LC/MS Crossroads. Jerry Pappas Sales Representative 265 Davidson Avenue Somerset, NJ

LC/MS Crossroads Jerry Pappas Sales Representative 265 Davidson Avenue Somerset, NJ 08873 jerry.pappas@thermo.com 732-698-2778 1

Comparison of Quads and Traps Ion Traps Quadrupoles Mass Separation in time Mass Separation in space High sensitivity Full Scan Lower sensitivity Full Scan Lower sensitivity SIM and SRM Offer multiple stages of MS n High sensitivity SIM and SRM Offers Only MS or MS/MS Parent and neutral loss scans 2

LCQ Instrumentation Classic Duo Deca 3

Duo/Deca Comparisons LCQ DUO 400um capillary 2 octopoles One rotary pump LCQ DECA 500um capillary 1 square quadrupole & 1 octopole 2 rotary pumps Deca: approximately 10 x better signal than Duo 4

5 Current LCQ Generation

Advantage/XP Comparisons 450um Ion Transfer Tube Orthogonal Probes 550um Ion Transfer Tube Orthogonal Probes XP: approximately 10 x better signal than Advantage 6

LCQ MS n Quadrupole Ion Trap LC Pump ESI Quadrupole Ion Trap Ion optics Detector Syringe Pump Quadrupole refers to the shape of the ion confining field inside the trap and not the shape of or number of electrodes in the trap. 7

Mass Spectrometry Simplified G M S D enerate ove elect etect Ion production Ion optics Mass filter Electron multiplier 8

The Mass Spectrum Light, all colors Prism Red Green Blue Ions, various masses Mass Spectrometer 100 200 300 9

Trace produced by summing all observed masses in each scan Total Ion Chromatogram or TIC 10

Ionization vs. Fragmentation API CI EI Soft Ionization Hard No Fragments Fragments 11

EI and CI Mass Spectra of Ephedrine 100 EI 58 % Relative Intensity 50 0 0 20 40 60 80 100 120 140 160 180 100 50 CI 148 (MH) 166 MW = 165Th 0 0 20 40 60 80 100 120 140 160 180 m/z 12

Ionization Techniques 200,000 ESI 15,000 1,000 APCI Molecular Weight GC PBI TSP FAB Non Polar Polar 13

What is API? Atmospheric Pressure Ionization Source Types: 1. Electrospray Ionisation (ES) Solution phase process (for the most part). 2. APCI (Atmospheric Pressure Chemical Ionization) - Gasphase process. Source Purpose: 1. Ionize the analyte (APCI) or transport ion in solution to the gas phase. 2. Desolvate sample flow for introduction into mass spectrometer. 3. Baffle the first vacuum region of the MS from atmospheric pressure in the source. 4. Pump away neutrals and opposite charged ions which would otherwise interfere with the analysis of the desired polarity. 14

LCQ Classic/Duo/Deca API Probes Electrospray Ionization (ESI) Peek insulator Atmospheric Pressure Chemical Interface (APCI) 15

LCQ Advantage/XP API Probes Electrospray Ionization (ESI) Atmospheric Pressure Chemical Interface (APCI) Orthogonal ESI & APCI probes 16

Chemistry Considerations ESI: Ions formed by solution chemistry Good for Thermally labile analytes Good for Polar analytes Good for Large Molecules (Proteins / Peptides) APCI: Ions formed by gas phase chemistry Good for Volatile / Thermally Stable Good for Non-polar analytes Good for Small Molecules (Steroids) 17

ESI Versatility Advantage/XP (Right: Picture represents a low flow position, <50uL/min) A-F Positions for increased ruggedness 1-5 Positions (Left: Picture represents a high flow position) 18

Electrospray Basic Layout Heated Capillary ESI Needle /- 5 kv Solvent evaporation and ion release Taylor Cone 19

APCI Position on Advantage/XP In/Out Movable Corona Discharge Pin Total control for any flow rate (200ul/min - 2000ul/min) 20

