[BioC] package for protein MS analysis (SELDI-TOF)

[Hooiveld, Guido]

Hi Laurent,
Thanks for the suggestions, and pointing me to the respective BiocViews (which until now i was not aware of).

Guido

-----Original Message-----
From: Laurent Gatto [mailto:laurent.gatto at gmail.com] 
Sent: Friday, February 04, 2011 20:01
To: Hooiveld, Guido
Cc: bioconductor (bioconductor at stat.math.ethz.ch)
Subject: Re: [BioC] package for protein MS analysis (SELDI-TOF)

Dear Guido,

I can think of two packages that might be helpful. xcms, a Bioconductor package, and msProcess, available on CRAN. Other packages in the Proteomics (Software > BiologicalDomains > Proteomics) and MassSpectrometry (Software > AssayTechnologies > MassSpectrometry) BiocViews might also be of interest.

Hope this helps.

Best wishes,

Laurent

On 2 February 2011 21:12, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
> Dear list,
>
> Through a collaboraring group I am about to get a pilot SELDI-TOF dataset consisting of spectra of ~ 80 plasma samples. I am relatively new to the analyses of these type of data (I am more into microarray analysis and regarding MS only know the software provided by the manufactor BioRad [ProteinChip data manager], which is somewhat of a black box), and therefore I wondered whether someone more experienced with proteomics work could point me to a package / paper / website that describes the current analyses strategy for these type of data.
>
> I do know about the BioC package PROcess, and also found this thread 
> in the archive
> http://article.gmane.org/gmane.science.biology.informatics.conductor/2
> 6426 but considering the fact the developments in handling of mass 
> spec data go fast I have the feeling the algorithms available through PROcess could be somewhat outdated (but please correct me if I am wrong).
>
> Any feedback would be very much appreciated!
>
> Guido
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group Division of Human Nutrition 
> Wageningen University Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> email:      guido.hooiveld at wur.nl<mailto:guido.hooiveld at wur.nl>
> internet:   http://nutrigene.4t.com<http://nutrigene.4t.com/>
> http://www.researcherid.com/rid/F-4912-2010
>
>
>
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[ Laurent Gatto | slashhome.be ]