Analyzing proteomics data

Question

[datanerd]

Hi All,

I am analyzing a proteomics adatset on 7 different disease group. and would like to check for proteins which might be present for absent in one specific group when compared to the others. Is there a way/tool anyone is familiar with that I can use/work with

It SILAM quantitative proteomics dataset run on QE machine and normalized using MAXquant software.

Thanks in adavnce!!!

Mamta

[Sukhi Singh]

You should mention what kind of proteomics dataset are you working with, it's a vast field. More details mostly never harm :)

[aeinsights]

Hi Mamta, We can help you for your analysis. Can you please more information on this? Let us understand if our platform http://bioelm.com can help on this.

Thanks.

Answer 1

[Benn]

I use limma for statistical analysis of maxquant normalized (label free ms) data. Make contrasts with a control group if you have it.

[sbt_gvs]

@Benn do you have any sample code on how to start this. I have normalized quant values and trying to do differential proteomics and pathway analysis. Can you help with how to go about it ?