This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Normalization And Differential Expression Analysis Of Mass Spectrometry Data

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?

mass-spec differential-expression normalization r proteomics
• 9,102 views • link
updated by Woa Woa • written by Ali Ali

1 answer

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
• 66 views • link
written by Woa Woa

Log in to answer this question.

More posts like this