M‐H)‐
or (M+Na)+ ions
• Choosing correct matrix is difficult
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Fast Atom Bombardment Source
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Atmospheric Pressure Ionisation
• Most important and widely used LC / MS technique
• API two types – Electrospray – Atmospheric Pressure Chemical Ionisation
• > 99% new LC/MS use API source • Ionisation takes place outside vacuum region
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Atmospheric Pressure Ionisation
• API coupled to LC or CE or Nanospray • Handle wide range of flow rates • Produce Intense (M+H)+ ions • Very little fragmentation
‐
Need MS/MS for structural information
• Applicable to wide range of compounds • Sample must be in solution
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Advantages of API
• Soft ionisation (gives the molecular weight)
• Sensitive (low pg amounts routinely)
• Robust, simple, run routinely 24 hr/day
• Wide range of flow rates (nanospray to analytical)
• Wide range of applications (drugs, proteins)
• Wide range of industries
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Electrospray Ionization (ESI)
• Softest ionisation technique
• ESI is a liquid phase ionization process
• Best for polar non‐volatile compounds (proteins, peptides, nucleic acids, Pharmaceuticals, natural products)
• Can produce multiply charged ions allowing determination of high molecular weight proteins
• Ions are ejected from charged vapour droplets to gas phase producing (M+H)+ or (M‐
H)‐
ions
• Strongly affected by salts & detergents
• Not very tolerant of non‐volatile salts
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Electrospray Ionization
• Sample dissolved in polar, volatile buffer (no salts) and pumped through a stainless steel capillary (70 ‐
150 μm)
at a rate of 10‐100 μL/min• Coupled to LC at a flow range of 2‐1000 ul/min,
nanospray (10 nL/min – 2 uL/min)
• Strong voltage (3‐4 kV) applied at tip along with flow of nebulizing gas causes the sample to “nebulize”
or
aerosolize
• Ion formation occurs as the droplets in the aerosol decrease in size resulting in ions being ejected into the
gaseous phase
• ESI is a concentration dependent process
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Electrospray ion source
• The LC eluent is sprayed (nebulized) into a chamber at atmospheric pressure in the presence of a strong electrostatic field and heated drying gas.
• The heated drying gas causes the solvent in the droplets to evaporate.
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Desorption of ions from solution
++++ +
++++
++ + +
++++
++
+++
Liquid5 kv
+++++
+++
++
+++++
++++
+
++ + + + ++
+++++++
+
++ ++
+++ +
Droplet
Formation
Droplet
Evaporatio
n
Coulombic
Explosion
Ion Evaporation
Molecularion
H+
+++++
• As the droplets shrink, the charge concentration in the droplets increases.• The repulsive force between ions with like charges exceeds the cohesive
forces and ions are ejected (desorbed) into the gas phase. • Useful for analyzing large biomolecules
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Electrospray Ionization
• Can be modified to “nanospray”
system with flow < 1 mL/min
• Very sensitive technique, requires less than a picomole of material
• Strongly affected by salts & detergents• Positive ion mode measures (M + H)+
(add formic
acid to solvent)• Negative ion mode measures (M -
H)-
(add ammonia
to solvent)
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Positive or Negative Ion Mode?
• If the sample has functional groups that readily accept H+ (such as amide and amino groups found in peptides and proteins) then positive
ion
detection is used
• Acidic conditions protonate all basic side chains (Lys, Arg, His) and N-terminus -
(Acetic acid
increase ionization while trifluoroacetic acid suppresses it)
• If a sample has functional groups that readily lose a proton (such as carboxylic acids and hydroxyls as found in nucleic acids and sugars) then negative
ion detection is used
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Peptide Masses From ESI: Multiply Charged Ion
m/z = (MW + nH+)n
m/z = mass-to-charge ratio of each peak on spectrumMW = MW of parent moleculen = number of charges (integer)H+ = mass of hydrogen ion (1.008 Da)
Each peak is given by:
ESI spectrum ofHEW LysozymeMW = 14,305.14
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Peptide Mass Calculation From ESI
1431.6 = (MW + nH+)
n
Charge (n) is unknown, Key is to determine MWChoose any two peaks separated by 1 charge
1301.4 = (MW + [n+1]H+)
[n+1]
2 equations with 2 unknowns - solve for n first
n = 1301.4/130.2 = 10
Substitute 10 into first equation - solve for MW
MW = 14316 - (10x1.008) = 14305.9 14,305.14
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Atmospheric Pressure Chemical Ionization (APCI)
• Used for wide range polarity of compounds
• HPLC eluent (up to 2ml/min flow rate) is vaporized at up to 600 C
• The Corona discharge needle ionizes solvent molecules
• A combination of collisions and charge transfer reactions between the solvent and the analyte results in the transfer of a proton to form either (M+H)+ or (M-H)- ions
• Compounds can be thermally degraded
• Multiply charged ions are rare
• More tolerant to salts
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APCI Ion Source• The LC eluent is sprayed
through a heated (250°C – 400°C) vaporizer at atmospheric pressure.
