Introduction to Organic Mass Spectrometry sep2007

Introduction to Organic Mass Spectrometry : Introduction to Organic Mass Spectrometry Jonathan A. Karty, Ph.D. September 10-12, 2007


The Wonderful World of Mass Spectrometry : The Wonderful World of Mass Spectrometry Mass Spectrometry arises at the union of chemistry and physics Most mass spectrometers started out life as physics apparati These presentations are meant only as the briefest introduction to mass spectrometry Consider registering for C612 in the spring


Why Mass Spectrometry : Why Mass Spectrometry Information is composition-specific Very selective analytical technique Most other spectroscopies can describe functionality present, but not absolute formula MS is VERY sensitive MSF personnel dilute NMR samples 1:500 Sub femtomole sensitivity has been demonstrated


Three Questions : Three Questions Did I make my compound? Molecular weight is an intrinsic property of a substance Did I make anything else? Mass spectrometry is readily coupled to chromatographic techniques How much of it did I make? Response in the mass spectrometer is proportional to analyte concentration (R = α[M]) Each compound has a unique response factor


Common MS Applications : Common MS Applications Quick product identification (TLC plate) Confirmation of elemental composition Much more precise then EA Selective detector for GC/HPLC Hybrid instruments can multiply peak capacities Reaction monitoring Crude reaction mixture MS Stable isotope labeling Enantiomer ratio measurement by kinetic method


Mass Spectrometer Components : Mass Spectrometer Components Inlet Get samples into the instrument Source Ionize the molecules in a useful way Mass Analyzer Separate the various ions by m/z ratio Detector Converts ions into electronic signal or photons Data system Photographic plates to clusters of computers


Important Concepts to Remember : Important Concepts to Remember Mass spectrometers analyze gas-phase ions, not neutral molecules If your molecule cannot ionize, MS cannot help MS is not a “magic bullet” technique MS can tell you composition of an ion Connectivity of the atoms in that ion is much more challenging Although MS requires a vacuum, it cannot be performed in an information vacuum All conclusions drawn with ANY analytical technique must be validated by other analyses Deriving useful information from MS data often requires some foreknowledge of the system under investigation


Molecular Weight Calculations : Molecular Weight Calculations The molecular weight of a compound is computed by summing the masses of all atoms that comprise the compound. Morphine: C17H19NO3 = 12.011(17)+1.008(19)+14.007+15.999(3) = 285.34 Da Yet this is not the mass we observe 285.136 is observed be EI-MS


Monoisotopic vs. Average Masses : Monoisotopic vs. Average Masses Most elements have a variety of isotopes C  12C is 98.9% abundant, 13C is 1.1% abundant For C20, 80% chance 13C0, 18% chance 13C1, 2% chance 13C2 Sn has 10 naturally occurring isotopes (7 @ >5% abundance) F, P, Na, Al, Co, I, Au have only 1 natural isotope Mass spectrometers can often resolve these isotopic distributions Molecular weight is usually calculated assuming a natural distribution of isotopes Monoisotopic masses for multi-isotope species are computed using most intense isotopes of all elements For morphine, monoisotopic mass = 285.1365


C6H5Cl Mass Spectrum : C6H5Cl Mass Spectrum Monoisotopic mass = 112.00743 amu Average mass = 112.557 amu Electron has a mass of 0.00055 amu


Charge State Determination : Charge State Determination Mass spectrometrists use 2 units of mass Dalton  1 Da = 1 amu (1/12 of a 12C atom) Thompson  1 Th = 1 Da/z (z is electron charge) Thompson is more correct when referring to data from a mass spectrum For a +1 ion, m/z in Th ≈ mass in Da High molecular weight ions generated by ESI and MALDI often carry more than one charge Determined by measuring spacing between adjacent isotopes (e.g. 12C and 13C) (charge = 1/spacing) 0.33 Th between isotopes, +3 charge


Charge State Examples : Charge State Examples 915.2247 915.4818 915.7363 915.9765 916.2311 916.4857 505.3506 506.3584 507.3566 1086.0433 1086.5515 1086.0444 1087.5529 1088.0460 +1 1.00 0.51 +2 0.25 +4


