all about mass spectrometry.

1. Mass Spectrometry Mussarat Jabeen

3. Smallest scale

4. Destructive technique

5. Useful for identification of speciesAccording to the IUPAC (International Union of Pure and Applied Chemistry), it is the branch of science dealing with all aspects of mass spectroscopes and results obtained with these instruments.

6. Mass Spectrometry Contents Brief History of Mass Spectrometry Nobel prize pioneers Mass spectrometer Structural analysis and Fragmentation Patterns interpretation of mass spectrum Applications of mass spectrometry

7. 1897 1919 1934 1966 Mass Spectrometry Brief History of Mass Spectrometry J.J. Thomson. Discovered electrons by cathode rays experiment. Nobel prize in 1906. Francis Aston recognized 1st mass spectrometer and measure z/m of ionic compounds. First double focusing magnetic analyzer was invented by Johnson and Neil. Munson and Field described chemical ionization.

8. 1968 1975 1985 1989 Mass Spectrometry Electrospray Ionization was invented by Dole, Mack and friends. Atmospheric Pressure Chemical Ionization (APCI) was developed by Carroll and others. F. Hillenkamp, M.Karas and co-workers describe and coin the term matrix assisted laser desorption ionization (MALDI). w. Paul discovered the ion trap technique.

9. Mass Spectrometry Nobel prize pioneers

10. Mass Spectrometry Mass spectrometer

11. Mass Spectrometry Understanding Mass Spectrometry In a mass spectrometer, the same thing is happening, except it's atoms and molecules that are being deflected, and it's electric or magnetic fields causing the deflection. It's also happening in a cabinet that can be as small as a microwave or as large as a chest freezer.

12. Mass Spectrometry Mass spectrometer is similar to a prism. In the prism, light is separated into its component wavelengths which are then detected with an optical receptor, such as visualization. Similarly, in a mass spectrometer the generated ions are separated in the mass analyzer, digitized and detected by an ion detector.

14. Ionization source

15. Mass analyzer

18. Mass Spectrometry Direct infusion or injection sample introduction technique Frequently used due to high efficiently Used in coupling techniques like GC-MS and HPLC-MS

20. Deprotonation

21. Cationization

22. Transfer of a charged molecule to the gas phase

23. Electron ejection

25. Mass Spectrometry Deprotonation Give net negative charge of 1- by removal of one proton Used for acidic species like phenols, carboxylic acid, sulfonic acid etc. Used in MALDI, APCI and ESI

26. Mass Spectrometry Cationization produces a charged complex by non-covalently adding a positively charged ion like alkali metal ion or ammonium ion to a neutral molecule. Used for Carbohydrates Used in MALDI, APCI and ESI

27. Mass Spectrometry Transfer of a charged molecule to the gas phase Cation from solution to gas Used in MALDI or ESI

28. Mass Spectrometry Electron ejection Electron is ejected to give positive ion Usually for non-polar compounds with low molecular weights like anthracene.

29. Mass Spectrometry Electron capture a net negative charge of 1- is achieved with the absorption or capture of an electron. Used for halogenated compounds

31. Nanoelectrospray Ionization (NanoESI)

32. Atmospheric Pressure Chemical Ionization (APCI)

33. Atmospheric pressure photoionization (APPI)

34. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)

35. Fast Atom Bombardment (FAB)

36. Electron Ionization (EI)

37. Chemical Ionization (CI)

39. Mass Spectrometry Electrospray Ionization (ESI) The sample solution is sprayed from a region of the strong electric field at the tip of a metal nozzle maintained at a potential of anywhere from 700 V to 5000 V. The nozzle (or needle) to which the potential is applied serves to disperse the solution into a fine spray of charged droplets. Either dry gas, heat, or both are applied to the droplets at atmospheric pressure thus causing the solvent to evaporate from each droplet For example peptides, proteins, carbohydrates, small oligonucleotides, synthetic polymers, and lipids

41. very low flow rates

43. Mass Spectrometry Atmospheric pressure photoionization (APPI) it generates ions directly from solution with relatively low background and is capable of analyzing relatively nonpolar compounds. APPI vaporized sample passes through ultra-violet light. APPI is much more sensitive than ESI or APCI.