LC Flow Rates ESI: APCI: 3 µl/min - 1mL/minute Optimal Flow Rate: 200 µl/min Generally, higher flow rates require higher heated capillary temperatures and higher gas flow rates. 200 µl/min - 2mL/minute. Optimal Flow Rate: 500 µl/min Generally, higher flow rates require more sheath and auxiliary gas, but do not require higher heated capillary temperatures. 21

Theoretical Increase in Response Conc max = D 2 Column 1 D 2 Column 2 Col. Diameter mm 4.6 3.0 1.0 Flow Rate ml/min 1 0.5 0.2 0.05 < 10 µl / min Theoretical Increase 1 2.3 2.0 Capillary 5 21 22

Acids Bases LC Additives Do not use inorganic acids (may cause source corrosion) Formic and acetic acid are recommended Do not use alkali metal bases (may cause source corrosion) Ammonium hydroxide is recommended Surfactants (surface active agents) Detergents and other surface active agents may suppress ionization Trifluoroacetic Acid (TFA) May enhance chromatographic resolution, but causes ion suppression in both negative and positive ion mode Isopropyl Alcohol May Enhance Negative Ion Formation 23

Buffers (ph) Avoid using non-volatile HPLC additives such as: Alkali Metal Phosphates Borates Citrates Keep Buffer concentrations below 20 mm using volatile salts such as ammonium acetate. When using buffers, more frequent cleaning of the heated capillary and API stack will be necessary 24

LC/MS Additives and Buffers Summary Acetic Acid Formic Acid Ammonium Hydroxide Ammonia Solutions Trichloroacetic Acid (< 0.1% v/v) Trifluoroacetic Acid (< 0.1% v/v) Isopropyl Alcohol (10% of organic phase) Ammonium Acetate Ammonium Formate Proton Donors Proton Acceptors Chromatographic Separation Negative ion formation Buffers 25

Common LC/MS Solvents Methanol Acetonitrile Water Isopropanol Dichloromethane Chloroform Hexane 26

Effects of Solvents and Additives on ESI Solvent System 50/50 ACN/H2O 0.1% NH4OH 50/50 MeOH/H2O 0.1% NH4OH 50/50 ACN/H2O 0.02% TFA 50/50 ACN/H2O 0.05% TFA 50/50 ACN/H2O 0.1% TFA 50/50 MeOH/H2O 0.02% TFA 50/50 MeOH/H2O 0.05% TFA 50/50 MeOH/H2O 0.1% TFA 50/50 MeOH/H2O 10mM NH4OAc 50/50 MeOH/H2O 5mM NH4OAc 50/50 ACN/H2O 0.1% Formic 50/50 ACN/H2O 1% Acetic 50/50 MeOH/H2O 0.1% Formic 50/50 MeOH/H2O 1% Acetic 100 ACN 100 MeOH 100 H2O 50/50 ACN/H2O 50/50 MeOH/H2O Tyr-Gly-Gly-Phe-Leu Leucine Enkephalin 0 100000 200000 300000 400000 500000 Counts (protonated ion species) 27

API Stack LCQ Classic, LCQ DUO, LCQ DECA LCQ DECA XP, LCQ Advantage 28

Ion Transfer Tube and Removal Tool Ion transfer tube Removal tool Heated capillary 29

Vent Prevent Mechanism Heated Tube in-situ Heated Tube removed Tungsten Vent Prevent 30

Ion Optics First multipole Lens Intermultipole Lens Second multipole Lens IONS IN IONS OUT Octapole Mount Vacuum Baffle Analyzer Mount 31

Multipole Potential Wells Mass Range Trans Efficiency Octapole Square Quadrupole Round Quadrupole 32

33 Mass Analyzer (Ion Trap)

Vacuum System Every mass analyzer must operate under vacuum in order to minimize both ion/molecule and molecule/ molecule collisions. At atmospheric pressure, the mean free path of a typical ion is only ca. 52 nm and at 1 mtorr,, it is 40 m. Without vacuum, the ions produced in the source won t make it to the detector. The LCQ vacuum is maintained by a both rotary and turbomolecular pumps 34

