Mathew A Beale Thank for the quick reply. Well, one thing i forgot to mention is my algae-synechococcus is a prokaryotic cell (cyanobacteria). So, polyadenylated ends will be similar to bacteria.

As Mathew pointed out, you can separate the reads by mapping to reference organisms (it is a common practice). If you want to have an estimate how well that is likely going to work, you could simulate a mix of transcriptome reads from both species (with the appropriate error rate & read length distribution; for example use https://github.com/bcgsc/NanoSim for simulating MinION reads; there are different tools for other sequencing platforms) and align the simulated reads back to the two reference genomes and analyze the results.

Katharina Hoff Thanks

For exoproteome analysis you should choose a shot-gun proteomics approach. For quantitation you may follow a label-free method, before thinking about chemical or isotopic labeling methods, as cost may be an issue.

You should have a look to the following articles, that describe a very interesting method using gel electrophoresis for protein preparation before enzyme digestion:

Article Functional distinctness in the exoproteomes of marine S ynec...

Article Taking the Shortcut for High-Throughput Shotgun Proteomic An...

I would firstly perform exoproteome analysis for your algae and bacteria in separate, then in co-culture condition.

Good luck.

Newton Verbisck Thanks for informative articles. The whole point of my experiment is to find out the functional proteoms exported during co-culture and by whom. I understand it sounds easy in the question but is really difficult to separate them out in co-culture system