How to do analysis of proteomics data acquired from LC-MS ?

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Romana Stopková Popular answer

By the way LFQ normalization (inbuilt in MS) is not enough. Data/samples may still have different sizes. Definitely normalize first and then PLGEM it :)

Pavel Stopka

Hi We use PLGEM statistics (Power Law Global Error Model) and it works well. Originally it was adopted from microarrays because LC-MS and microarray data have similar statistical distribution. Look at our latest paper: Article Differential regulation of vaginal lipocalins (OBP, MUP) dur...

Good thing is that PLGEM runs under BIOCONDUCTOR package/project in R software. Also it is important to have datasets with similar size and distribution. Otherwise you have to use normalization procedures before computing. If this is the case you may use 'PreprocesCore' routine normalization also within BIOCONDUCTOR. All descibed in our paper above (http://rdcu.be/vSys ) or in this one Article On the tear proteome of the house mouse (Mus musculus muscul...

Romana Stopková

Saurabh Kumar

Thanks Pavel Stopka and Romana for your suggestion.

I was trying to take the interaction of the over expressed and unique proteins through STRING database and then make the network in the cytoscape. Then i will choose important proteins on the basis of topological properties to make short network and then doing GO through BINGO and ClueGo. Any important comment on this to make the analysis more correct. Can i use DAVID for the bacterial data?

Rajesh Durairaj

Dear Saurabh Kumar,

I agree with Dr. Paval Stopka and Dr. Romana Stopkova valuable suggestions.

As par your interest, Need to collect the log P values of GO ID of the differential expression of proteins using their respective UniProt ID (By David/ Panther/ GO consortium/BiNGO/Gorilla servers-based on organisms). After, remove the redundant entries of GO and make the list of GO with P-values submit to REVIGO server (http://revigo.irb.hr/) according to mentioned algorithm. Then the result output linked to Cytoscape plugin and furnish the differential protein network based on molecular function.

As well as you can try to VENN analysis for the study.

Kindly check this article GO analysis:

Muthukumar, S., Rajkumar, R., Rajesh, D., Saibaba, G., Liao, C. C., Archunan, G., ... & Gulyas, B. (2014). Exploration of salivary proteins in buffalo: an approach to find marker proteins for estrus. The FASEB Journal, 28(11), 4700-4709.

Hope it is useful.