• The gas-phase solvent molecules are ionized by electrons discharged from a corona needle.
• The solvent ions then transfer charge to the analyte molecules through chemical reactions (chemical ionization).
• The analyte ions pass through a capillary sampling orifice into the mass analyzer.
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APCI ‐
Schematic
. . . . . ..
. . . . . ..M
S
S
SH
MSH
S
MH
SH
S
Ionization producessolvent ions
Corona DischargeNeedle
Solvent ions react with analyte moleculesto form analyte ions by charge transfer
MHMHSH
SHS
APCI +ve ion mode
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APPI Ion Source
• Vaporizer converts the LC eluent to the gas phase.
• A discharge lamp generates photons.
• The energy ionizes analyte molecules while minimizing the ionization of solvent molecules.
• The resulting ions pass through a capillary sampling orifice into the mass analyzer.
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Matrix Assisted Laser Desorption Ionisation
• Similar process to FAB
• Sample is dissolved in matrix, which absorbs light from a short pulse of laser of a specific wavelength.
• The sample becomes ionised and extracted towards the mass analysers
• Coupled to Time of Flight MS
• Not coupled to LC • High mass range achievable
• Calibrants may be external or included in sample
• Reproducibility issues
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MALDI Ionization
++
+
+
-
--
++
+
+
-
---++
Analyte
Matrix
Laser
+++
• Absorption of UV radiation by chromophoric matrix and
ionization of matrix
• Dissociation of matrix, phase change to super‐compressed gas,
charge transfer to analyte molecule
• Expansion of matrix at supersonic velocity, analyte trapped in
expanding matrix plume (explosion/”popping”)
+
+
+
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MALDI
• Unlike ESI, MALDI generates spectra that have just a singly charged ion
• Positive mode generates ions of M + H
• Negative mode generates ions of M ‐
H
• Generally more robust than ESI (tolerates salts and nonvolatile components)
• Easier to use and maintain, capable of higher throughput
• Requires 10 μL of 1 pmol/μL sample
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MALDI Sample Limits
• Phosphate buffer < 50 mM
• Ammonium bicarbonate < 30 mM
• Tris buffer < 100 mM
• Guanidine (chloride, sulfate) < 1 M
• Triton < 0.1%
• SDS < 0.01%
• Alkali metal salts < 1 M
• Glycerol < 1%
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Separate ions based on their mass-to-charge ratio (m/z)
Operate under high vacuum (keeps ions from bumping into gas molecules)
Key specifications are resolution, mass measurement accuracy, and sensitivity.
Several kinds existQuadrupole
Time-of-flight
Ion traps are most used.
Mass analyzers
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Quadrupole Mass Analyzer
• Consists of four parallel metal rods with different charges
• Uses a combination of radio frequency and DC
• voltages to operate as a mass filter.
• Lets one mass pass through at a time.
• All other ions are thrown out of their original path
• Can scan through all masses or sit at one fixed mass
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Hyperbolic Quadrupoles
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mass scanning mode
m1m3m4 m2
m3
m1
m4
m2
single mass transmission mode
m2 m2 m2 m2m3
m1
m4
m2
Quadrupoles have variable ion transmission modes
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Principle of Time of Flight Analyzer
• A uniform electromagnetic force is applied to all ions at the same time, causing them to accelerate down a flight tube.
• Lighter ions travel faster and arrive at the detector first, so the mass-to- charge ratios of the ions are determined by their arrival times.
• Time-of-flight mass analyzers have a wide mass range and can be very accurate in their mass measurements.
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Mass Spec Equation (TOF)
mz
2Vt2=
m = mass of ion L = Flight tube lengthz = charge of ion t = time of travelV = voltage
L2
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Flight time and transients/second as a function of mass*
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TOF mass calibration
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Ion Trap
• Consists of a circular ring electrode plus two end caps
that together form a chamber.
