Question: A package to analyse Quantitative proteomics study
gravatar for Roopa Subbaiaih
3.7 years ago by
United States
Roopa Subbaiaih130 wrote:

Hi All,

Is there a good package which analyses quantitative proteomics study, particularly label free approach? Please let me know.

Thanks in advance, Roopa




ADD COMMENTlink modified 3.7 years ago by Laurent Gatto980 • written 3.7 years ago by Roopa Subbaiaih130
gravatar for Laurent Gatto
3.7 years ago by
Laurent Gatto980
United Kingdom
Laurent Gatto980 wrote:

It would be useful to have a bit more information regarding the type of label-free and what kind of analysis you are after. In terms of statistical analysis, standard packages can be applied to proteomics data, but you might also want to have a look at MSstats in particular. In terms of MS data processing, for MS2 label-free (peptide/spectral counting), you could look at MSnID, msmsTests and MSnbase. For MS1 quantitation, I think the best solution would be to try xcms that is usually used for metabolomics data. You could also use a third party software and then import the data into R as MSnSet instances using readMSnSet or readMSnSet2 from MSnbase, that will manage the quantitative data and meta-date and provide support for various analyses. 

As a general introduction to R/Bioc for proteomics, you could look at the RforProteomics package vignette.

Hope this helps.


ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Laurent Gatto980
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