be a huge difference between organic oranges in one of these Whole Foods type/straight-from-the-farm, and "conventional" varieties at normal grocery. It's a consideration.
There are studies that check keto-acids during the different seasons. I may have included the paper which deals with virus infected plants. Basically, sun-ripened fruits will have more keto-acids. Location where grown will be an important factor; sunny California compared to cooler areas. Now it would be interesting to know whether organically grown have increased levels. You would think by providing the plants with inputs high in the amino acids would increase the keto-acids. I think the melon studies subjected melon cubes to amino acids to increase aroma volatiles. As organically grown fruit have different inputs than conventional, you may see a difference here. Nice to know; not that I want to pay extra for my oranges. Useful for growers to know that certain inputs can increase the levels of keto acids be they organic or conventional grown.
Glad that you are using lc/ms. Now that we are clear on which keto acids you are looking for; you need to ensure that you select the appropriate column for the method. The lab may already have one. You don't want an old one. Test the column beforehand ensuring there are no issues with resolution. You don't want an old column that has not been properly maintained. Columns are expensive, so determine which one you require so that it can be ordered before you start and not during your experiment. As mentioned previously, the manufacturer of the instrument can provide advice on column selection for the method you are using.
Find out who the guru in lc/ms is in the lab. You will need assistance and guidance, as setting up the right conditions for your sample can take time, to get just right. You want to do this as efficiently as practical otherwise you will run out of time. It is one thing learning the theory however totally new ball game when it is hands on. You will need someone knowledgeable in the art to help you troubleshoot.