[BioC] Mass spectrometry data analysis

[Wolfgang Huber]

Dear James

these people used DESeq for a differential abundance analysis of MS data:

Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.
Castello A, Fischer B, et al.
Cell. 2012 Jun 8;149(6):1393-406. doi: 10.1016/j.cell.2012.04.031. Epub 2012 May 31.

System-wide identification of RNA-binding proteins by interactome capture.
Castello A, et al.
Nat Protoc. 2013 Mar;8(3):491-500. doi: 10.1038/nprot.2013.020. Epub 2013 Feb 14.

and here is a paper that used vsn for iTRAQ:

Addressing accuracy and precision issues in iTRAQ quantitation.
Mol Cell Proteomics. 2010 Sep;9(9):1885-97. doi: 10.1074/mcp.M900628-MCP200. Epub 2010 Apr 10.
Karp NA, Huber W, Sadowski PG, Charles PD, Hester SV, Lilley KS.


Hope this helps -

	Wolfgang

El Apr 2, 2013, a las 5:16 pm, James W. MacDonald <jmacdon at uw.edu> escribió:

> Hi all,
> 
> I see lots of packages in BioC for the analysis of raw mass spectrometry data, but I don't see anything offhand for the differential analysis of these data. In addition, the googles seem only to point towards proprietary analysis software.
> 
> I have been handed a data set comprised of spectral counts (rather than say, area under the curve), and wonder if anybody has experience with this type of data, and might have pointers to useful software.
> 
> Best,
> 
> Jim
> 
> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
> 
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