• For liquid chromatography to be initiated, the mobile phase solution and all samples must be fully dissolved / soluble at all times.
• Ammonium acetate would be flushed from the column using an AQUEOUS solution, not an organic one. If you are running RP methods and want to flush buffer from the system (and you should be doing this every day), then please flush your system with a mostly water based solution (example: 90% Water / 10% MeOH), not 100% organic solution. Once the buffer has been rinsed from the column, a high concentration of mostly organic solvent (stronger) should be slowly introduced to remove any bound material from the column.
• Your mobile phase contains no water, yet it does contain a wide array of organic solutions plus ammonia acetate and TEA?? What are you doing and what column are you doing it with?? This does not sound like chromatography.

It does sound like your column or the tubing connection leading to and from it may be plugged. For now, place the guard column aside (which is not needed at all) and disconnect the column inlet fitting from the column. Point the disconnected line (from your injector) into a glass beaker (e.g. 150 ml) and run a premixed solution of 90% Water / 10% MeOH through it at an appropriate flow rate for several minutes. Observe the pressure and flow. It should flow with minimal back pressure. If so, and your column is a RP column (e.g. C18), then connect it back to the system, disconnect the column outlet line and position the column outlet over the beaker. Run the same liquid at a low initial flow rate through the column and observe the pressure over time. It may rise initially, but should stabilize at some point (yes, you may reverse the column if needed after trying the above).

Please provide us with more information about what you are doing. Details such as the exact column type and dimensions, flow rate, isocratic or gradient conditions, inj volume and inj solution, detector settings, sample TYPE, observed back pressure under the conditions specified above, and anything else you think is important to include. Once we have this basic info, we will be in a better position to provide advice.

Detach column, and run line directly to detector, make sure the plug is not in the detector.  If it is you will need to flush detector (see manufacturer recommendations on flushing detector).

Re-install column leaving detector side open so you can see if mobile phase is coming out of column.

Use 50/50 Acetonitrile/water - start off at low flow (.2 mL/min).  Is anything coming out of column?  If yes let it flow for an hour, and then try ramping up the flow slowly.

If this doesn't work flip column and repeat ( backflushing is done by reversing the column)

Desperation move if nothing else works: Sometimes columns have a pre-filter frit at the head of the column, remove the fitting at the head of the column - replace pre-filter if possible - or sonicate in 50/50 Acetonitrile/water.

Finally - don't ever use that mixture again.  You need a portion of your mobile phase to be aqueous when using salt buffers.

In reference to the last sentence in Peter Philbrook's comment: if possible, can you give us more information about your experiment?  The solvent system is very unusual, and there may be better combinations for your analysis.

 Many thanks for your helpful and informative replies. 

Bill Letter, I will try flushing my column using your suggestion. To clarify, a.acetate is dissolved in a methanol/isopropanol mixture and then, depending upon how many litres of total mobile phase we are wanting, some of this mixture is mixed in with the ACN:Dioxane mix. I personally did not setup this method, a post-doc in our group recently developed it for our lab, but the original method is in the following publication:  

(Nomura AM et al (1997) Serum micronutrients and prostate cancer in Japanese Americans in Hawaii. Cancer Epidemiol Biomarkers Prev, 6, 407-12.) 

He has also not had any complications using this method, but I will bring this up with them regardless. Thank you for raising this. 

The column is a C18 sphereclone 5u 250*4.6mm. We are using it to separate and quantify retinyl esters from liver tissue. Flow rate 1ml/min, 100% isocratic flow of mobile phase, 10ul inj volume, 325nm detection wavelength. 

Peter Philbrook, many thanks for the advice, I will run according to your suggestions. And please see above as to what I have mentioned about the a.acetate; but thank you also for voicing this concern.

Adam: Thank you for the additional info.

I do not have access to the paper you reference so can only say that the method appears to be illogical and not follow fundamental chromatography principles. *It would be nice to see a chromatogram with peaks and all of the settings too. 

You mentioned that you are running in an isocratic mode. If not coupled to a secondary wash method after each run (*not incorporated into the analysis run), then this will lead to column fouling, poor chromatography and/or clogs even when a method utilizing good fundamentals is used. A gradient method might be much better.

The clog issue you have is rather minor compared to the problems that the proposed method itself has. I teach chromatography and train scientists in method development and based on the information you have provided so far,  I would not use it.

With a simple keyword search I found numerous related RP methods (e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483537/). Note: I am not recommending any method, just suggesting that there are more appropriate ways to separate these compounds via RP methods.

because it is reverse phase system,then you can work with 100 % water,flush 100% water only until you get start pressure ,i think this is the only way to regenerate the system!

I wonder about your guard column: why does it not behave the same as your column does?

Is it of same chemistry like the column?

Do they have  identical  history?

If not- may some sample or mobile-phase residue, retained on the guard column, was swept to the column and blocked it?