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Clogging of the H-ESI spray needle is generally caused by the presence of non-volatile components in the injected samples. If the non-volatile components of the samples are not removed during sample preparation, they will be injected onto the column where they will gradually bleed off over time into the detector. They may also be directly introduced by the use of non-volatile buffers in the mobile phase. Non-volatile buffers should be avoided in LC-MS analysis because the spray needle will clog frequently and in addition the MS optics will quickly become contaminated.

Clogging issues may be worsened when using a divert valve or bypass valve. This is because when the valve switches to waste the LC flow to the needle is stopped, causing the residual liquid in the hot needle to quickly evaporate. This in turn causes the non-volatile components to deposit on the inner wall of the tubing which will eventually clog it.

When using a divert or bypass valve, the issue may be fully resolved by adding another HPLC pump to supply make-up flow through the needle when the column eluent is bypassed. The second pump is connected to the divert valve or bypass valve so that when the eluent is diverted to waste, clean solvent flows through the needle to help keep it clean. Alternatively, sample preparation procedures should be modified to reduce the amount of non-volatile components in each sample injection.

Possible Cause: System was vented because of a main power failure
A main power failure has the same consequence as switching off with the main power circuit breaker switch. If the power is available again, the system is started up automatically: the pumps are switched on and the vacuum is created. If the system has been vented during the mains failure, it is necessary to bake out the system to obtain the operating vacuum. See “Baking Out the System” on page 8-12. If the log file of the data system shows a reboot of the system and the pressure reading in the Tune software shows a bad vacuum, this indicates that the system was vented. In case of frequent but short power failures we recommend that you install an uninterruptible power supply (UPS). If main power failures occur frequently while the system is not attended (for example, in the night), we recommend that you install a power fail detector.

Possible Cause: Vacuum leak
Refer to pages 7-5 and 8-12 in Operator's Manual

The UHV chamber heating control may have failed. During general operation of the mass spectrometer, the temperature of the UHV chamber is not regulated. Only during a system bakeout, electric power is supplied to the heating elements of the UHV chamber. The heating always operates at maximum power. Thus, failure of the heating control does not lead to a dangerous overheating of the mass spectrometer. If the Exactive Series mass spectrometer does not work as expected, use the Tune software for error diagnosis:

  • The messages window displays real-time information about the statuses of the instrument, the control service, or other programs. If the heating was terminated, the window displays a corresponding error message.

In case of a failure of the UHV chamber heating control, shut down the mass spectrometer as described on page 6-8. To prevent permanent damage to components of the Exactive Series mass spectrometer, Thermo Fisher Scientific recommends that you call a Thermo Fisher Scientific field service engineer.

A turbomolecular pump may be switched off because of one of the following reasons:

  • Turbomolecular pump is blocked
  • Failure of fans in turbomolecular pump

Each of the above reasons might lead to an overheating of the pump. When overheated, a turbomolecular pump switches off automatically to prevent its destruction. This overheating protection prevents the outbreak of a fire and minimizes the risk of destructing the pump. If the Exactive Series mass spectrometer does not work as expected, use the Tune software for error diagnosis:

  • The instrument status window displays real-time status information for the instrument components. All parameters are arranged in a tree view. In addition to showing numerical values of parameters (for example, pump speeds or component temperatures), the instrument status window uses icons to indicate the statuses of system components.
  • The messages window displays real-time information about the statuses of the instrument, the control service, or other programs. It might display additional information.

In case of an overheated turbomolecular pump, shut down the mass spectrometer as described on page 6-8. To prevent permanent damage to components of the Exactive Series mass spectrometer, Thermo Fisher Scientific recommends that you call a Thermo Fisher Scientific field service engineer.

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