Ion Optics (Operating Pressures) 1.3 torr 760 torr 1.7x10-3 torr 2.0 x10-5 torr (1.0x10-5 torr He) 60 m 3 /hr 100 L/sec 3.5x10-3 torr He 220 L/sec 35

Steps to Ion Trap Scan Functions Trapping- all scans Isolation- SIM and MS n Excitation- MS n Ejection- all scans 36

Helium as a Damping Gas Without Helium With Helium He collision He He He He 37

38 Discovery of the Effects of Helium

39 Helium as a Damping Gas

Ion Trap Resolution Effect of Damping Gas Traps injected ions by removing kinetic energy Damps ion motion to center of trap Result... Increase in resolution and sensitivity 40

Helium Effect Helium flowing into trap S#:1 RT:0.00 AV:1 SM:7G NL:2.50E7 T: p Full ms 524.3 80 60 40 20 525.3 0 514 516 518 520 522 524 526 528 m/z Abundance100 Relative S#:23-32 RT:0.71-1.00AV:10 SM:7G NL:5.61E7 T: p Full ms 80 60 40 20 195.15 Abundance100 Relative 1522.04 1621.97 1322.06 1721.89 524.26 1222.14 1821.95 1122.21 1921.88 1022.09 0 500 1000 1500 2000 m/z Helium shut off and not flowing into trap S#:1 RT:0.02 AV:1 SM:7G NL:9.70E6 T: p Full ms 100 Relative Abundance 80 60 40 20 522.6 523.0 521.8 521.2 523.9 520.7 S#:23-32 RT:0.39-0.54AV:10 SM:7G NL:2.80E7 T: p Full ms 0 0 514 516 518 520 522 524 526 528 500 1000 1500 2000 m/z m/z 100 Relative Abundance 80 60 40 20 1620.79 1520.26 1720.44 1320.95 1220.75 523.01 1919.96 1120.90 192.17 41

Ion Trap Stability Diagram The region shaded blue indicates a (DC) and q (RF) values which provide stable trajectories in the r-direction The region shaded yellow indicates the z-stable a and q combinations The green area where the r- and z-stable regions overlap indicates the a and q combinations under which ions will be stable in the trap 42

Stability Diagram for Commercial Traps V qz = k ( m/ e) 43

LCQ Scan-Out (Ejection) Rates Normal Scan (5500 amu/sec) Common full, SIM, or MS n (SRM and CRM) scanning Resolution (FWHM) = 0.50, Mass Accuracy = ± 0.05 Zoom Scan (280 amu/sec) Increases resolution and mass accuracy across a narrow range (allows charge state determination) Resolution (FWHM) = 0.15, Mass Accuracy = ± 0.02 Turbo Scan (55,000 amu/sec) Decreases total scan time of a full scan, thus increasing number of scans across a chromatographic peak Resolution (FWHM) = 3.0, Mass Accuracy = ± 0.5 Used for better quantitation due to an increase of scans across a chromatographic peak 44

What is AGC and Why Is it Important? Camera AE LCQ Series AGC Too much light degrades the image stored on film, causing a loss of color and image resolution. Too little light results in dark picture with no fine details visible. Cameras with high quality light meters and AE controls produce high quality pictures over a wide dynamic range of lighting conditions. Controls amount of ions (light) entering the ion trap (film) Too many ions degrade the spectral quality in the trap, causing loss in mass resolution and mass assignment. Too few ions result in poor sensitivity to low level or minor components. AGC ensures excellent quality MS, SIM and MS/MS spectra, as well as excellent sensitivity over a wide dynamic range. 45

Automatic Gain Control (AGC) Prescan before the analytical scan - Measures the # of ions in the trap for a pre-defined time (10 ms) -Allows software to determine optimum ion injection time 46

