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@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 spec data go fast I have the feeling the algorithms available through PROcess could be somewhat outdated (but please correct me if I am wrong).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 > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- [ Laurent Gatto | slashhome.be ]