• Ions entering the chamber are “trapped”
there by
electromagnetic fields.• Scanning field can eject ions
of specific m/z • Advantages
– MS/MS/MS….. – High sensitivity full scan
MS/MS
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Ion Trap Mass Analyzer
Top View
Cut away side view
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Ion Trap Mass Aanalyzer
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Comparison of Quads and Traps
SRM: selected reaction monitoringSingle Ion Monitoring (SIM)
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Tandem Mass Spectrometry
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72
InletInlet DetectDetectMass
AnalyzeMass
AnalyzeIonizeIonize
MSMS
InletInlet FragmentFragmentMass Analyze
Mass AnalyzeIonizeIonize
MassAnalyze
MassAnalyze DetectDetect
MS1MS1 CollisionCell
CollisionCell MS2MS2
MS/MSMS/MS
MS vs. MS/MS
GCHPLCCE
Separation Identification
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73
CH3 COCH3 CH3 COCH3
Sample Inlet
Sample Inlet
CH3 +COCH3 CH3+COCH3
Ionization& Adsorption
of Excess Energy
Ionization& Adsorption
of Excess EnergyMass AnalysisMass Analysis
CH3 C+OCH3 CH3 C+OCH3
+COCH3+COCH3
+CH3+CH3
+COH+COH
Fragmentation(Dissociation)Fragmentation(Dissociation)
DetectionDetection
Mass Spectrometry
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Mass Spectrometry
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Collision‐Induced Dissociation
CID (collosion‐induced) or CAD (chemically activated)
Generate
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Tandem Mass Spectrometry
• Purpose is to fragment ions from parent ion to provide structural information
about a molecule
• Allows separation and identification of compounds in complex mixtures
• Uses two or more mass analyzers/filters separated by a collision cell filled with Argon or
Xenon
• Collision cell is where selected ions are sent for further fragmentation
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77
Ion source MS-2MS-1
Mixture of ions
Single ion
Fragments
What is Tandem MS?
• Uses 2 (or more) mass analyzers in a single instrument
– One purifies the analyte ion from a mixture using a magnetic field.
– The other analyzes fragments of the analyte ion for identification and quantification.
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78
Applications of Tandem MS
• Biotechnology & Pharmaceutical– To determine chemical structure of drugs and drug
metabolites.– Detection/quantification of impurities, drugs and their
metabolites in biological fluids and tissues.– High through‐put drug screening– Analysis of liquid mixtures– Fingerprinting
• Nutraceuticals/herbal drugs/tracing source of natural products or drugs
• Clinical testing & Toxicology– Inborn errors of metabolism, cancer, diabetes, various
poisons, drugs of abuse, etc.
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Tandem in Space
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80
Tandem in Space MS
Triple Quatrupole
Hybrid InstrumentsESI‐QTOF
Electrospray ionization source + quadrupole mass filter + time‐of‐flight mass analyzer
MALDI‐QTOFMatrix‐assisted laser desorption ionization + quadrupole + time‐of‐flight mass analyzer
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Ion‐Source CID with a Single and a Triple Quadrupole MS
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Tandem Mass Spectrometer
TOF
NANOSPRAY TIP
IONSOURCE
HEXAPOLECOLLISIONCELL
HEXAPOLE
HEXAPOLE
QUADRUPOLE
MCPDETECTOR
REFLECTRONSKIMMER
PUSHER
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Tandem MS
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What is MS/MS?
MS/MS+
+
+ +
+
1 peptide selected for
MS/MS
The masses of all the pieces give an MS/MS spectrum
Peptidemixture
Have only masses to start
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Interpretation of an MSMS spectrum to derive structural information is analogous to solving a
puzzle
+
+
+ +
+
Use the fragment ion masses as specific pieces of the puzzle to help piece the intact molecule back together
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MS Detectors
• Early detectors used photographic film• Today’s detectors (ion channel and electron
multipliers) produce electronic signals via 2o electronic emission when struck by an ion
• Timing mechanisms integrate these signals with scanning voltages to allow the instrument to report which m/z has struck the detector
• Need constant and regular calibration
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Mass Detectors
Electron Multiplier (Dynode)
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+e-
primary ion
e-
e- e-L
D
-1000V
-100V
L >> D
Ions are detected with a microchannel plate
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MS‐MS Scan Modes
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Product ion scans
• There are two types of product ion scans:
• Full Scan
Product ion are used for qualitative applications to obtain structural information.
• Selected Reaction Monitoring Product ion scans are used for Quantitative target analysis
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What are product ion scans?
• Product ion scans are also know as daughter ion scans
• Q1 is set to allow only the transmission of one m/z
• The parent ion collides with Argon gas in Q2 to create fragment or product ions
• Product ions are scanned through Q3
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What are precursor ion scans ?
• Precursor ion scans are also known as parent ion scans
• Q3 is set to allow only a fragment ion of one m/z to pass
• Q1 is scanned • The precursor ions collide with Argon gas in
Q2 to create fragment or product ions • Only those compounds which give that
specific fragment ion are detected
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Precursor ion scans
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What are neutral loss scans ?
