[Psidev-ms-dev] item Paul ion trap

[pierre-alain b. <pie...@is...>]

Hi all,

one action item was to clarify the existence, relevance and position of 
the Paul ion trap term.

Marcus Macht from Bruker did help in this, and here is the explanation 
and proposal:


We have the following terms discussed here:
-    Quadrupole ion trap
-    Paul ion trap
-    Linear trap
-    Ion trap


-    The term "quadrupole ion trap" refers to the nature of the fields 
inside an ion trap and NOT to the geometry of the analyzer.
-    A quadrupole ion trap, in its _classical_ design, and as described 
by Paul is made of a circular electrode and 2 end-caps electrodes. It is 
NOT constituted by a quadrupole (i.e. 4  linear or curved rods) with 2 
end caps electrodes.
-    The Paul ion trap is synonym to the classical quadrupole ion trap.
-    The linear trap (as in LTQ or Qtrap for instance) has the geometry 
of a quadrupole + end caps electrodes and generates quadrupolar ion trap 
fields. It is a quadrupole ion trap.
-    Both Paul ion trap an linear trap are quadrupole ion traps.

We should therefore have in the PSI-MS CV:
   +-quadrupole ion trap
      +-Paul ion trap (classical quadrupole ion trap with circular 
electrode such as in : Bruker Esquire, HCT, amaZon; Thermo LCQ; Shimadzu 
LC-IT-TOF and Axima Resonance (MALDI), Agilent/Varian 500-MS)
      +-Linear quadrupole ion trap (such as in ABSCIEX QTRAPs, Thermo LTQs)


Now about the term ion trap in the current CV:
In the PSI-MS CV, the term "ion trap" is not correctly positioned. It is 
a generic term with a correct definition for a generic term. The term as 
defined now should includes Orbi and FTICR as childs, though. And the 
synonym "IT" should become a synonym of quadrupole ion trap (as it is 
mostly used and marketed in that context). If we keep the term we should 
make the following (concentrate on the ion trap part):

Here is therefore the proposal:

mass analyzer
+-Time of Flight
+-quadrupole mass filter
+-magnetic sector
+-ion trap
    +-image current detection based ion trap <!-- new term -->
       +-Orbitrap <!-- note that this refers to the analyzer, not the 
instrument name, which is correctly defined in the CV -->
       +-FTICR (Penning cell)
    +-mass selective scanning detection based ion trap <!-- "renamed" 
quadrupole ion trap -->
       +-Paul ion trap (classical quadrupolar ion trap with circular 
electrode)
       +-Linear ion trap
          +-radial ejection linear ion trap
          +-axial ejection lineal ion trap

The term Pal ion trap should therefore not be obsolete.

Suggestions for the CV:
[Term] id: MS:XXXXXXX
name: image current detection based ion trap
def: "Ion trap analyzer where ions are moving in an orbit which 
trajectory frequency can be measured as an image current " [PSI:MS] 
is_a: MS:1000264 ! ion trap

[Term] id: MS:XXXXXXX
name: mass selective scanning detection based ion trap
def: "Ion trap analyzer where ions are m/z selectively ejected from the 
trapping device and detected outside of it " [PSI:MS]
is_a: MS:1000264 ! ion trap

[Term]
id: MS:1000484
name: orbitrap
def: "An ion trapping device that consists of an outer barrel-like 
electrode and a coaxial inner spindle-like electrode that form an 
electrostatic field with quadro-logarithmic potential distribution. The 
frequency of harmonic oscillations of the orbitally trapped ions along 
the axis of the electrostatic field is independent of the ion velocity 
and is inversely proportional to the square root of m/z so that the trap 
can be used as a mass analyzer." [PSI:MS]
is_a: MS:XXXXXXX ! image current detection based ion trap

[Term]
id: MS:1000079
name: fourier transform ion cyclotron resonance mass spectrometer
def: "A mass spectrometer based on the principle of ion cyclotron 
resonance in which an ion in a magnetic field moves in a circular orbit 
at a frequency characteristic of its m/z value. Ions are coherently 
excited to a larger radius orbit using a pulse of radio frequency energy 
and their image charge is detected on receiver plates as a time domain 
signal. Fourier transformation of the time domain signal results in a 
frequency domain signal which is converted to a mass spectrum based in 
the inverse relationship between frequency and m/z." [PSI:MS]
synonym: "FT_ICR" EXACT []
is_a: MS:XXXXXXX ! image current detection based ion trap

[Term]
id: MS:1000297
name: Paul ion trap
def: "A device that permits the trapping of ions by means of an 
alternating current voltage. The ejection of ions with a m/z less than a 
prescribed value and retention of those with higher mass depends on the 
application of radio frequency voltages between a ring electrode and two 
end-cap electrodes to confine the ions in a circular path. The choice of 
these voltages determines the m/z below which ions are ejected." [PSI:MS]
synonym: "quadrupole ion trap" RELATED []
is_a: MS:XXXXXXX ! mass selective scanning detection based ion trap

[Term]
id: MS:1000291
name: linear ion trap
def: "A two dimensional ion trap in which ions are confined in the axial 
dimension by means of an electric field at the ends of the trap." [PSI:MS]
is_a: MS:XXXXXXX ! mass selective scanning detection based ion trap


Note: I do have a doubt whether we need to separate a FT cell (Penning 
cell) where ions are detected as image current from the older FT-ICR 
where ions in teh Penning cell are detected while hitting the walls of 
the cell, but I suspect it is ok to leave like this.

Pierre-Alain