I doubt that fatty acid composition of phospholipids can be used as a taxon-identifying criteria. Different organisms share the same set of fatty acids, it's pretty universal. Moreover, for such organism as plants, fungi, bacteria, fatty acid composition of lipids can vary considerably within a single species depending on the environmental conditions, first of all, temperature. 

You can use PLFA to determine Gram+/- bacteria, fungi, some mycorrhiza, actinobacteria, I think archaea as well, and some other groups. There is quite a lot of literature on the different fatty acids you can use to identify different microorganisms.

You use a standards on your gas chromatograph to determine at what time the fatty acids of interest appear in the future samples you will run. I think you should be able to buy standards from the company of your gas chromatograph.

Thanks for the answers.

@ Aimeric Blaud, could you please share the literature you know with me. Actually, we have received some PLFA results from a laboratory, but it still need to convert them in those groups you have talked about, but until now I have not figured out how to move on to that step.

I found this http://www.ncbi.nlm.nih.gov/pubmed/24623527 quite related to my research questions but they only focused on bacteria and Fungi.

Thanks again.

PLFA is used as a taxonomic phenotypic marker for bacterial isolates by comparing the new isolates with reference strains. Severe standard growth conditions are required for reliable comparisons.  However as far as I know bacterial cells (at least in some species) are reported to change the composition of fatty acids of the cellular membrane according to the growth conditions (e.g. C sources). These aspects should be taken into consideration when using PLFA in the study of environmental microbial communities.

PLFA is used as biochemical markers and broad indicators of microbial community at a coarse level. There is bias, such as variability in the amount of fatty acids between organisms, same fatty acids shared between organisms. Knowing these limitations and the ones mentioned in the previous answer, PLFA remains a useful tool to gather semi-qualitative and semi-quantitative data in the shift in microbial community.

 If I understand your problem, you received a list of fatty acids (FA) but you do not know to which organisms they correspond. I guess the FA in the files you received are named following the usual nomenclature: e.g. C15:0, cycC17:0 etc. What is important is to select FA that are specific to bacteria or fungi and do not take the ones shared by other organisms such as plants. You can use the following FA:

Gram+ bacteria: i-C15:0, a-C15:0, i-C16:0, brC17:0, i-C17:0, aC17:0

Gram- bacteria C16:1(9)cis, C16:1(11)cis, cycC17:0, cycC19:0

Bacteria: C15:0, C17:0, 10me-C16:0

Actinobacteria: 10meC18:0

Fungi: C18:1, C18:2

More details and references in an article I published in 2012 in Applied Soil Ecology (53, 1-9; you can find the pdf on my RG).

You can find more information about PLFA and FA to use in the articles bellow, but there are plenty of articles using PLFA and you can follow the FA that they selected as there is a limited number of FA that you can use so they are more or less always the same between articles.   

“A Citation classics”…:

Frostegård, Å., Tunlid, A., Bååth, E., 2011. Use and misuse of PLFA measurements in soils. Soil Biology and Biochemistry 43, 1621–1625. doi:10.1016/j.soilbio.2010.11.021

Basics and key articles about PLFA

Frostegard, A., Tunlid, A., Baath, E., 1993. Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Applied and Environmental Microbiology 59, 3605–3617.

Schutter, M.E., Dick, R.E., 2000. Comparison of fatty acid methyl ester (FAME) methods for characterizing microbial communities. Soil Science Society of America Journal 64, 1659–1668.

Zelles, L., 1999. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biology and Fertility of Soils 29, 111–129. doi:10.1007/s003740050533

Zelles, L., Bai, Q.Y., 1994. Fatty acid patterns of phospholipids and lipopolysaccharids in environmental samples. Chemosphere 28, 391–411. doi:10.1016/0045-6535(94)90136-8

Article about FA (PEL method) for archaea:

Gattinger, A., Höfle, M.G., Schloter, M., Embacher, A., Böhme, F., Munch, J.C., Labrenz, M., 2007. Traditional cattle manure application determines abundance, diversity and activity of methanogenic Archaea in arable European soil. Environmental Microbiology 9, 612–624. doi:10.1111/j.1462-2920.2006.01181.x

Thanks a lot to everyone who answers my question. They were really useful