A "blank" run would consist of mobile phase only. No one can answer your questions without additional information. Please provide us with your actual HPLC and MS conditions so we can better understand what your actual sample is (lipids can stick to everything!) and what your method is.

If you have not done so already, run with a flow restrictor in place of the actual column to rule it out as a source of contamination. You may have contaminated the MS source too (or no contamination at all, just looking at debris from poor quality washes??), but please provide us with more information before we start guessing at the cause.

Bill is right, more information are needed.

Additionally you may check if your solvents are contaminated (use a fresh bottle), clean everything well prior change anything. Also clean the spray chamber/check for dirt. You may also clean the MS capillary which connects the spray chamber with the internal part of the MS instrument. It yould be a contaminated needle, tubing, whatever had contact to something which hardly dissolves in your solvent system and flushed out only slowly. But this is just guessing!

Thank you. 

I will keep in mind your suggestions and work again.

Sangita

 Bill and Marcus are right. You need to provide more information on what type of sample you are working with.

In addition to what is already said look if the transfer capillary is contaminated and try cleaning it. Inspect the spray needle and the column for possible contamination. Look for contamination in the sample injection needle (they are one major source).

Hope this helps 

Hey,

Thats true, additional information is required. Can you text the make and model of the instrument? I have one doubt, while running the blank, Did u pass it through a column or you run the blank without column by just keeping union? and is there any other thing present in the blank other than mobile phase?

Additonally to Bharath's answer, there are certain cleaning procedures which should be perfomed to guarantee maximum performance (provided by the company, sometimes they also offer cleaning mixtures/preparation). Expecially for the transfer capillary, do not clean it as you think, clean as how the company suggests!

The MS instrument needs to be tuned again after cleaning the capillary for sure. This may take few hours prior you can start your analysis again. This is performed by the instrument/software automatically and andjusts e.g. sensitivity, baseline and noise to certain levels which are preset in the internal setup of the instrument.

And yes, try to run w/o the column to ensure that you can exclude this as a source of contaminations as Rahul suggested.

Thank you all.