LC-MS/MS using the Q-Trap The hybrid linear ion trap mass - PDF document

LC-MS/MS using the Q-Trap The hybrid linear ion trap mass spectrometer (Q TRAP MS) from MDS Sciex Articles that describe this mass spectrometer: - Hager JW, Le Blanc JC. J. Chromatrogr. A , 2003 ; 1020 (1) : 3-9 - Le Blanc JC, Hager JW, Ilisiu AM, Hunter C, Zhong F, Chu I. Proteomics , 2003; 3(6) : 859-69 - Hager JW, Le Blanc JC. Rapid Commun. Mass Spectrom. 2003 ; 17(10) :1056- 64. Willy Bienvenut Cours de 3 eme cycle Romand 03/03/04 Q Trap (Quadrupole – linear trap) The Q-trap MS 1

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Triple quadrupole mass spectrometer Q0 Q1 Q2 Q3 Skimmer N 2 CAD Gas Exit lens Aux AC Ion accumulation Detector Q0 Q1 Q3 Q2 Fragmentation Q 0 : ion accumulator (on/off) Normal quadrupole or linear ion trap Entrance plate Q 1 : First quadrupole 3x10 -5 Torr Q 2 : Fragmentation cell Q 3 : third quadrupole or linear ion trap 3

Q-Trap utilisation modes Q0 Q1 Q2 Q3 Q-Trap mode Q1 Q2 Q3 Q1 scan Resolving (scanning) RF-only RF-only Q3 scan RF-only RF-only Resolving (scanning) Triple quadrupoles (Q1 & Q3) Resolving (scanning) Fragment Fragment resolving (scanning) Product ion Resolving (fixed) Fragment Fragment resolving (scanning) Precursor ion Resolving (scanning) Fragment Resolving (fixed) Neutral loss scan Resolving (scanning) Fragment Fragment resolving (scanning) Multiple reaction monitoring Resolving (fixed) Fragment Resolving (fixed) Enhance MS RF-only RF-only Trap scan Enhance multiply charged ions RF-only RF-only Trap scan Enhance resolution RF-only RF-only Trap scan Enhance produced ion Resolving (fixed) Fragment Trap scan MS 3 Resolving (fixed) Fragment isolate/Fragment/Scan Mode Triple Quad. MS/MS Q0 Q1 Q2 Q3 • Only 1 ion pair is stable at any one time. • Poor scanning efficiency. • Very efficient for MRM . • Very selective scans available. 4

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Standard ESI-MS/MS modes Q-Trap mode Q1 Q2 Q3 Enhance MS RF-only RF-only Trap scan Enhance resolution RF-only RF-only Trap scan Enhance produced ion Resolving (fixed) Fragment Trap scan 7

Alternative survey scan: the PIS scan The precursor ion scan approach: Looking for well defined ions m/z values Usual approach for small molecules detection and quantitation, e.g. drugs and metabolites. Adaptable to low MW peptide fragments such as immonium ions Corresponding AA I/L V W P S y 1 (R) Ac-K p-Y m/z ions 86 72 159 70 60 175 216 216 AA A R Q D C N E G H I L K M F P S T W Y V % in SWISS- 1.1 PROT 7.72 5.24 4.28 5.27 1.60 3.92 6.54 6.90 2.26 5.88 9.56 5.96 2.36 4.06 4.88 6.98 5.58 8 3.13 6.66 TIC (Total Ion Current) EMS ER EPI 1 EPI 2 EPI 2 8

TIC PIS 86 ER EPI 1 EPI 2 Extraction of the data from the acquired files 9