The most important module that needs to be optimized for lowest carry
over is the autosampler.
To provide lowest possible carry over we recommend:
• Prime flush pump daily for three minutes with appropriate solvent
previous to the first run.
• Set needle wash in flush port to at least 10 seconds.
• Use injector program as injection mode with additional injector valve
switching (figure 3) if carry over is significantly higher than 0.01 %.
If compounds that need a high percentage of organic phase are
analyzed, it is recommended to switch the injection valve at the high
percentage of organic phase after the last peak has eluted. It is also
recommended to switch the injection valve again after the start conditions
for the mobile phase have stabilized. This ensures that in the bypass groove the gradient start conditions are given, which is especially
important for flow rates below 0.5 ml/min.
• For samples where needle outside cannot be cleaned sufficiently
with water or alcohol use wash vials with an appropriate solvent.
With an injector program several wash vials can be used for cleaning.
"Flush port" on the Agilent 1200-series (Well plate sampler waste valve or Prime purge valve?). Are you referring to the Prime Purge valve located on the pump head? If so, this valve should be opened each time you wish to change mobile phase solution; change bottles or manually purge the system of bubbles or liquid. Normal position is closed. We normally open this valve at the start of each day to wash mobile phase from all of the channels (one at a time) through the system to waste to remove gas which has bleed into the system when not in use. Note: This is a very delicate needle valve and should be opened one or two turns at most, using your fingers (not a wrench). Turn counter-clockwise to Open. Turn clockwise to close and just snug it closed, do not turn the valve so hard that you have trouble opening it again. You will damage it. You can check to confirm it is closed by looking for liquid to exit through the waste tubing connected to it. When closed, no liquid should come out of that line.
Carry Over: If your instrument has been properly maintained (a worn injector rotor seal will cause sample carry-over), then you should not have any issues with sample carry over with an Agilent 1200-Series Autosampler at all. They utilize a needle/pump flow through design so carry over is not possible 99.9% of the time. The entire flow path from needle, needle seat, loop, injector pump to column is continuously washed (not true of other HPLCs) so any left over material is continuously flushed out during your method. The outside of the needle is the only area left "unwashed", but this is rarely and issue, and if needed, a dip (described later) can help. This fantastic autoinjector design works great, but does increase system volume (we can discus how to improve that aspect later on, if needed). The most significant way you can induce carryover in this type of system is to not understand how it works and use the wash vial. Do not use the wash vial feature. It is not needed, except under rare circumstances. Do not program the injector to do anything but inject the sample as designed. We often see chromatographers who have no experience or formal training using HP or Agilent HPLC systems have carry over issues with these modules because they are so used to having these problems with other brands of systems (esp Waters). They have not received proper training in how to use these A/S with their different designs, so make things worse by using a wash vial. By learning how they work, you can make better decisions how to use them. ;)
If you would like to read more about how to troubleshoot and reduce sample carryover (carry-over) in HPLC and LC-MS systems for this and many other HPLC brands, please read the attached article link, "Carry-Over (Carryover) Contamination in HPLC and LC-MS Systems ". *The information contained within it has been taught by my to thousands of scientists over the years as part of fundamental chromatography training and service classes. I think it will answer most of your questions.
http://hplctips.blogspot.com/2015/02/carry-over-carryover-contamination-in.html
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