In order to extract the FAAs in the sample, 2 g of flour should be suspended in 17 ml of 0.2 M perchloric acid and 5 ml of methanol. The mixture should be homogenized at 12000 rpm for 2 min and kept in an ultrasonic (35 kHz) bath for 15 min and then should be centrifuged at 3250 g for 30 min. The supernatant should be filtered through Whatman 42 paper and filled into an Eppendorf tube. Samples then tightly should be capped and store at -18 °C until analysis.
Methods including the addition of acids and alcohol-water media are best for free amino acids extraction. I have used trichloroacetic acid (TCA) that denaturizes gluten proteins and keeps them out of the extraction solution, but you have to be careful with its concentration and contact time to prevent acidic hydrolysis that can alter your results. Polysaccharides, especially starch in the case of flour, are kept away from the extraction solution by using ethanol or methanol water mixtures (70 to 80% at least might be advisable)
In any case, try to validate all details of your selected method before applying it to investigation, especially if you are using spectrophotometrical analysis (ninhydrin method or ultraviolet measurement of aromatic amino acids). By the way, do not forget to centrifuge properly your extraction solutions to avoid an important alteration of your results.