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/26426
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in handling of mass spec data go fast I have the feeling the algorithms available through PROcess could be somewhat outdated (but please correct me if I am wrong).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@wur.nl<mailto:guido.hooiveld@wur.nl>
internet:   http://nutrigene.4t.com<http://nutrigene.4t.com/>
http://www.researcherid.com/rid/F-4912-2010



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