What is Resolution? : Resolution is the ability to separate ions of nearly equal mass/charge e.g. C6H5Cl and C6H5OF @ 112 m/z C6H5Cl = 112.00798 amu (all 12C, 35Cl, 1H) C6H5OF = 112.03244 amu (all 12C, 16O, 1H, 19F) Resolving power of 4600 required to resolve these two Two definitions Resolution = Δm / m (0.015 / 112.03 = 0.00013 or 1.3*10-4) Resolving power = m / Δm (112.03 / 0.015 = 7,468 or 7.5*10+3) High resolution, high accuracy MS can replace elemental analysis for chemical formula confirmation MAT-95 is capable of 60,000 resolving power LCT is capable of 5,000 resolving power High resolution facilitates high precision measurements Typical resolving powers for the MAT-95 in the MSF EI/CI: 4,000 - 6,000 ESI: 3,000 - 7,000 What is Resolution?


Resolving Power Example : Resolving Power Example All resolving powers are FWHM C6H5OF C6H5Cl


Mass Accuracy : Mass Accuracy Mass spectrometer accuracy often reported as a relative value ppm = parts per million (1 ppm = 0.0001%) 5 ppm @ m/z 300 = 300 * (5/106) = ±0.0015 Th 5 ppm @ m/z 3,000 = 3,000 * (5/106) = ±0.015 Th High resolving power facilitates precise mass measurements Mass accuracies for MSF instruments MAT-95: <5 ppm is standard precision (int. calib.) LCT: <50 ppm (ext. calib.), <5 ppm (int. calib.) Quadrupole (API III and GC-MS): ±0.2 Da (absolute) Biflex MALDI-TOF: depends on mass range Under 3,000 Da w/ internal calibration: 60 ppm Over 3,000 Da w/ internal calibration: 200 ppm


Formula Matching Basics : Formula Matching Basics Atomic weights are not integers (except 12C) 14N = 14.0031 amu; 11B = 11.0093 amu; 1H = 1.0078 amu 16O = 15.9949 amu; 19F = 18.9984 amu; 56Fe = 55.9349 amu Difference from integer mass is called “mass defect” or “fractional mass” Related to binding energy of the nucleus Sum of the mass defects depends on composition H, N increase mass defect Hydrogen-rich molecules have high mass defects Eicosane (C20H42)= 282.3286 O, Cl, F, Na decrease it Hydrogen deficient species have low mass defects Morphine, (C17H19NO3) = 285.1365


More Formula Matching : More Formula Matching Accurate mass measurements narrow down the possible formulae for a particular molecular weight 301 entries (150 formulae) in NIST’02 @ nominal MW 321 4 compounds within 0.0016 Da (5 ppm) of 321.1000. Mass spectrum and user info complete the picture Isotope distributions indicate/eliminate elements (e.g. Cl, Br, Cu) User-supplied info eliminates others (e.g. no F, Co, I in reaction) Suggested formula has to make chemical sense C6H28O2 is not reasonable nor is Cl3H2Co4 Isomers are not distinguished in this analysis


Inlets available at IU : Inlets available at IU Direct insertion probe Direct infusion Gas chromatograph Liquid chromatograph Source design influences inlet choice GC is not practical with MALDI LC is not compatible with CI LC and ESI are natural match


Sources : Sources


Electron Ionization (EI) : Electron Ionization (EI) Gas phase molecules are irradiated by beam of electrons Interaction between molecule and beam results in electron ejection M + e-  M+• + 2e- 70 eV electrons have de Broglie wavelength near that of chemical bonds Radical species dominate EI is a very energetic process Molecules often fragment right after ionization


EI Diagram : EI Diagram Image from http://www.noble.org/Plantbio/MS/iontech.ei.html


EI Advantages : EI Advantages Simplest source design of all Very high yield (up to 0.1% ionization) Simple, robust ionization mechanism Even noble gases are ionized by EI Fragmentation patterns can be used to identify species NIST ’05 library has over 190,000 70 eV spectra Interpretation allows functionalities to be deduced in novel compounds


