Hi,

I guess a bit more background with regard to the type of data you're referring to would be helpful: I assume you are talking about MS data?

And what are your specific questions: would you like to identify proteins, identify phosphopeptides, or quantify phosphopeptides (and proteins)?

Thanks in advance for providing some more information!

Hi Eef :

Thanks for your response.

Our primary goal is to identify all phosphorylation sites that significantly differ (up or down regulated) between the treated and control group. I would also subsequently like to do some pathway mapping.

Its Label- Free Quantitative Profiling.

Hello Ayanabha,

Have you read this paper, "Perseus A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research" by Stefka Tyanova and Juergen Cox? It is a good guide for analysing proteomic data & should help you if you are analysing your data using MaxQuant software.

Good luck.

Best,

Peter

Thanks Peter