Anion-cation balance in particle phase I'm now analysising the water-soluble ions in atmopsheric aerosol. With ultrasonic concussion and filtering impurity, the anion and cation from the particle sample are examined  in Ion Chromatography System(IC) separately.  

We test $\ce{Cl-, SO4^2-, NO3-}$ and $\ce{Ca^2+, Mg^2+, Na+, NH4+, K+}$ as 8 major ion species to quantify the concentration level and seasonal variation in the sampling area.  

But when I combine the anion and cation data together for same particle sample, the ratio of [ Total charge of anion]/[Total charge of cation] are much larger than  1. 

In my opinion, the cation and anion inside particle should keep the balance of charge. The 8 ion species I choose should take up the majority of the total water-soluble ions (added with $\ce{F-}$, organic acid radical, etc).    

I have also searched some paper, some results  of their ion-sample are also not keep the balance, but some observed. 

Are the ratio of (+-)charges differed by sampling sites? The anion especially $\ce{SO4^2-}$ are larger comparing with the cation species. Are there any missing cation that I have not deteced?
Yes, you have left out one very important cation from your cation/anion balance: $\ce{H+}$

The primary pathway for new particle formation in the atmosphere is the photo-oxidation, via hydroxyl radicals, of volatile reduced sulfur species to form very non-volatile sulfuric acid.  For the most part then, new particles start out as puny droplets of sulfuric acid and grow via accretion, etc. from there.  

I recommend measuring the pH of the filtered aerosols, and I strongly suspect that will account for your missing cations.  

If I have missed the point of the question, please feel free to ask for any clarifications in the comments.