EI Disadvantages : EI Disadvantages Fragmentation often makes intact molecular ion difficult to observe Analytes must be in the gas phase Not applicable to most salts Labile compounds not amenable to EI Databases are very limited NIST’05 only has 163,000 unique compounds Interpreting EI spectra is an art EI only generates positive ions


EI Mass Spectrum : EI Mass Spectrum Figure from Mass Spectrometry Principles and Applications E. De Hoffmann, J. Charette, V. Strooband, eds., ©1996


Chemical Ionization (CI) : Chemical Ionization (CI) Ion-molecule reactions are used to ionize analyte molecules An EI source operated at high pressure is used to generate reactive ions in a plasma CH4  CH5+, C2H5+, C3H7+ C4H10  C4H9+ and C3H7+ NH3  NH4+ and [NH4—(NH3)n]+ clusters Variety of other gases available to tune ionization efficiency and specificity Even electron species are often created CI less energetic than EI Less fragmentation observed


Methane Positive CI : Methane Positive CI CH4 + e-  C2H5+, CH5+, C3H7+, CH3+ Source operated at 1 torr, 120 eV electrons Source must be tightly sealed to maintain plasma Analyte is present at <0.1% concentration of methane Analyte must be in the gas phase Methane plasma can ionize a large variety of organic molecules It is the default gas in the Mass Spectrometry Facility Plasma can cause undesired reactions with analyte


Three Types of Ions by PCI : Three Types of Ions by PCI Protonation: M + C2H5+  (M+H)+ + C2H4 Molecule needs basic site (e.g. heteroatom, pi bond) Hydride abstraction: M + C2H5+  (M-H)+ + C2H6 Alkanes often exhibit this mechanism Charge exchange: M + C2H5+  M+• + C2H4 + H• Often observed with metals or if CI conditions are not maintained Mechanism can be facilitate study of ionization potentials by using multiple reagent gases For complex molecules, more than one of these mechanisms can happen Energetics of each reaction determine ratios


Electron Capture Negative Ionization (ECNI) : Electron Capture Negative Ionization (ECNI) Electrons leftover from CI often have low energy (<15 eV) These electrons can be captured by electronegative groups (e.g. F, Cl, Br) Radical anions formed (M-•) ECNI can be performed in a standard CI source ECNI is VERY selective Allows analysis of chlorinated pollutants in complex matrices Prof. Ron Hites at IU used this technique quite often in his research


Advantages of CI : Advantages of CI Lower energy ionization process increases chance of observing intact molecular ion Intact ion needed for formula confirmation Positive and negative ions can be generated with relative ease Choice of reagent gas can make CI extremely selective Range of reagent gases enable analysis of very wide array of compounds


Disadvantages of CI : Disadvantages of CI More complex source design Many more variables to manage Reagent gas choice, source pressure, etc. Plasma contaminates source quickly Multiple reactions between gas and analyte can make spectra complex Fragmentation patterns are not straightforward No NIST database for CI mass spectra


CI Example 1 : CI Example 1 Figure from Mass Spectrometry, A Textbook J. Gross, ed. © 2004


Electrospray Ionization (ESI) : Electrospray Ionization (ESI) Dilute solution of analyte (~1 mg/L) infused through a fine needle in a high electric field Highly charged, very small droplets are created As solvent evaporates, ions are ejected to lower droplet charge/area ratio (or droplet explodes) Nebulizing gas accelerates drying Free ions are directed into the vacuum chamber Ion Source Voltage depends on solvent Usually ±2500 – ±4500 V +HV makes positive ions, -HV makes negative ions High surface tension liquids need high voltage


ESI Picture : ESI Picture


ESI Source Diagram : ESI Source Diagram 3 – 4 kV 760 torr 1 torr 10-3 torr 10-6 torr 45 V 5 V