44. Mass Spectrometry Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) the analyte is first co-crystallized with a large molar excess of a matrix compound, usually a UV-absorbing weak organic acid. Irradiation of this analyte-matrix mixture by a laser results in the vaporization of the matrix, which carries the analyte with it. The matrix plays a key role in this technique. The co-crystallized sample molecules also vaporize, but without having to directly absorb energy from the laser. Molecules sensitive to the laser light are therefore protected from direct UV laser excitation.

45. Mass Spectrometry Fast Atom Bombardment (FAB) Immobilized 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 analyzers Used for large compounds with low volatility (eg peptides, proteins, carbohydrates) Solid or liquid sample is mixed with a non-volatile matrix (eg glycerol, crown ethers, nitrobenzyl alcohol)

51. Quadrupole Ion Trap

52. Linear Ion Trap

53. Double-Focusing Magnetic Sector

54. Quadrupole Time-of-Flight Tandem MS

56. Mass Spectrometry Quadrupole Ion Trap The quadrupole ion trap typically consists of a ring electrode and two hyperbolic endcap electrodes. The motion of the ions induced by the electric field on these electrodes allows ions to be trapped or ejected from the ion trap. In the normal mode, the radio frequency is scanned to resonantly excite and therefore eject ions through small holes in the endcap to a detector. As the RF is scanned to higher frequencies, higher m/z ions are excited, ejected, and detected.

57. Mass Spectrometry Linear Ion Trap The linear ion trap differs from the 3D ion trap as it confines ions along the axis of a quadrupole mass analyzer using a two-dimensional (2D) radio frequency (RF) field with potentials applied to end electrodes. The primary advantage to the linear trap over the 3D trap is the larger analyzer volume lends itself to a greater dynamic ranges and an improved range of quantitative analysis.

58. Mass Spectrometry Double-Focusing Magnetic Sector the ions are accelerated into a magnetic field using an electric field. A charged particle traveling through a magnetic field will travel in a circular motion with a radius that depends on the speed of the ion, the magnetic field strength, and the ion’s m/z. A mass spectrum is obtained by scanning the magnetic field and monitoring ions as they strike a fixed point detector.

59. Mass Spectrometry Quadrupole Time-of-Flight Tandem MS Time-of-flight analysis is based on accelerating a group of ions to a detector where all of the ions are given the same amount of energy through an accelerating potential. Because the ions have the same energy, but a different mass, the lighter ions reach the detector first because of their greater velocity, while the heavier ions take longer due to their heavier masses and lower velocity. Hence, the analyzer is called time-of-flight because the mass is determined from the ions’ time of arrival. Mass, charge, and kinetic energy of the ion all play a part in the arrival time at the detector.

60. Mass Spectrometry Quadrupole Time-of-Flight MS Quadrupole-TOF mass analyzers are typically coupled to electrospray ionization sources and more recently they have been successfully coupled to MALDI. It has high efficiency, sensitivity, and accuracy as compared to Quadrupole and TOF analyzer.

61. Mass Spectrometry Detectors used in mass spectrometer Faraday Cup Photomultiplier Conversion Dynode Array Detector Charge (or Inductive) Detector Electron Multiplier

62. Mass Spectrometry Faraday Cup A Faraday cup involves an ion striking the dynode (BeO, GaP, or CsSb) surface which causes secondary electrons to be ejected. This temporary electron emission induces a positive charge on the detector and therefore a current of electrons flowing toward the detector. not particularly sensitive offering limited amplification of signal is tolerant of relatively high pressure. – Ions are accelerated toward a grounded “collector electrode” – As ions strike the surface, electrons flow to neutralize charge, producing a small current that can be externally amplified. – Size of this current is related to # of ions in – No internal gain -> less sensitive

63. Mass Spectrometry Photomultiplier Conversion Dynode the secondary electrons strike a phosphorus screen instead of a dynode. The phosphorus screen releases photons which are detected by the photomultiplier. Photomultipliers also operate like the electron multiplier where the striking of the photon on scintillating surface results in the release of electrons that are then amplified using the cascading principle. is not as commonly Life limit is high as compared to others.

