Mass analyzer systems and methods for their operation

1. A mass analyzer system comprising:

a sample support having a sample surface;

an optical system configured to irradiate a sample on the sample surface with a pulse of energy such that the pulse of energy strikes a sample on the sample surface at an angle substantially normal to the sample surface;

a MALDI ion source comprising;

a first electrode spaced apart from the sample support;

a second electrode spaced apart from the first electrode in a direction opposite the sample support holder;

a third electrode spaced apart from the second electrode in a direction opposite the first electrode; and

a power source electrically coupled to the sample support, the first electrode, the second electrode, and the third electrode and configured to:

apply a first potential to the sample surface and a second potential to at least one of the first electrode and the second electrode to establish a non-extracting electric field at a first predetermined time substantially prior to striking a sample on the sample surface with a pulse of energy to form sample ions, the non-extracting electrical field substantially not accelerating sample ions in a direction away from the sample surface;

change the electrical potential of at least one of the sample surface and the first electrode to establish a first extraction electric field at a second predetermined time subsequent to the first predetermined time, the first extraction electric field accelerating sample ions in a first direction away from the sample surface, the first extraction electric field accelerating sample ions in a first direction away from the sample surface along a first ion optical axis that is substantially coaxial with the pulse of energy; and

apply a third potential to the second electrode to focus ions in a direction substantially perpendicular to the first direction;

an ion deflector configured to deflect ions from the first ion optical axis and onto a second ion optical axis;

a first time-of flight positioned between the ion deflector and a timed ion selector;

the timed ion selector being positioned between the first time-of flight and a collision cell, the timed ion selector being positioned to receive ions traveling along the second ion optical axis and being configured to select ions for transmittal to the collision cell;

a second time-of-flight positioned between the collision cell and a first ion detector;

an ion mirror positioned between the second time-of-flight and the first ion detector; and

a third time-of-flight positioned between the ion mirror and a second ion detector.

2. The mass analyzer system of claim 1 , comprising a temperature controlled surface disposed in the ion source.

3. A method of operating a mass analyzer system having two or more modes of operation and an ion source comprising a sample support having a sample surface, a first electrode spaced apart from the sample support, a second electrode spaced apart from the first electrode in a direction opposite the sample support holder, and a third electrode spaced apart from the second electrode in a direction opposite the first electrode, the method comprising the steps of:

selecting for a first mode of operation a first position of a time-focus plane of the ion source by application of a first electrical potential difference between the sample surface and the first electrode, by applying a first electrical potential to the sample surface and a second electrical potential to the first electrode, the direction z being substantially normal to the sample surface;

irradiating a sample on the sample surface with a pulse of energy at an irradiation angle that is substantially normal to the sample surface to form sample ions by matrix-assisted laser desorption/ionization;

focusing sample ions in a direction substantially perpendicular to the direction z by application of a third electrical potential to the second electrode;

extracting sample ions in the direction z along a first ion optical axis which is substantially coaxial with the pulse of energy;

deflecting sample ions from the first ion optical axis and onto a second ion optical axis for mass analysis using the first mode of operation on sample ions deflected onto the second ion optical axis;

changing the mode of operation of the time-of-flight mass analyzer to a second mode of operation; and

selecting for the second mode of operation a second position of a time-focus plane of the ion source by application of a first electrical potential difference between the sample surface and the first electrode, by applying a fourth electrical potential to the sample surface that is substantially equal to the first electrical potential and applying a fifth electrical potential to the first electrode;

irradiating a sample on the sample surface with a pulse of energy at an irradiation angle that is substantially normal to the sample surface to form sample ions by matrix-assisted laser desorption/ionization;

focusing sample ions in a direction substantially perpendicular to the direction z by application of a sixth electrical potential to the second electrode;

extracting sample ions in a direction substantially normal to the sample surface along a first ion optical axis which is substantially coaxial with the pulse of energy; and

deflecting sample ions from the first ion optical axis and onto a second ion optical axis for mass analysis using the second mode of operation on sample ions deflected onto the second ion optical axis.

4. The method of claim 3 , wherein one of the mode of operation comprises collision induced dissociation using an ion optics assembly comprising a first ion lens disposed between a retarding lens and an entrance to a collision cell, the respective step of deflecting sample ions from the first ion optical axis and onto a second ion optical axis for mass analysis using said mode of operation comprising:

substantially focusing sample ions to a focal point in the first ion lens and forming after the focal point in the first ion lens and before the entrance to the collision cell a substantially collimated ion beam of sample ions at a first collision energy by:

establishing a decelerating electrical field to decelerate sample ions entering the retarding lens by applying a first electrical potential to an electrode of the retarding lens;

establishing an accelerating electrical field between the retarding lens and the first ion lens to accelerate sample ions from the retarding lens and into the first ion lens by applying a second electrical potential to an electrode of the first ion lens; and

establishing a decelerating electrical field between the first ion lens and the entrance of the collision cell to decelerate sample ions from the first ion lens by applying a third electrical potential to the entrance of the collision cell.