Characteristics of ESI Ions : Characteristics of ESI Ions ESI is a thermal process (1 atm in source) Little fragmentation due to ionization (cf EI) Solution-phase ions are preserved in MS e.g. organometallic salts ESI ions are generated by ion transfer (M+H)+, (M+Na)+, or (M-H)-, rarely M+• or M-• ESI often generates multitply charged ions (M+2H)2+ or (M+10H)10+ Most ions are 500-1500 m/z ESI spectrum x-axis must be mass/charge (m/z or Th, not amu or Da)


Advantages of ESI : Advantages of ESI Gentlest ionization process Greatest chance of observing molecular ion Very labile analytes can be ionized Molecule need not be volatile Proteins/peptides easily analyzed by ESI Salts can be analyzed by ESI Easily coupled with HPLC Both positive and negative ions can be generated by the same source


ESI Disadvantages : ESI Disadvantages Analyte must have an acidic or basic site Hydrocarbons and steroids not readily ionized by ESI Ag+ ionization does allow ESI of some non-polar analytes Molecule must be soluble in polar, volatile solvent ESI is less efficient that other sources Most ions don’t make it into the vacuum system ESI is very sensitive to contaminants Solvent clusters can dominate spectra Distribution of multiple charge states can make spectra of mixtures hard to interpret Polymer mass spectra Peaks from different charge states and different numbers of monomers can overlap


ESI Examples : ESI Examples C26H18O4 (M+H)+ myoglobin (M+10H)10+ (M+13H)13+


Matrix-Assisted Laser Desorption/Ionization (MALDI) : Matrix-Assisted Laser Desorption/Ionization (MALDI) Analyte is mixed with UV-absorbing matrix 1,000:1 to 100,000:1 matrix:analyte ratio Analyte does not need to absorb laser A drop of this liquid is dried on a target Analyte incorporated into matrix crystals Solvent free techniques do exist Spot is irradiated by a laser pulse Irradiated region sublimes, matrix is promoted to the excited state Charges exchange between matrix and analyte in the plume UV lasers (337 nm and 355 nm) most common Ions are accelerated toward the detector


MALDI Diagram : MALDI Diagram Image from http://www.noble.org/Plantbio/MS/iontech.maldi.html


Common MALDI Matrices : Common MALDI Matrices


MALDI Advantages : MALDI Advantages Relatively gentle ionization technique Very high MW species can be ionized Molecule need not be volatile Very easy to get femtomole sensitivity Usually 1-3 charge states, even for very high MW species Positive or negative ions from same spot


MALDI Disadvantages : MALDI Disadvantages MALDI matrix cluster ions obscure low m/z (<600) range Analyte must have very low vapor pressure Pulsed nature of source limits compatibility with many mass analyzers Coupling MALDI with chromatography is very difficult Analytes that absorb the laser can be problematic Fluorescent-labeled species Some chromophores can be used for photoionization (LDI)


MALDI Example : MALDI Example (Ubiq+H)+ (Ins+H)+ (Ubiq+2H)2+ (ACTH 7-38+H)+ (ACTH 18-37+H)+


Fast Atom Bombardment (FAB) : Fast Atom Bombardment (FAB) Analyte suspended in polar, non-volatile liquid matrix (1:1000 analyte:matrix) Glycerol, 3-nitrobenzyl alcohol Beam of high energy, high mass atoms/ions is aimed at drop Xe @ 8 keV or Cs+ @ 20 keV Very few species can be analyzed by FAB that can’t ionize by ESI


Mass Analyzers : Mass Analyzers


Time-of-Flight (TOF) : Time-of-Flight (TOF) All ions are given the same kinetic energy at the same time Excellent choice for MALDI Ions then drift through a field-free region Lower m/z ions travel faster than higher m/z ions Theoretically unlimited mass range +1 Ion > 1,000,000 Th by MALDI-TOF Reflectron allows 2 passes down same flight tube