64. Mass Spectrometry Array Detector detects ions according to their different m/z, has been typically used on magnetic sector mass analyzers. The primary advantage of this approach is that, over a small mass range, scanning is not necessary and therefore sensitivity is improved.

65. Mass Spectrometry Charge (or Inductive) Detector Charge detectors simply recognize a moving charged particle (an ion) through the induction of a current on the plate as the ion moves past Detection is independent of ion size.

67. made up of a series (12 to 24) of aluminum oxide (Al2O3) dynodes

68. Used for increasing potentialIons strike the first dynode surface causing an emission of electrons. These electrons are then attracted to the next dynode held at a higher potential and therefore more secondary electrons are generated.

69. Mass spectrometer Vacuum in the Mass Spectrometer All mass spectrometers need a vacuum to allow ions to reach the detector without colliding with other gaseous molecules or atoms. If such collisions did occur, the instrument would suffer from reduced resolution and sensitivity.

71. Fragmentation peaks

72. Base peak

73. Isotopic peaks.

74. Mass spectrometer Molecular ion (Parent ion) the peak corresponding to the mol wt of the compound The peak of an ion formed from the original molecule by electron ionization, by the loss of an electron, or by addition or removal of an anion or cation and also known as parent peak, radical peak.

75. Mass spectrometer Fragmentation peaks The peaks observed by fragments of compounds. The molecular ions are energetically unstable, and some of them will break up into smaller pieces. The simplest case is that a molecular ion breaks into two parts - one of which is another positive ion, and the other is an uncharged free radical. The uncharged free radical won't produce a line on the mass spectrum. Only charged particles will be accelerated, deflected and detected by the mass spectrometer. These uncharged particles will simply get lost in the machine - eventually, they get removed by the vacuum pump.

76. Mass Spectrometry Base peak The most intense (tallest) peak in a mass spectrum, due to the most abundant ion. Not to be confused with molecular ion: base peaks are not always molecular ion and molecular ion are not always base peaks.

78. Homolytic bond cleavage

79. Heterolytic fragmentation

80. Alpha cleavage

81. Beta-cleavage

82. Inductive cleavage

83. Retro Diels-Alder Cleavage

84. McLafferty rearrangement

85. Ortho effect

86. Onimum Reaction

88. Mass Spectrometry Homolytic bond cleavage A type of ion fragmentation in which a bond is broken by the transfer of one electron from the bond to the charged atom, the other electron remaining on its starting atom. The movement of one electron is signified by a fishhook arrow. The fragmentation of a ketone is shown in the figure.

89. Mass Spectrometry Heterolytic bond cleavage type of ion fragmentation in which a bond is broken by the transfer of a pair of electrons from the bond to the charged atom The movement of 2 electrons is signified by a double-barbed arrow and also referred to as charge-induced fragmentation.

90. Mass Spectrometry Alpha cleavage Alpha cleavage occurs on α-bonds adjacent to heteroatoms (N, O, and S). Charge is stabilized by heteroatom. Occurs only once in a fragmentation (cation formed is too stable to fragment further) For example in alcohols, aliphatic ethers, aromatic ethers, cyclic compounds and aromatic ketones etc.

91. Mass Spectrometry Beta-cleavage Fission of a bond two removed from a heteroatom or functional group, producing a radical and an ion. Also written as β-cleavage. For example allylic fragmentation.

92. Mass Spectrometry Inductive cleavage If an electron pair is completely transferred towards a centre of positive charge as a result of the inductive effect, shown schematically by the use of a double-headed arrow, then the ion will fragment by inductive cleavage. The figure illustrates this for a radical cation ether.

