The difference between plasma and serum is coagulant factor presence in plasma, not serum. So, if you wish to measure factors other than coagulants, you can use both serum and plasma. However, I myself prefer to use serum because the more pure sample, the more accurate measurement. Serum lacks some proteins.
It is analyte and method specific. We did some work at USDA to compare serum and plasma for vitamin and mineral analyses. One change is the slight dilution that occurs in plasma due to anticoagulant changing osmolality and drawing fluid from RBS. We find that heparin plasma gives best reproducibility for carotenoids and vitamin A, E with freeze-thaws. Some EIAs are affected by anticoagulants.
I agree with Joanna and Seyyed, it depends on the analyte to be determined. For example toxic trace elements as lead, cadmium and mercury are bond preferably on erythrocytes, therefore for its determination, the whole blood is prefered.
In case of metabolite analysis both serum and plasma would show effective result.Serum is found to be more sensitive . In order to determine biochemical markers ,serum would be a better source. In case of protein estimation serum lacks many proteins hence plasma holds better.
Our study shows that reproducibility was good in both serum and plasma. As long as the same blood preparation procedure is used, either matrix should generate similar results in clinical and biological studies. However, the higher metabolite concentrations in serum, make it possible to provide more sensitive results in biomarker detection.
I agree with the others that it depends on type of analyte. Plasma can be prepared by different ways. When used citrate, Ca2+ is missing in the plasma – it should be taken into consideration. Heparin does not influence calcium level. As wrote Prabasheela, lower level of proteins in serum is another factor.
I have good experience with heparinized plasma when oxidative stress and antioxidants determined. I prefer the heparinized plasma because the preparation seems to be better reproducible when samples processed in a small lab. Subjectively, I have better experience with plasma but I did not fully compare the two types of samples.
Both plasma and serum are good. Those who often used plasma is because they needed the erythrocytes or whole blood for some other analysis. Otherwise the serum is easy and cheap to obtain and also gives good results.
We have found better reproducibility of carotenoids in freeze/thaw samples using heparin plasma. Serum is cleaner for estrogen metabolites by LC-MS-MS. See the following article:
Carotenoids, retinol and tocopherols in blood: Comparability between serum and plasma (Li-heparin) values.
Effect of heparin and citrate on measured concentrations of various analytes in plasma
Differences between Human Plasma and Serum Metabolite Profiles