Time-of-Flight Theory : Time-of-Flight Theory From Physics 1: ΔX= voTOF + ½aTOF2 Ions drift after they exit the source ΔX same for all ions (typically 0.5m - 2.5 m) From Physics 1: KE = ½mv2 All ions accelerated by the same electric field From Physics 2: KE = z*E = ½mv2 Thus v = [(2*E*z)/m)]½ ~19 kV in Biflex III (1 kTh ion, v ≈ 60 km/sec) ~5 kV in in LCT (1 kTh ion, v ≈ 31 km/sec) Flight time measured with sub-nsec resolution TOF α v-1 and v-1 α (m/z)½ TOF α (m/z)½


TOF Diagram : TOF Diagram Reflector Detector Linear Detector Lens Target Extraction Plate Flight Tube Entrance Reflectron 337 nm Nitrogen laser


TOF Advantages : TOF Advantages Multiplexing advantage (all ions detected at once) High mass accuracy and resolving power possible Reasonable performance for cost <5 ppm and >20,000 resolving power commercially available ($150k-$300k) High mass, low charged ions not a problem


TOF Disadvantages : TOF Disadvantages High vacuum required for resolution and accuracy (<10-7 torr) Not applicable to volatile analytes Must be recalibrated often Temperature and voltage fluctuations alter flight times Long flight tubes for high resolving power can make instruments large Adaptation to continuous sources (EI, CI, ESI) can be tricky


Double Focusing (BE sector) : Double Focusing (BE sector) High kinetic energy (5 keV) ions are separated by a homogeneous magnetic field (B-sector) Lorentz force and right-hand rule (F=q*vXB) Only one radius of curvature will make it into the detector Kinetic energies are focused by electrostatic analyzer (E-sector) Magnetic field and/or ion kinetic energy are both variable Mass spectrum is constructed by scanning the B sector or the acceleration voltage B and E sectors can be arranged in many different geometries IU-MSF has a B-E sector instrument


BE Sector Equations : BE Sector Equations r = radius of curvature E = ion kinetic energy m/z = ion mass/charge ratio B = magnetic field strength r = radius of curvature E = ion kinetic energy m/z = ion mass/charge ratio V = voltage between plates Magnetic sector is scanned for wide-range mass spectra Electric sector (ion kinetic energy) is scanned for high accuracy, narrow mass range scanned


MAT-95 XP (BE Sector) Diagram : MAT-95 XP (BE Sector) Diagram Source Detector Electrostatic Analyzer (focuses ion energies) Magnetic Analyzer (separates ions by m/z) m/z 335 m/z 345 m/z 325 m/z 336 ion with a little excess energy


BE Sector Advantages : BE Sector Advantages RP of 60,000 and sub-ppm mass accuracy commercially available Can separate nearly isobaric ions Often used for chlorinated pollutant analysis BE sector instrument helped discover THG Molecular formula of unknown substance in a syringe determined with MAT-95 instrument BEFORE it was characterized by other techniques Gold standard for small molecule MS Often used as replacement for EA


BE Sector Disadvantages : BE Sector Disadvantages High vacuum (<10-7 torr) required Limited mass range (~1,000 or ~3,500 m/z) Instrument is very large and complex Radii of the sectors is on order of 20 cm Number of parameters to control requires highly trained operator Scanning nature of analyzer limits compatibility with rapidly changing analytes Faster scans lower mass accuracy Instrument is quite expensive ($300k-$500k)


Quadrupole Mass Filter (QMF) : Quadrupole Mass Filter (QMF) QMF has radio frequency (RF) field between 4 rods Rods can be cylindrical or hyperbolic Ion motions governed by set of Mathieu equations (2nd order differential equations) RF field has DC (few kV) and AC (several kV @ ~1-4 MHz) components A narrow range of m/z’s have stable trajectories through the quadrupole


Quadrupole Diagram : Quadrupole Diagram Movie URL: http://www.youtube.com/watch?v=8AQaFdI1Yow%20&%20mode=related%20&%20search=


Quadrupole Mass Filter 2 : Quadrupole Mass Filter 2 Ratio of DC and AC components of the RF fields determines resolution Unit resolution (peaks 0.5 Da wide) can be obtained with reasonable sensitivity Isotope patterns of highly charged species (≥ 3) cannot be resolved Peaks widths as low as 0.1 Da can be obtained with some newer instruments QMF with no DC offset acts as a focusing element passing nearly all ions Amplitude of the AC portion determines m/z passed by QMF Spectrum is created by scanning the m/z passed by the quadrupole and measuring ion current 201.0, 201.25, 201.5, 201.75, 202.0, etc.


