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gels, it can be used to identify positions of modified or labelled bases that might not be

picked up by the Sanger dideoxy sequencing method.

Structural information can be obtained on almost any type of organic molecule, on an

instrument that is suitable for that type of sample. This includes investigation of organic

compounds on a magnet sector MS where two double-focussing magnetic sector

machines can be combined into a four-sector device coupled through acollision cell.

The general procedure is that a mixture of ions is generated in the ion source of the

mass spectrometer as normal and the ions are allowed to pass through the first mass

Q1

R 1

C C

H

N C

HH

CN

OR 2 O R 3 OR 4

H 2 NCOCCNC 2 H

HH HH

R 1

C C

H

N C

HH

CN

OR 2 O R 3 OR 4

H 2 NCOCCNC 2 H

HH HH

Q2

Q3

Collision cell

MS-2, separation of

fragment ions

MS-1

Selection of

Ions precursor ion

Detector

(a)

(b)

Fig. 9.21Quadrupole MS sequencing. An ion of a particularm/zvalue is selected in the first quadrupole, Q1, as

in Fig. 9.5, but instead of being detected, it passes through the second quadrupole, Q2, where it is subjected to

collision with the collision gas. The Q3 acts like a second quadrupole mass spectrometer, MS-2, to scanm/z

to obtain a spectrum of the fragment ions. The collision cell, Q2, is frequently a radio frequency (RF)-only

quadrupole containing the appropriate collision gas. No mass filtering occurs here, the RF merely constrains

the ions to allow a greater number of collisions to occur. The fragmentation depicted here is at the peptide bond

and one of the fragments will retain the charge, resulting in either a y-series or a b-series ion (see Fig. 9.22).

380 Mass spectrometric techniques