5. The method of claim 4 , wherein:

the retarding lens comprises a first electrode, a second electrode and a third electrode, the first electrical potential being applied to the first electrode, the second electrode, or both; and

the first ion lens comprises said third electrode, a fourth electrode and a fifth electrode, the second electrical potential being applied at least to the third electrode.

6. The method of claim 5 , wherein sample ions are substantially focused to a focal point between the third electrode and the fourth electrode.

7. The method of claim 4 , further comprising:

changing the first collision energy to a second collision energy different from the first collision energy; and

substantially focusing sample ions to the focal point in the first ion lens and forming after the focal point in the first ion lens and before the entrance to the collision cell a substantially collimated ion beam of sample ions at the second collision energy by:

establishing a decelerating electrical field to decelerate sample ion entering the retarding lens by applying a fourth electrical potential to an electrode of the retarding lens, the fourth electrical potential being substantially equal to the first electrical potential;

establishing an accelerating electrical field between the retarding lens and the first ion lens to accelerate sample ions from the retarding lens and into the first ion lens by applying a fifth electrical potential to an electrode of the first ion lens; and

establishing a decelerating electrical field between the first ion lens and the entrance of the collision cell to decelerate sample ions from the first ion lens by applying a sixth electrical potential to the entrance of the collision cell.

8. The method of claim 3 , wherein one of the modes of operation comprises performing collision induced dissociation at different collision energies using a an ion optics assembly comprising a first ion lens disposed between a retarding lens and an entrance to a collision cell, the respective step of deflecting sample ions from the first ion optical axis and onto a second ion optical axis for mass analysis using said mode of operation comprising:

forming a substantially collimated ion beam of sample ions at a first collision energy by:

applying a decelerating electrical potential to the retarding lens, by applying a first electrical potential to an electrode of the retarding lens;

applying an accelerating electrical potential difference between the retarding lens and the first ion lens, by applying a second electrical potential to an electrode of the first ion lens; and

applying a decelerating electrical potential difference between the first ion lens and the entrance to the collision cell, by applying a third electrical potential to the entrance of the collision cell;

changing the first collision energy to a second collision energy different from the first collision energy;

forming a substantially collimated ion beam of sample ions at the second collision energy by:

applying a decelerating electrical potential to the retarding lens, by applying a fourth electrical potential to an electrode of the retarding lens, the fourth electrical potential being substantially equal to the first electrical potential;

applying an accelerating electrical potential difference between the retarding lens and the first ion lens, by applying a fifth electrical potential to an electrode of the first ion lens; and

applying a decelerating electrical potential difference between the first ion lens and the entrance to the collision cell, by applying a sixth electrical potential to the entrance of the collision cell.

9. The method of claim 8 , wherein sample ions are substantially focused to a focal point a distance F from an entrance to the retarding lens.

10. The method of claim 9 , wherein the distance F varies within less than about .±.4% when the difference between the first collision energy and the second collision energy is less than about 5000 electron volts.

11. The method of claim 9 , wherein the distance F varies within less than about .±.2% when the difference between the first collision energy and the second collision energy is less than about 5000 electron volts.

12. The method of claim 9 , wherein the distance F varies within less than about .±.1% when the difference between the first collision energy and the second collision energy is less than about 5000 electron volts.

13. The method of claim 8 , wherein sample ions are substantially focused to a focal point within the first ion lens.

14. The method of claim 8 , wherein: the retarding lens comprises a first electrode, a second electrode and a third electrode, the first electrical potential being applied to the first electrode, the second electrode, or both; and the first ion lens comprises said third electrode, a fourth electrode and a fifth electrode, the second electrical potential being applied at least to the fourth electrode.

15. The method of claim 14 , wherein sample ions are substantially focused to a focal point between the third electrode and the fourth electrode.

16. The method of claim 8 , wherein the fourth electrical potential is within about .±.5% of the first electrical potential.

17. The method of claim 8 , wherein the fourth electrical potential is within about .±.2.5% of the first electrical potential.

18. The method of claim 8 , wherein the step of changing the collision energy comprises substantially fixing one of a source potential at which sample ions are formed or the electrical potential on the entrance to the collision cell; and changing the other.

19. The method of claim 18 , wherein the step of changing the collision energy comprises substantially fixing a source potential at which sample ions are formed and changing the electrical potential on the entrance to the collision cell.