47 No AGC Spectrum of Ultramark 1621, Caffeine, MRFA Calibration Mixture space charging

48 Spectrum of Ultramark 1621, Caffeine, MRFA Calibration Mixture with AGC

AGC (Ion Population Control) ~ 300 Ions ~ 1500 Ions ~ 3000 Ions ~ 6000 Ions 100 524.3 100 524.4 100 524.5 100 524.8 Relative Abundance 80 60 40 525.3 20 20 20 20 526.5 526.3 526.3 527.5 527.5 0 0 0 0 522 530 522 530 522 530 522 m/z Relative Abundance 80 60 40 Good Resolution 525.4 m/z Relative Abundance 80 60 40 525.5 m/z Relative Abundance 80 60 40 m/z 525.7 Poor Resolution 526.7 530 49

Calculation of Ion Time Constant During Prescan AGC Prescan Signal = Number of Ions x Multiplier Gain x Prescan Time (3 x 10 5 counts) (10 ms) Calculated Ion Time = (how long the gate lens is open ) Target Value AGC Prescan Signal 50

Triplicate Injection of 5 nmol of MRFA (AGC ON) Unscaled TIC (counts) Injection Time (ms) 2.0E08 1.8E08 1.6E08 1.4E08 1.2E08 1.0E08 8.0E07 6.0E07 4.0E07 2.0E07 0.0E00 60 50 40 30 20 10 Unscaled TIC 0 100 200 300 400 500 600 Scan Number Injection Time Scaled TIC (counts) 0 8.0E08 7.0E08 6.0E08 5.0E08 4.0E08 3.0E08 2.0E08 1.0E08 0.0E00 0 100 200 300 400 500 600 Scan Number Scaled TIC 0 100 200 300 400 500 600 Scan Number 51

7 Isolation of Ions Ion we wish to isolate 0.0 q z 0.908 Ions at different q z values oscillate at different frequencies (ω o ) ω o q z Ω 2 2 52

Isolation Waveforms ~ m/z 200 q axis.908 500 Hz 16 msec q axis.908 53

Why MS/MS or MSn? Signal to Noise Improvement Intensity Signal Noise S/N 0 1 2 3 4 5 6 Stages of Analysis 54

MS/MS Parameters Precursor ion m/z Excitation voltage Excitation q z Intensity Precursor ion Σ(Product ions) 0.0 1.0 2.0 3.0 4.0 Excitation Voltage (V) 77001-1285 970219 55

Resonant Excitation q z Value q z Fragment ions not trapped Product Ion m/z Range Fragmentation Energy 0.0 0.225 0.908 1/4 q z 0.0 0.30 0.908 1/3 q z 0.0 0.45 0.908 1/2 56

Ion Trap Scan Functions 1. Collect 3. Fragment 2. Isolate 4. Eject 57

Summary (Ion Trap Functions) 1)Collection 2)Isolation 3)Excitation 4)Ejection For Scans: All By: Ring Electrode Method: Alternating RF frequency (760 khz) at a set amplitude along with He dampening gas traps and cools the ions to the center of the trap. 58

Summary (Ion Trap Functions) 1)Trapping 2)Isolation 3)Excitation 4)Ejection For Scans: SIM, MS n By: Endcap Electrodes Method: a) Tailored waveform applied to all ions in the trap except ion of interest b) Thus, only ions of interest remain in the trap. 59

Summary (Ion Trap Functions) 1)Trapping 2)Isolation 3)Excitation 4)Ejection For Scans: MS n By: Endcap Electrodes Method: a) Cool ion of interest back to set q value (default = 0.25). b) Apply custom RF waveform in resonance with the set q value, activation time (default = 30 msec), and optimized activation amplitude. 60

Summary (Ion Trap Functions) For Scans: All 1)Trapping 2)Isolation 3)Excitation 4)Ejection By: Ring Electrode Method: Ramp ring RF power to increase the q values of all ions in desired scan range, low mass to high mass. (i.e. Mass Selective Scanning) Also, ramp the RF amplitude on the endcap electrodes to consolidate the ions to a group (Resonance Ejection) 61

