I want to find a chemoattractant present in spent media which possible is a small unknown molecule. Please suggest me ways to extract the desired fraction and remove the other interfering contaminants and also the sample preparation.
Without knowing more about the molecule, you can't really extract it. Standard isolation methods are liquid-liquid or solid phase extracting. To perform these, you first need to know the chemical properties of the molecule. Will it be retained by water or by hydrophobic compounds? Based on that you can optimize extraction conditions and the solvents you use, i.e. buffered water, low/high pH water, methanol, acetonitrile, ethers, etc. Without knowledge about what kind of molecule you're looking for, you can't extract and perform LC-MS (as LC-MS also requires settings to optimize for hydrophillic/hydrophobic/polar compounds, e.g. which type of column & mobile phases you use).
As Gido Snaterse says, you should know a little bit about the physical and chemical behavior of the molecule. Sometimes I had good results with GPC (Gel-Permeations-Chromatographie) to get rid of matrix and unwanted stuff, cleaning up samples quite good and taking fractional samples for sample-preparation and further analyses. Possibly your sample is fluorescent or UV-active, so you can grab your sample-slot (ret.-time) by GPCing and monitoring it, when it drops out from your GPC-coloumn. So you caught ur molecule and it should be ready to go on with the molecule of interest. Good Luck!
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