Few years ago, I made a shampoo utilizing chamomile flowers for a science fair but I did not publish that research. I became interested in chamomile (which is considered by many as a medicinal plant). Here is a paper which will be interesting for your work. Good luck.
Flavonoids could be extracted with MeOH. After HPLC investigation of the
concentrated extracts, the extract could be applied to PPC with BAW, 15% HOAc and then BEW (n-BuOH/EtOH/H2O = 4:1:2.2). Components isolated can be purified by preparative HPLC (solvent system: MeCN: H2O = 20:80 and 22:78) and Sephadex LH-20 column chromatography (solvent system: 70% MeOH). Later Qualitative HPLC analyzes of the isolated compounds could be performed using Shim-pack CLC-ODS [I.D. 6.0 x 150 mm], at a flow-rate of 1.0 ml/min, detection wavelength of 190-530 nm and eluent of MeCN/HOAc/H3PO4/H2O (6:8:3:83) for anthocyanins, and 190-360 nm and MeCN/H2O/H3PO4 (22:78:0.2) for other flavonoids. In quantitative HPLC analyses, each 0.2 g of perianth can be extracted with 2 ml of 5% HOAc for anthocyanins, and 2 ml of MeOH for other flavonoids. The extracts later can be directly analyzed with HPLC systems.
To better extract the flavonoids from your matrix, first you need to develop an efficient method. If you are looking for polar flavonoids, I suggest to go for microwave assisted extraction using aqueous ethanol as solvent.
The extract can further be purified suing preparatory HPLC to isolate compound of interest.