Figure 1. Main Steps in Measuring with a Mass Spectrometer (9).

Ionization: the process by which an atom or a molecule acquires a negative or positive charge by gaining or losing electrons. In Mass Spectrometry, sample analytes in the source become (+ or -) charged molecules or molecule fragments and the mass spectrometer detects their abundance on the basis of their mass-to-charge (m/z) ratios.

Primary Reagent Gas Ion Formation:

CH4 + e- --> CH4

+ + 2e

-

Secondary Reagent Ion Formation:

CH4 + CH4+

--> CH5+

+ CH3

CH4 + CH3+

--> C2H5+

+ H2

Analyte Ion Formation:

M + CH5+

--> CH4 + [M + H]+

(protonation)

AH + CH3+

--> CH4 + A+

(H - abstraction)

M + CH5+

--> [M + CH5]+

(adduct formation)

A + CH4+

--> CH4 + A+

(charge exchange)

Scheme 1. Steps involved in analyte ion formation in chemical ionization MS.

Scheme 2. Negative ion electron capture ionization: Resonance Electron Capture.

Scheme 1

Scheme 2

Scheme 3. Negative ion electron capture ionization: Dissociative Electron Capture.

Figure 2. Matrix-Assisted Laser Desorption Ionization (Closed circles are analyte molecules) (16).

Scheme 3

Figure 2

Figure 3. Schematic diagram of an ESI-MS source of an early instrument in John Fenn’s laboratory (21) that uses a counter-current flow of drying gas that excludes solvent vapor from the ion-gas mixture that enters the vacuum system via free jet expansion at the exit of glass capillary, each end which is metallized so that it can be maintained at any desired potential. The field required to “electrospray” the sample solution can be achieved with the spray needle while the metallized entrance of the capillary is at the required potential “below” ground. Ions entering the capillary are in a potential well. Rapid flow of gas through the capillary drags ions out of that potential well to the potential at which the metallized exit of the capillary is maintained. External parts of the apparatus are at ground to eliminate operator hazard (21).

Figure 3

Figure 4. Models for formation of solute ions in ESI. Top: Charged Residue Model. Offspring droplets from a first Rayleigh Instability continue to evaporate solvent, undergo a second Rayleigh Instability, and disrupt (21). Continued evaporation-disruption episodes ultimately produces droplets with only 1 solute molecule. As the last solvent evaporates from the ultimate droplet the remaining solute molecule becomes a free gas-phase ion. Bottom: Ion Evaporation Model. Before ultimate droplets containing only 1 solute molecule are formed, the field at a droplet's surface becomes intense enough to lift a solute ion from the droplet surface into the ambient gas (21).

Figure 4

Figure 5. Schematic Diagram of a Sector Mass Analyzer (9).

Figure 5

Figure 6

Figure 6. Basic components of linear (upper) & reflecting (lower) TOF mass spectrometers (15).

Figure 7. Schematic diagram of the quadrupole mass analyzer or quadrupole mass filter (23).

Figure 7

Figure 8. Schematic of the 3D ion trap (23). Electric field E is generated by a quadrupole of endcaps & a ring electrode

Figure 9. Quadrupole ion trap with a positively charged particle, surrounded by a cloud of positively charged particles (25). Electric field E is generated by a quadrupole of endcaps (a, positive) & ring electrode (b). Pictures 1 & 2 show 2 states during an AC cycle.

Figure 8

Figure 9

Figure 10. Mechanical model of the ion trap (23).

Figure 11. Trajectory of a trapped ion (24). Projection onto the x-y plane illustrates planar motion in 3-dimensions with a trajectory like a flattened boomerang.

Figure 10

Figure 11

Figure 12. ThermoFinnigan LTQ linear ion trap mass spectrometer (26).

Figure 13. Scheme to apply DC, RF trapping, & AC excitation voltages to operate a 2-D ion trap (18).

Figure 12

Figure 13

Figure 14. Ion cyclotron resonance in the Penning trap (28). Left panel illustrates trap electronic circuitry. Center & right panels illustrate ion motion in a 2 in. cubic Penning trap in a homogeneous magnetic field.

Figure 15. Ion cyclotron resonance (29).

Figure 14

Figure 15

Figure 16. Fast Fourier Transformation of transient image current (29).

Figure 16

Figure 17. Cutaway view of the Orbitrap mass analyzer (30). Ions are injected into the Orbitrap at the point indicated by the red arrow with a velocity perpendicular to the long axis of the Orbitrap (the z-axis). Injection at a point displaced from z = 0 gives ions potential energy in the z-direction. Ion injection at this point on the z-potential is analogous to pulling back a pendulum bob and releasing it to oscillate.

Figure 17

Figure 18

Figure 18. Schematic Diagram of a Triple Stage Quadrupole Tandem Mass Spectrometer (31).

Figure 19. Schematic diagram of the QTOF tandem mass spectrometer (34).

Figure 19

Figure 20. Tandem mass spectrometry on the Finnigan LTQ linear ion trap (35).

Figure 20

Figure 21. Diagram of QTRAP instrument ion path (36). Q1 is a standard Rf/DC quadrupole mass filter. Q3 can be operated as an Rf/DC quadrupole or a linear ion trap MS.

