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4 New Reference Mass Introduction Procedure
Reference Mass Solution Operation with a new Top Plate – For Use with TOF or Q-TOF
LC/MS Instruments ONLY!
PLEASE NOTE: These instructions apply only to 6200 Series TOF and 6500 Series Q-TOF
LC/MS systems with an HPLC-Chip/MS interface. Do not use the reference mass solution
with 6400 Series Triple Quad or 6300 Series Ion Trap LC/MS Systems.
When performing accurate mass measurements on a TOF or Q-TOF instrument, it is desirable
to add compounds which ionize under the analysis conditions and provide known accurate
mass values ("reference masses") in real time so the mass values in the acquired spectra may
be corrected for short-term variations. This document provides a description for performing
this function on Agilent TOF or Q-TOF instruments outfitted with a G4240 HPLC-Chip/MS
Interface and operated in positive ion polarity. You need a modified top plate for the HPLC-
Chip/MS interface assembly and chemicals to make solutions of reference mass compounds.
After applying the solutions to an absorbent wick on the underside of the top plate, the IRM
compounds slowly evaporate and are ionized, providing signals for correction of the mass
assignments.
In order to operate successfully using this modified top plate, the drying gas supply to the
LC/MS system must be altered so that air (oxygen) is present in the drying gas and the flow
out of the ionization region is restricted. If this alteration has not been performed but this
modified top plate is installed, the spray from the Chip will be erratic and unstable. The
complete instructions for this alteration are in part number G1995-90000 (instructions for
G1995A Low Background Site Preparation kit). If you have not made this alteration to the
drying gas supply, it is not recommended to use the modified top plate.
The major differences from the previous generations of top plates are the replacement of the
conductive brushes on the top and the addition of a contained absorbent wick on the bottom.
The brushes close off the slot in the top plate while still allowing for insertion and ejection of
the HPLC-Chip. This minimizes the entry of outside air and contaminants into the ionization
region, lowering the abundance of background ions produced and detected by the instrument.
The wick holds the IRM solution. You do not need to dismount the Chip cube in order to install
the modified top plate.
Preparation of the IRM solutions
The example below assumes you wish to use two internal reference mass standards; however,
it is possible to omit either one if desired. The solution of internal reference mass standard(s)
in acetonitrile (ACN) is applied to the wick and allowed to dry. Then the high mass solvent (FC-
Page 24 of 33
18 July 2011
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