93. Mass Spectrometry Retro Diels-Alder Cleavage A multicentered ion fragmentation which is the reverse of the classical Diels-Alder reaction employed in organic synthesis that forms a cyclic alkene by the cycloaddition of a substituted diene and a conjugated diene. In the retro reaction, a cyclic alkene radical cation fragments to form either a diene and an alkene radical cation or a diene radical cation and an alkene. Depending on the substituents present in the original molecule, the more stable radical cation will dominate.

94. Mass Spectrometry McLafferty rearrangement An ion fragmentation characterised by a rearrangement within a six-membered ring system. The most usual configuration is for a radical cation formed by EI to undergo the transfer of a γ- hydrogen atom to the ionisation site through a ring system as shown here. The distonic radical cation so formed can break up by radical-site-induced (α), or charged site-induced fragmentation as shown in the figure. For example ketones, carboxylic acid and esters.

95. Mass Spectrometry Ortho effect The interaction between substituents oriented ortho, as opposed to para and meta, to each other on a ring system, can create specific fragmentation pathways. This permits the distinction between these isomeric species. The diagram shows a case in which only the ortho isomer can undergo the rearrangement.

96. Mass Spectrometry Onium Reaction Onium Ion: A hypervalent species containing a non-metallic element such as the methonium ion CH5+. It includes ions such as oxonium, phosphonium, and nitronium ions. Mostly observed in cationic fragments containing a heteroatom as charge carrier, e.g. oxonium, ammonium, phosphonium and sulphonium ions. The onium reaction is not limited to alkyl substituents acyl groups can also undergo the onium reaction

97. Mass Spectrometry CO Elimination Cyclic unsaturated carbonyl compounds and cationic carbonyl fragments which resulted from an a-cleavage tend to eliminate CO . If there is more than one CO group present sequential elimination of all CO groups is possible. From carbonyl compounds CO elimination reaction takes place like in aldehyde, ketones and phenols etc

99. Nitrogen Rule

102. Mass Spectrometry Isotopic effect

103. Mass Spectrometry Mass spectra (examples) Alkanes Strong M+ (but intensity decreases with an increase of branches. Carbon-carbon bond cleavage loss of CH units in series: M-14, M-28, M-42 etc

104. Mass Spectrometry Alkanes

105. Mass Spectrometry Cycloalkanes Strong M+, strong base peak at M-28 (loss of ethene) A series of peaks: M-15, M-28, M-43 etc Methyl, ethyl, propyl with an additional hydrogen give peaks

106. Mass Spectrometry Alkenes Strong M+ Fragmentation ion has formula CnH2n+ and CnH2n-1 -Cleavage A series of peaks: M-15, M-29, M-43, M-57 etc

107. Mass Spectrometry Alkynes Strong M+ Strong base peak at M-1 peak due to the loss of terminal hydrogen Alpha cleavage

108. Mass Spectrometry Aromatic Hydrocarbons Strong M+ Loss of hydrogen gives base peak McLafferty rearrangement Formation of benzyl cation or tropylium ion

109. Mass Spectrometry Alcohols M+ weak or absent Loss of alkyl group via a-cleavage Dehydration (loss of water) gives peak at M-18

110. Mass Spectrometry Phenols Strong M+ M-1 due to hydrogen elimination M-28 due to loss of CO M-29 due to loss of HCO (formyl radical)

111. Mass Spectrometry Ethers M+ weak but observable Loss of alkyl radical due to a-cleavage B-cleavage( formation of carbocation fragments through loss of alkoxy radicals) C-O bond cleavage next to double bond Peaks at M-31, M-45, M-59 etc

112. Mass Spectrometry Aldehyde M+ weak, but observable (aliphatic) Aliphatic : M-29, M-43 etc McLafferty rearrangement is common gives the base peak A-cleavage B-cleavage

113. Mass Spectrometry Aldehyde M+ strong (aromatic) Aromatic: M-1 (loss of hydrogen) M-29 (loss of HCO) McLafferty rearrangement is common A-cleavage B-cleavage

114. Mass Spectrometry Ketones Strong M+ A series of peaks M-15, M-29, M-43 etc Loss of alkyl group attached to the carbonyl group by a-cleavage Formation of acylium ion (RCO+) McLafferty rearrangement