Figure 21

Figure 22. Structures of cocaine, benzoylecgonine (BEG), and the pentafluoropropyl (PFP) ester derivative of BEG (38).

Figure 22

Figure 23

Figure 23. Mass spectra of the pentafluoropropyl ester derivatives of benzoylecgonine & d3- benzoylecgonine (38).

Figure 24. Gas chromatographic/selected ion monitoring MS analyses of the pentafluoropropyl ester derivatives of benzoylecgonine & d3-benzoylecgonine (38).

Figure 24

Figure 25. Structure of Tacrolimus (FK506)

Figure 25

Figure 26. Collision-induced dissociation spectra of (A) Tacrolimus & (B) internal standard (39).

Figure 26

Figure 27. Chromatograms from blood extracts with multiple reaction monitoring of (A) Tacrolimus supplemented blood, (B) blank blood, & (C) Patient sample containing Tacrolimus (39).

Figure 27

Figure 28. ESI/MS analyses of Li+ adducts of ceramide species from insulinoma cells (A) and tandem mass spectrum of [M + Li]+ of 24:1-CM (B) (40).

Figure 29. Neutral losses of water and formaldehyde from [M + Li]+ of 24:1-ceramide (40).

Figure 28

Figure 29

Figure 30. Thapsigargin-induced ceramide accumulation in INS-1 insulinoma cells. Ceramide species in control cells (A) or cells treated with thapsigargin (B) were analyzed as Li+ adducts by ESI/MS/MS scanning for constant neutral loss of m/z 48 (40).

Figure 30

Figure 31. Detecting CFTR gene mutations by using primer oligo base extension (41).

Figure 31

Figure 32. MALDI/TOF/MS of primer oligo base extension products to detect CFTR mutations (41).

Figure 32

Figures 33-34

Figure 33. Western blot INS-1 cell iPLA2ß (42).

Figure 34. MALDI/TOF/MS of tryptic digest of 70kDa iPLA2ß immuno-reactive protein expressed by INS-1 cells (42).

Figure 35. Tandem mass spectrum of the [M+2H]+2 ion m/z 955.03 in LC/ESI/MS analyses of tryptic peptides from a 70 kDa iPLA2β digest (42). Upper panel illustrates the peptide sequence & expected y- and b-series ions. Deviations of the observed m/z values are also indicated. The QTOF data system converted the observed data into singly charged equivalents to facilitate interpretation.

Figure 35

Table 2. Partial list of MRMs monitored for a set of 100 drugs in post-mortem toxicologic analyses of blood in Herrin GL, et al. J. Anal. Tox. 29: 599-607 (2005) (43).

Table 2

Figure 36. QTRAP LC/MS/MS results for drugs in a post-partum sample plotting ion current for all MRMs vs. LC retention time in Herrin GL, et al. J. Anal. Tox. 29: 599-607 (2005) (43).

Figure 36

Figure 37. Detection and confirmation of the presence of benzoylecgonine in a post-mortem blood sample by the QTRAP LC/MS/MS system using MRM and then IDA of an EPI scan (43).

Figure 37

Figure 38. (A). Total ion chromatogram of a solution of 10 antipsychotic drugs in methanol; (B) Underlying amisulpride Q3-only enhanced mass spectrum (EMS); (C) Corresponding extracted ion chromatogram; and (D) Enhanced product ion (EPI) spectrum of amisulpride. From Sauvage FL, et al., & Marquet P. Clin. Chem. 52: 1735-42 (2006) (44).

Figure 38

Figure 39. Comparison of LC/MS/MS, GC/MS, and HPLC/DAD in general unknown drug screening of 36 clinical specimens that yielded a total of 130 positive identifications of 89 different compounds. From Sauvage FL, et al., & Marquet P. Clin. Chem. 52: 1735-42 (2006) (44).

Figure 39

Table 3. Partial list of mass spectrometric and chromatographic characteristics of benzodiazepines from Quintela O, et al., & Marquet P. Clin. Chem. 52: 1346 –1355 (2006) (45).

Table 3

Figure 40. LC/MS/MS chromatogram of MRM on a Triple Stage Quadrupole of benzodiazepines from Quintela O, et al., & Marquet P. Clin. Chem. 52: 1346 –1355 (2006) (45).

Figure 40

Figure 41. Drugs of abuse identified in a sample of oral fluid by LC/MS/MS on a Triple Stage Quadrupole with MRM and heavy isotope-labeled internal standards from Øiestad EL, et al. Clin. Chem. 53: 300-309 (2007) (46).

Figure 41

Figure 42. LC/MS/MS drug screening on a QTOF with IDA from MS to MS/MS. (A) TIC in MS. (B) Extracted ion chromatogram for [M+H]+ of methadone (RT indicated by arrow in Panels A and B). (C) and (D) MS/MS spectra of methadone at two different collision energies. (D) TIC of the three MS/MS channels (47).

Figure 42

Table 4. (A) Drug findings in urine samples with LC/TOF/MS screening and LC/FTMS confirmation together with the measured masses. (B) Comparison of the number of drug candidates in a database of 7640 drugs using 3 mass search windows. [Ojanperä I, et al., & Witt M. J. Anal. Tox. 29: 34-40 (2005)] (48).

Table 4