Tune Page convection gauge pressure < 1.5 torr? Ion gauge Pressure <2.0x10-5 torr? 62

ESI Calibration Solution Caffeine stock: MFRA stock: Ultramark stock: 10 ml acetonitrile 1 mg/ml in methanol Dissolve 3.0 mg MRFA in 1 ml 50:50 methanol:water Measure 10 υl of Ultramark 1621, and dissolve it in ESI calibration solution ESI calibration solution Into a clean vial pipette 100 µl of caffeine stock, 5 µl of MRFA stock and 2.5 ml of Ultramark stock. Add 50 µl of glacial acetic acid and 2.34 ml 50:50 methanol:water 63

64 Ion Trap Animation

The Eighth Generation Triple Quad TSQ 15, TSQ 45, TSQ 46, TSQ 70, TSQ 700, TSQ 7000, TSQ, TSQ Quantum 65

Smaller because 8degrees 90 Degree Square quad collision cell 25 cm quad TSQ 7000 25 cm quad 25 cm quad Quantum 25 cm quad 90 degrees 66

HyperQuads TM Hyperbolic Quadrupoles TSQ 7000 1993 to 2000 r 0 = 4 mm L = 250 mm TSQ Quantum 2001 to r 0 = 6 mm L = 250 mm Forms Pure Quadrupolar Fields Reduces Fringing Effects Significantly Improves Resolution Improves Transmission Improves Peak Shapes 67

Quadrupole Mass Analyzer The ion is transmitted along the quadrupole in a stable trajectory Rf field. The ion does not have a stable trajectory and is ejected from the quadrupole. 68

How does the Quadrupole work? The quadrupole consists of four parallel rods. The opposing rods have the same polarity while adjacent rods have opposite polarity. Each rod is applied with a DC and an RF voltage. Ions are scanned by varying the DC/Rf quadrupole voltages. Only ions with the selected mass to charge ratio will have the correct oscillatory pathway in the Rf field. -ve ve 69

Effect of Peak Width On Transmission HYPERQUAD ROUND RODS % T r a n s m i s s i o n 100 80 60 40 20 0 2 1.5 0.7 0.5 0.2 0.1 Peak Width FWHM 70

Effect of Peak Width on Resolution Resolution 12000 10000 8000 6000 4000 2000 Quad 0.7 FWHM Quad 0.1 FWHM Sector Quantum operating at 0.1 FWHM at m/z 1000 R = 10,000 Quantum, API 4000, Ultima at 0.7 FWHM at m/z 1000 R = 1428 R is relatively flat across m/z 0 0 200 400 600 800 1000 1200 m/z 71

The Power of Resolution Separation of ions with same nominal m/z value Unequivocal determination of charge state (ESI) High resolution precursor ion selection for MS/MS High resolution product ion for charge state determination 72

Effect of changing resolution on peak shape 1.0 FWHM 0.7 FWHM 0.5 FWHM 0.3 FWHM 0.2 FWHM 0.1 FWHM 73

Resolution vs. Intensity 1.0 FWHM 0.7 FWHM 0.5 FWHM 2.5e6 2.1e6 1.9e6 74

Resolution vs. Intensity 0.3 FWHM 0.2 FWHM 0.1 FWHM 1.5e6 1.4e6 0.8 e6 75

Quadrupole Mass Analyzer If one MS scan between m/z 100 and 500 is completed in one second, then each m/z will be allowed to pass for 2.5 ms. 1000 ms = 2.5 ms/amu 400 amu To detector 76

Quadrupole Mass Analyzer And, for the same peak, for example, the quadrupole performs 5 complete scans from 100 500 Da each taking 1 sec. 100 500 Da 100 500 Da 100 500 Da 100 500 Da 100 500 Da 77 5 sec

Ion Trap Pre-Scan The length of time that the trap stays open to collect ions is determined by a pre-scan which measures total ion current (prevents space charging, so no ghost peaks ) Pre-Scan 78 5 sec

