Hello Farah Farah

Great to hear you have a dataset but could you please tell us all a bit more about it such as:

Which instrument did you acquire it on?

How many conditions did you compare and how many replicates (both biological and technical) were performed?

Have you searched the data against a protein database yet? And if so, what software (Mascot? MaxQuant? Proteome Discoverer etc?) did you use?

There are many available analyses available including Perseus (that can be used with output results from MaxQuant), Proteome Discoverer has good options, and there are a number of very nice R packages on BioConductor and GitHub.

Tell us a bit more and I'm sure someone can help you out.

Best,

Peter

Hello Peter,

Thanks for your kind reply.

The instrument is Orbitrap Fusion Mass Spectrometer, and the dataset is coming from Proteome Discoverer tool (using Sequest).

There are three conditions (conA, conB, control), and each condition has three replications.

I need to know, beside protein-protein interaction network analysis, what other analyses (e.g. deferentially expressed protein analysis, etc) are applicable and necessary to do on this dataset to obtain useful information? (because it is from an immunoprecipitation experiment, so, it is not a large dataset)

or for bait-prey technologies, only p-p interaction network analysis is applicable and informative??

Thanks for the help.