Normalization And Differential Expression Analysis Of Mass Spectrometry Data

Question

[Ali]

I am looking for a software platform, preferably an R package, for normalization and differential expression analysis of Mass Spectrometry data.

For transcription profiles, I use limma package that is really great in both normalization and differential expression analysis based on linear models and Bayesian statistics.

However I have no idea about a similar package for proteome profile.

Does anyone have a good recommendation?

Answer 1

[Woa]

For proteomics data Limma is often used too. Depending on what type of labelling you're using, you can use the followings:

1. DanteR: runs on R with a gui: http://omics.pnl.gov/software/danter
2. R package "Isobar": http://bioinformatics.cemm.oeaw.ac.at/index.php/downloads-left/88-isobar-r-package-for-analysis-of-quantitative-proteomics-data
3. http://www.msstats.org/ I guess there are some more, consult some recent reviews on software libraries used in Proteomics. For example: http://www.sciencedirect.com/science/article/pii/S1570963913001039 and http://www.sciencedirect.com/science/article/pii/S1570963913001866

[Woa]

You can see some R code examples of Linear Models used in quantitative Proteomics in the appendix of this PhD thesis(not mine) http://unsworks.unsw.edu.au/fapi/datastream/unsworks:8135/SOURCE02