Ion Trap Pre-Scan Cont d Across a peak 5 sec. wide the trap might fill and empty 5 times. So, a group of ions are collected ca. every 1 sec each group is then ejected to the detector, smaller ions first. 1 sec 1 sec 1 sec 1 sec 1 sec 79 5 sec

Comparison of Quads and Traps For the quadrupole, each m/z is scanned (sequentially) to the detector for 2.5 ms. But for a trap, each m/z (and all m/z at the same time) is/are collected for ca. 750 ms (taking pre-scan and interscan times into account) and then scanned to the detector. 80

Comparison of Quads and Traps At any one particular instant, a quad will only scan/look for only one m/z. All other m/z will be ignored. In this example, each m/z is scanned for 2.5 ms. A trap will fill similar to filling a glass with water. All ions entering the trap will be collected until the trap fills with a pre-defined amount of ions (AGC target value). 81

Comparison of Quads and Traps So, for full scan MS, a trap will give better sensitivity because there are more ions representing each m/z arriving at the detector for each scan. 82

How Much More??? Accounting for pre-scan/interscan timing, the trap produces ca. 300 times (750 ms/2.5 ms) for the collection of each m/z compared to a quadrupole (i.e 2 orders of magnitude). 83

But What if I wanted to pass (filter) only one m/z ion to the detector (i.e. SIM or SRM) then I could spend more time on that ion 84

Comparison of Quads and Traps Yes, on a quadrupole, interscan times are relatively short and so the quadrupole remains fixed on that one ion a duty cycle of close to 100% But a trap will still only collect ions in batches - and prescan/interscan times afford a duty cycle of about 75% 85

What is a Duty Cycle? Definition:- Time taken to acquire 1 scan and be ready to acquire the next one Duty Cycle Scan 1 ISD Scan 2 Interscan delay (ISD) is the time taken to return all system voltages to the start values and reach a stable state This is dead time and should be minimized 86

In Addition While the beam instrument is continuously detecting one particular m/z a trap builds a curve from an average over each collection time and the points are least frequent at the most important region for quantitation (the take off ). 87

For Example SRM of 5 pg Alprazolam with LCQ Deca gives a %RSD of 6.11 while SRM of 750 fg Alprazolam with TSQ 7000 gives a %RSD of 1.87. Signal to noise ratio (S/N) are similar (20:1 and 28:1 respectively). 88

Relative Abundan ce 100 90 80 70 60 50 40 30 20 10 0 %RSD 6.11 RT: 4.26 SN: 20 SRM 5pg Alprazolam with LCQ Deca 100 SRM 750fg Alprazolam with TSQ RT: 4.41 SN: 28 90 80 70 60 50 40 %RSD 1.87 30 20 10 89 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 Time (min)

The Effect of Ion Trap Scan Speeds on Quantitative Performance In general, faster scanning produces more points across a chromatographic peak, hence better precision and lower LOQ s. In fact, for an ion-trap, scan speed refers only to the time taken to scan ions from the trap during mass analysis. Scan speed does not refer to the total analytical cycle. In an ion trap device, an MS n analytical scan comprises at least four events: 90

The Effect of Ion Trap Scan Speeds on Quantitative Performance 1- AGC Pre-scan 2- Ion Injection (usually the rate-determining step) 3- Isolation and activation of the parent ion within the trap 4- Scanning the ions out of the trap (mass analysis) 91

MS Scan Function Ion isolation Mass Analysis Ion Activation Ion Injection AGC Prescan Analytical Scan 92

Scan Terminology Prescan Mass Analysis Prescan Mass Analysis Prescan Mass Analysis 1st Microscan 2nd Microscan 3rd Microscan Save Data Complete Scan Cycle 93

The Effect of Ion Trap Scan Speeds on Quantitative Performance The injection time constitutes the majority of the total scan time. For good quantitative reproducibility, it is necessary to take enough points to precisely determine the chromatographic peak particularly at the take-off point. Increasing the scan speed in the trap does not significantly increase the number of data points taken across the peak. 94