115. Mass Spectrometry Esters M+ weak but generally observable Loss of alkyl group attached to the carbonyl group by a-cleavage Formation of acylium ion (RCO+) McLafferty rearrangement Acyl portion of ester OR+ Methyl esters: M-31 due to loss of OCH3 Higher esters: M-32, M-45, M-46, M-59, M-60, M-73 etc

116. Mass Spectrometry Carboxylic acids Aliphatic carboxylic acids: M+ weak but observable A-cleavage on either side of C=O M-17 due to loss of OH M-45 due to loss of COOH McLafferty rearrangement gives base peak

117. Mass Spectrometry Aromatic carboxylic acids: M+ Strong A-cleavage on either side of C=O M-17 due to loss of OH M-18 due to loss of HOH M-45 due to loss of COOH McLafferty rearrangement gives base peak

118. Mass Spectrometry Amines M+ weak or absent Nitrogen rule obey A-cleavage

119. Mass Spectrometry Nitriles M+ weak but observable M-1 visible peak due to loss of termiminal hydrogen

120. Mass Spectrometry Nitro Compounds M+ seldom observed Loss of NO+ give visible peak Loss of NO2+ give peak

121. Mass Spectrometry Alkyl chloride and alkyl bromides Strong M+2 peak For Cl M/M+2 = 3:1 F or Br M/M+2 = 1:1 A-cleavage Loss of Cl or Br Loss of HCl or HBr

122. Mass Spectrometry Alkyl chloride

124. Measuring nanoparticle size

125. Pharmacokinetics

126. Protein characterization

127. Space exploration

128. Isotope dating and tracking

129. Molecular weight

130. Bonding

132. Mass Spectrometry Protein characterization Mass spectrometry is an important emerging method for the characterization of proteins. The two primary methods for ionization of whole proteins are electrospray ionization (ESI) and (MALDI). Space exploration Mass spectrometers are also widely used in space missions to measure the composition of plasmas. For example, the Cassini spacecraft carries the Cassini Plasma Spectrometer (CAPS),[44] which measures the mass of ions in Saturn's magnetosphere. Isotope dating and tracking Mass spectrometry is also used to determine the isotopic composition of elements within a sample. Differences in mass among isotopes of an element are very small, and the less abundant isotopes of an element are typically very rare, so a very sensitive instrument is required. These instruments, sometimes referred to as isotope ratio mass spectrometers (IR-MS).

133. Mass Spectrometry Molecular weight Molecular weight can be determined by mass spectrometry. Actual number of carbons, hydrogen, oxygen etc By using relative intensities(peak hight), we can easily calculated the actual numbers of C,H,O etc atoms. Bonding Bonding can be studied by fragmentation patterns for example, beta cleavage is possible only if double bonds or heteroatom present. Reaction mechanism Mass spectrometry is best technique to study reaction mechanism and intermediates produced in reaction, for example, in carboxylic acid and alcohols a peak at M-18 indicates that water is produced.

134. Mass Spectrometry Determination of Elements Bulk materials such as steel or refractory metals, elements are determined by low-resolution glow-discharge mass spectrometry. High-resolution GDMS has been used to study semiconductor materials. GDMS is considered virtually free of matrix effects. Detection limits in ICPMS as in Table

135. Mass Spectrometry Species Analysis Heavy metals in the environment are stored in complexes with humic acids, can be converted by microbes in different complexes, and can be transported in live animals and humans. This applies to many elements such as lead, mercury, arsenic, astatine, tin and platinum For example, tin and lead alkylates established in soil, water or muscle tissue by GC / MS after exhaustive alkylation or thermal spray, and ICP-LC/MS API methods.

136. Mass Spectrometry Environmental Chemistry the analysis of trace elements and compounds in environmental samples like air, water, soil etc because of its detection power, specificity and structural analysis functions Generally, sample preparation is at least one type of chromatography coupled with MS either offline or online like GCMS

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142. Instant notes of Analytical chemistry, D.Kealey.

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