Hi everyone,
I have a proteomics data and want to compare male-female mice protein expression levels. I need to find differentially expressed proteins between two group. Student's T test just compares the mean values and gives a p-number. But I want to find which protein's expression level is significantly upregulated or downregulated. So what test/method should I use?
Thanks for any contribution.
What kind of proteomic data do you have (Instrument/technique) ?... I mean for instance; gel-based proteomics such as 2D, well-separated proteins can easily be analyzed by using proper software like PDquest (BioRad). Any upregulated or down-regulated protein can be identified by spot analysis (comparing abundances) and filtered marker proteins can be identified after excising POI from the gel and subjecting it to MS (ESI-LC or MALDI). The more efficient way to do this is MS-based proteomic indeed. If you labeled peptides for relative quantification (TMT, ITRAQ, ICAT, SILAC, etc..) you can do even manual curation to determine the differentiation at the peptide level. On the other hand, if you have label-free data you can analyze them by benefiting from the proteomic-centric software for prefiltering (proteome discoverer, PLGS, progeneis QI, protein pilot, Paser, etc...)
For statistical comparison, I would prefer and suggest Perseus...
Thank you so much for the detailed explanation. I'm not sure about our data type, but obviously, it's not gel-based proteomics. Our proteins are label-free. And yes since we used Maxquant for the analysis, Perseus was recommended to me for the statistics. So I want to compare LFQ intensities of female and male mice and see which proteins are differentially expressed. So which test should I use on Perseus?
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