Scan speeds in ion traps Pre-scan Quantitation m/z 500 scanning 135-510 Isol /Activ // Download 80 80 0 msec Pre-scan 375 amu @ 13,000 60 60 msec amu/sec 30 30 Isol /Activ // Download Injection time 80 80 500 Pre-scan 375 60 60 msec amu @ 13,000 Total amu/sec scan time 30 30 610 Isol/Activ/ Download Injection 80 time 80 Scans // 10 10 sec 500 wide peak 16 16 375 amu @ 5500 Total amu/sec 70 scan time 70 670 Injection time Scans 500 // 10 10 sec wide peak 15 15 Total scan time 710 Scans // 10 10 sec wide peak 14 14 95

The Effect of Ion Trap Scan Speeds on Quantitative Performance The only significant way to increase the sampling rate across the peak is to reduce the injection time which can be achieved in two ways: 1- Set a lower max injection time which reduces the number of ions in the trap, hence sensitivity 2- Increase the efficiency of the source and lenses to improve the transmission of ions; I.e filling the trap to the same level in a shorter period of time. 96

Data Dependant Acquisition of MS n Spectra Data Dependant Acquisition: Intelligent decision-making software that selects precursor ion for MS n experiments based on user-define criteria. Critical for metabolite screening experiments. Scan event 1 Full-Scan MS Scan event 2 Full-Scan MS 2 Software selects most intense ion from scan event 1 as precursor ion for ms 2 experiment in scan event 2, provide that its intensity is above a user selected threshold m/z m/z 97

Dynamic Exclusion -- MS and MS/MS of Co-Eluters MS MS 407 452 MS MS/MS MS MS/MS MS MS MS Threshold 231 MS/MS 365 377 MS 407 452 Time m/z 206 255 MS/MS 377 m/z 98 m/z m/z

Comparison of Quads and Traps Major Strengths of Triple Quads SRM Sensitivity Neutral Loss Scan Mode Parent (Precursor) Scan Mode Major Strengths of the LCQ Deca XP Plus MS n Scan Mode Full Scan MS/MS Sensitivity Consecutive Reaction Monitoring (CRM) 99

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 Since both Q1 and Q3 are scanning, neutral loss scan mode is slower than any other mode 100

Neutral loss scans Neutral loss scans are used for screening experiments where a group of compounds all give the same loss H 2 N -m/z 84 H 2 N N -m/z 84 N N N H 2 N N H 2 N N H 2 N NH 2 N N -m/z 84 H 2 N NH 2 N HO N N -m/z 84 HO N 101

What are precursor ion scans? Precursor ion scans also known as parent ion scans Q1 is scanned Q3 is set to allow only a fragment ion of one m/z to pass; (Q3 fixed) ions collide with Argon gas in Q2 to create fragment or product ions Only those compounds which give that specific fragment ion are detected 102

Precursor ion scans Precursor ion scans are used for screening experiments where a group of compounds all give the same fragment ion m/z 162 N N H 2 N m/z 192 N H 2 N N H O N N m/z 192 N N N m/z 84 H 2 N H 2 N N N m/z 268 m/z 238 103

Comparison of MS n in a Triple Quad verses an Ion Trap Instrument. Triple Quad(nonresonant excitation): Acceleration voltage applied equally to all masses. Get a mix of ms 2, ms 3 ms n products. Ion Trap(resonant excitation): Excitation energy is in resonance with only one mass at a time. Fragments, once formed, can not be further excited unless they are purposely selected for next stage of MS. Allows one to take apart a molecule in a controlled, step-wise fashion. 104

Comparison of Quads and Traps Ion Traps Quadrupoles Mass Separation in time Mass Separation in space High sensitivity Full Scan Lower sensitivity Full Scan Lower sensitivity SIM and SRM Offer multiple stages of MS n High sensitivity SIM and SRM Offers Only MS or MS/MS Parent and neutral loss scans 105