• Both Q1 and Q3 are scanned together • Q3 is offset by the neutral loss under
investigation
• The precursor ions collide with Argon gas in Q2 to create fragment ions
• Only those compounds which give a fragment having that specific loss are detected
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Neutral loss scans
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Selectivity of Selected Reaction monitoring (SRM)
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Selected Reaction monitoring (SRM) Product Ion Scan
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Single Ion Monitoring (SIM)
• Single (or Selected) Ion Monitoring (SIM) is used as a quantitative scan whereby the molecular ion of the
analyte is monitored in a narrow amu window.
• E.g. Orphenadrine may be monitored at 269.9 +/– 0.3 amu (269.6 to 270.2)
• Other analytes or an internal standard may be monitored in sequential scans.
• SIM gives more sensitivity and better selectivity than monitoring Orphenadrine in full scan MS.
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SIM of Orphenadrine
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Protein Sequencing
"Bottom‐Up" Sequencing‐
(most common) a. Cleave protein into peptides.b. Send peptides into MS for sequencing
"Top‐Down" Sequencing‐
(difficult but fast) a. Send intact protein into mass spec.b. Fragment & sequence
Why peptides instead of proteins?1. Increased stability2. Better solubility3. Greater sensitivity4. Easier to sequence if < 20 amino acids5. Fewer (usually <1) translational modifications/peptide5. Cheaper instrumentation (proteins require an FTICR for sequencing)
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Breaking Proteins into Peptides
peptides
MPSER……
GTDIMRPAKID
……
HPLCTo MS/MSMPSERGTDIMRPAKID......
protein
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MS‐MS & Proteomics
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Proteolyzed Proteins Need Separation
Cleaved proteins yield a complex peptide mixture & must be separated prior to MS.
Separation Characteristics:1. Typically reverse phase (hydrophobicity).
May need multi‐dimensional separation.2. Remove contaminants i.e. detergents, salts3. Reduce complexity but overlapping peaks OK4. Couple directly to ESI/MS
a. Elute in smallest possible volumeb. Peak width of 10‐60 s
Ex: μscale‐
HPLC, capillary electrophoresis, microfluidic chips
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Amino Acid Sequencing and Protein Identification
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Breaking Protein into Peptides and Peptides into Fragment Ions
• Proteases, e.g. trypsin, break protein into peptides.• A Tandem Mass Spectrometer further breaks the
peptides down into fragment ions
and measures the mass of each piece.
• Mass Spectrometer accelerates the fragmented ions; heavier ions accelerate slower than lighter ones.
• Mass Spectrometer measure mass/charge ratio of an ion.
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Peptide Fragmentation by MS
• Peptides tend to fragment along the backbone.
• Fragments can also loose neutral chemical groups like NH3
and H2
O.
H...-HN-CH-CO . . . NH-CH-CO-NH-CH-CO-…OH
Ri-1 Ri Ri+1
H+
Prefix Fragment Suffix Fragment
Collision Induced Dissociation
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Peptide Fragmentation
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CID fragmentation
b‐ion production
(Michael Kinter and Nicholas E. Sherman, 2000 “Protein sequencing and identification using tandem mass spectrometry”,Wiley, New York)
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CIDCID fragmentationfragmentation
yy‐‐ionion productionproduction
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Peptide sequencing by MS/MSPeptide sequencing by MS/MS
(Standing 2003 Curr. Opin. Struct. Biol. 13, 595-601)
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Protein Identification by Tandem Mass Spectrometry
SSeeqquueennccee
S#: 1708 RT: 54.47 AV: 1 NL: 5.27E6T: + c d Full ms2 638.00 [ 165.00 - 1925.00]
200 400 600 800 1000 1200 1400 1600 1800 2000m/z
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Rel
ativ
e A
bund
ance
850.3
687.3
588.1
851.4425.0
949.4
326.0524.9
589.2
1048.6397.1226.91049.6489.1
629.0
MS/MS instrumentMS/MS instrument
Database search•Sequestde Novo interpretation•Sherenga
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DATABASE SEARCH
Police OfficerHeight: 5’7”
Weight: 160 lbs
Gender: male
Age: 35‐40
Fingerprints
Mass SpectrometristApprox. molecular weight: 30,000
Origin: bovine liver
Peptide mass list from MS analysis:
975.4832, 1112.5368, 632.3147,
803.4134, 764.3892
DATABASE OFKNOWN FELONS
PEPTIDE MASS DATABASEOF KNOWNPROTEINS
search search
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Sequence Tags from Peptide Fragmentation by MS/MS
•
peptide molecular weight (MW)•
partial sequence (region 2)
•
molecular wt before partial sequence (region 1)•
molecular wts after partial sequence (region 3)
A V I/L T
Peptide measured molecular wt = 1927.2
1108.13Partial Sequence- A-V-I/L-T-381.1
region 1 region 2 region 3
One sequence tag includes four components:
1546.11