How to clean an Agilent GCMS Ion Source

Document created by paulsalverda Employee on Nov 11, 2015Last modified by ryan_ohearn on Jun 2, 2016
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During the normal course of operation GCMS sources require cleaning due to sample throughput. This can be indicated by:

  • Loss in analyte response not improved by normal inlet and column maintenance.
  • Poor calibrant ion peak shapes during tuning, especially for the 502 ion.
  • Escalating tune repeller voltage.
  • Escalating tune Electron Multiplier voltage.


Sample residue, gas contaminants, and pump oil vapor all form an adsorbed organic film that must be removed. This film is often semi-insulating and causes a loss of the required electric fields necessary for optimum performance. Thoroughly cleaning all metal surfaces of the source removes this coating.  The care taken during this activity becomes more critical as our instruments become more sensitive.  The attached document contains the latest up-to-date way to do this, including tips and tricks you may have not seen before.  The R&D engineers added some very interesting tidbits!


Source cleaning is normal user maintenance and is only covered under the contract during scheduled preventative maintenance. Customers can add extra source cleaning visits onto their contract if they want Agilent to do it for them; customers may do it themselves if the symptoms point to that as the first step. Customers need to be trained on the best way to accomplish this recurring task, and this document is a good supplement to the information in the operations manuals and the available videos.

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