My model organism is Leishmania containing about 8000 total protein coding genes. I am performing LCMS based whole proteomics to do qualitative analysis under different conditions. What percentage of proteins should I aim to identify (percentage of the total proteins ) to get my experiments published.
That is a tough question to answer with a straight number because it is strongly dependent on you sample treatment, your workflow and most importantly on the dynamic range of the proteome. As you know the bottleneck in proteomics is really the huge abundance difference in the proteomes, that is why enrichment or fractionation techniques become more and more popular. So if you do classical shotgun you are very limited in the dynamic range. For example human cells encode ~20k proteins and in classical LCMS based workflows you identify 5000-8000, so roughly 25%. As bacteria have a lower dynamic range in their proteome, I would expect a higher coverage of their proteome. Best you check what other people got on E. coli and things like that, to get a feeling. Out of the blue I would say about +/- 50% proteome coverage should be achievable in simple systems.
I agree with Dr. Matin Eisinger. There is no cutoff for percentage of proteins found by proteomics to be publishable in any journals as far as I know. You have to prioritize your findings with your research aims/objectives. You will always find abundant proteins such as GP63 (MSP, or leishmaniolysin) in both amastigotes and promastigotes. We have studied membrane proteins by proteomics, and found stage specific proteins in log versus metacyclic promastigotes. Good luck.
Martin has provided an excellent answer. I would agree with him.
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