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Autosampler Contamination

Contamination in any chromatographic method is a complex problem to troubleshoot.  Extra peaks, often referred to as ghost peaks, in a blank or sample chromatogram can have a number of sources

  • Elution of analytes retained from a previous injection
  • Mobile phase contamination
  • Sample preparation
  • System contamination
  • Column contamination

This article will focus on autosampler contamination, how to determine if the autosampler is the source, and how to remedy the problem. 


The sample first makes contact with the HPLC system via the autosampler.  Contamination is often presented in the form of sample carryover as evidenced when injection of a solvent blank produces a mini-version of the previous sample’s chromatogram. 

Most carryover occurs in the rotor seal and is due to sample adsorption.  Extra peaks which are sharp are often due to sample contamination.  The appearance of broad, less efficient peaks within an otherwise good chromatogram may indicate the elution of highly retained species from previous injections (Figure 1).

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Figure 1: Identifying carryover and contamination.

It can be verified that the autosampler is the source of contamination by removing it from the flow path and carrying out a blank run to see if the ghost peaks disappear.  If the contamination peak is not present then the autosampler is the source. 

Conversely, if the contamination peak is present without an injection then contamination does not lie with the autosampler and other sources such as the rest of the system, solvents, and column etc. should be considered.

There are common contamination sites in an autosampler.  Figure 2 details these sites and remedial action which can be taken to remove and prevent further contamination.

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Figure 2: Sites of contamination and remedial action for autosamplers.
 

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Dr. Dawn Watson
 

This article was written by Dr. Dawn Watson.

Dawn received her PhD in synthetic inorganic chemistry from the University of Strathclyde, Glasgow. The focus of her PhD thesis was the synthesis and application of soft scorpionate ligands. As well as synthetic skills, this work relied on the use of a wide variety of analytical techniques, such as, NMR, mass spectrometry (MS), Raman spectroscopy, infrared spectroscopy (IR), UV-visible spectroscopy, electrochemistry, and thermogravimetric analysis.

Following her PhD she spent two years as a postdoctoral research fellow at Princeton University studying the reaction kinetics of small molecule oxidation by catalysts based on Cytochrome P450. In order to monitor these reactions stopped-flow kinetics, NMR, HPLC, GC-MS, and LC-MS techniques were utilized.

Prior to joining the Crawford Scientific and CHROMacademy technical team she worked for Gilson providing sales and support for the entire product range including, HPLC (both analytical and preparative), solid phase extraction, automated liquid handling, mass spec, pipettes, and laboratory consumables.

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