Baseline noise issue

[xiaoyu_fish]

We have a thermo finnigan LCQ instrument. Currently, I am just using the LC-PDA part. However, it gives high intensity noise (2000-5000uAU) during isocatic run and ~ 10000 uAU noise during gradient run. I have used water, IPA, pure acetic acid for washing the liquid displacement assembly. The pump seal also has been replaced with new ones. Beside, I tested all four propotioning valves, but the same baseline noise problem still exists. I tested the flow rate which is fine. However, if I premix two mobile phases (0.1% formic acid in water: 0.1% formic acid in ACN = 62:38) together and run isocratic, there is almost no baseline issue. Baseline noise in this case is ~ 100-200 uAU.

Is there anyone can give some suggestions? I really appreciate it. Thank you very much!

[tom jupille]

You have pretty much narrowed the problem down to a mixing issue. It would help to see if there is a pattern to the noise (and if so, is it synchronized with what the proportioning system is doing. [Instructions for linking chromatograms are here: viewtopic.php?f=1&t=2617 ]

Sometimes doing a "partial pre-mix" can make a big difference: try putting 10% ACN in A and 90% ACN in B, and adjust the A/B ratio appropriately (65:35 should be equivalent to the original 62:38).

[xiaoyu_fish]

Thank you, Tom!

Here is a previous blank run chromatogram. In first 15 min, it is isocratic. Afterwards, mobile phase B increased at 1ml/min.

http://tinypic.com/view.php?pic=2wnbkw0 ... CxVc9m9LCQ

I will try the partial premixing. Is it possible that is due to worn piston? Or the inlet module?

[xiaoyu_fish]

Partial premixing slightly helped the baseline noise issue. However, the problem still existed.

[tom jupille]

That looks to me like a proportioning valve issue. I know you said you tested it, so more detailed questions are in order: what did the "stairstep" test results look like? (http://www.lcresources.com/resources/TSWiz/hs450.htm )

[badger]

Ideas:

Try cleaning your flow cell, like take it out of the detector and wipe off the glass.
Also, is your method run at a high temperature? Is the tubing between your column and detector properly insulated?
Where do you get your water from? Is it filtered? Is your filtration system functioning properly?

[badger]

Sorry, just looked at your chromatogram. What Tom said is probably more applicable than my suggestions. That looks like systematic error from some faulty piece of equipment rather than random noise.

[xiaoyu_fish]

That looks to me like a proportioning valve issue. I know you said you tested it, so more detailed questions are in order: what did the "stairstep" test results look like? (http://www.lcresources.com/resources/TSWiz/hs450.htm )

Thank you, Tom and thank you, Badger. You guys' suggestions are very helpful. Actually I installed pump outlet seal and replaced the old check vavle seals. It helps reduce the noise for a little bit. Especially if I premixed the two mobile phases, there is almost no noise (~20 uAU). However, a new baseline noise problem showed up. It periodically shows spike noise with high intensity. I attached an image below. Is it likely a proportioning vavle problem? Any suggestions will be greatly appreciated.

http://i57.tinypic.com/2en6bs1.jpg

I will try to do the gradient proportioning vavle test when I can. Thank you very much.

[xiaoyu_fish]

After I switched the channel with purging several times, the spike seems gone now. I guess it is because some bubble trapped inside of the pump which takes time to be removed with a maximum flow rate, 2 ml/min. Thank you all the same!