QMF Advantages : QMF Advantages Very simple to implement Low cost (<$100k) Moderate vacuum required (~10-5 torr) Small size Many QMFs sent on spacecraft Very robust Can tune and calibrate monthly or less often Most common MS in service


QMF Disadvantages : QMF Disadvantages Limited mass range (up to m/z 4,000) Limited resolving power and mass accuracy Unit mass accuracy (+/- 0.2 Th for all ions) Unit resolution (0.5 Th wide) peak High resolving power, less sensitivity Scanning instrument limits ability to record rapidly changing inlets with wide mass ranges Quad can rapidly jump between m/z ratios, limited this problem for some analyses


Quadrupole Ion Trap (QIT) : Quadrupole Ion Trap (QIT) 2 types 3-D ion trap (take a quadrupole and wrap into a circle) 2-D trap (arrange 3 small quadrupoles to form a linear trap) Ions from source are trapped, then selectively ejected to the detector Performance is similar to QMF


Ion Trap Movie : Ion Trap Movie


Ion Trap Pros and Cons : Ion Trap Pros and Cons Very easily performs tandem mass spectrometry Price comparable to quadrupole systems Excellent sensitivity Scan time much shorter than a quadrupole Easily coupled to GC or LC Same cons as with QMF MS-MS fragments less than 30% parent mass are lost


Fourier Transform MS (FTMS) : Fourier Transform MS (FTMS) Ions placed in very strong magnetic field travel in a spiral Same magnets as MRI and NMR Frequency of oscillation is proportional to m/z ratio Vacuum <10-10 torr needed All ion m/z’s measured simultaneously Fourier transform on signal employed to determine frequencies of ion motion


FTMS Pros/Cons : FTMS Pros/Cons Highest resolving power available Dr. Clemmer’s FTMS has RP >800,000 Sub-ppm mass accuracy Large polymers can be analyzed by ESI Many tandem MS experiments possible High initial cost (>$750k) High maintenance cost for magnet Slow scan times (>1 sec for high resolution) limits utility with LC or GC Very complex instrument, requires highly skilled operator


Tandem Mass Spectrometry : Tandem Mass Spectrometry By stringing mass spectrometers together, new experiments are possible Daughter ion mode Isolate an ion with one MS, fragment it, then record mass spectrum of fragments Structural analysis of a molecule Parent ion mode Scan first mass spectrometer, leave 2nd mass spectrometer locked on diagnostic fragment Identify glycopeptides by looking for ions that give rise to 204 Th fragment (GlcNac)


Tandem Mass Spectrometry 2 : Tandem Mass Spectrometry 2 Neutral loss mode Scan first and second mass analyzers with a fixed offset Metabolite identification by looking for ions that lose a diagnostic functional group Quadrupole mass filter often first stage of tandem MS instruments Tandem MS greatly increases specificity for chromatography-MS experiments


Tandem MS Instrumentation : Tandem MS Instrumentation Triple quadrupole (QQQ) Most sensitive MS for LC-MS Q-TOF Gives advantages of both analyzers Ion trap Capable of MS10 FTMS TOF-TOF


Tandem MS of Peptides : Tandem MS of Peptides Peptide ions (<3,000 Da) will readily fragment if they are warmed up by collisions or ionization Under low energy conditions (<50 eV), peptide ions tend to fragment at the amide bond Amide bond fragmentation allows relatively facile interpretation of peptide tandem mass spectra


Peptide Ion Nomenclature : Peptide Ion Nomenclature a b c x y z b1 ion a1 ion y1 ion


Bradykinin (RPPGFSPFR) Fragmentation : Bradykinin (RPPGFSPFR) Fragmentation