Dear Muthamil Iniyan

I'm not a specialist in bacteria but maybe you will be interested in three papers. First denotes to global metabolic profiling of bacteria (E. coli):

http://www.ncbi.nlm.nih.gov/pubmed/18331064

Another protocol:

http://www.ncbi.nlm.nih.gov/pubmed/22608809

The last one is about ECMDB: The E. coli Metabolome Database

http://www.ncbi.nlm.nih.gov/pubmed/23109553

I think that this might help at beginning. UPLC-QTOF-MS or GC-QTOF-MS are good techniques for secondary metabolites discovery. However, it always depends on the chemical type of the compound. Currently it is very hard or even impossible to measure all low-molecular compounds (belonging to different chemical classes) using single protocol or equipment. Usually you need either to utilize different extraction protocols or combine several detection techniques. Therefore it depends on the type of compounds you are looking for.

I extract liquid part of culture with ethylacetate or the solid residue with methanol, acetone. Than I investigate the extracts by LC- QTof analysis and also by old fashioned TLC. Bacteria produce different amount of compounds, some only produce 1 main compound.....but in some strains you can find up to 30 compounds......what kind of bacteria do you have ?

I am concentrating on the metabolic profiling of actinomycetes by LC-ESI-MS analysis. I extracted the metabolites using ethyl acetate and did column fractionation. The active column fraction itself showing >20 mass peaks between 100-1000 Da.

I'm used to analyze streptomyces, actinomyces and e.coli. Besides MS data you'll need at least UV. With UV and high resolution MS you can try to do database search....if you have. Dictionary of Natural Products contains most of known actinomyces compounds....( but is expensive )