I had the same issue with Phenolic glycosides as I exhausted my list of potential ISTDs and there was always impeding interaction with my compounds of interest.
Depending on how many samples you have I would suggest you run each sample 3 to 5 times and take the average of the peak area. You might wanna use excel as some data analysis softwares require ISTD for quantification.
Internal standards are required for recovery calculations. You may use this in your standard curves to calculate the recovery percentage of your procedure. We should remember that the regular procedure does not yield complete recovery and thus we always have to adjust the curves accordingly. Based on the recovery of your standard curve analysis you can confirm the recovery and use this average value for your sample. If you have interaction issues with IS this is one way around. Note that the use of no internal standard will result in relative value with no reference point at all. Hope this helps.
Please read the following manuscript in attached file.The electronic version of this article is the complete one and can be found online at: http://www.plantmethods.com/content/4/1/16
Thank you Heshmat Soliman Aldesuquy for the manuscript link. I have already gone through the manuscript and the problem in my case is that I don't have the labelled phytohormone internal standard as stated in the manuscript. So my main problem is how to skip the internal standard thing in LCMS and if I carry out the hormone quantification without internal standard how far it is acceptable?