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• When it comes to eliminate in one step minute quantities of different proteins (anionic, cationic, hydrophobic, Ig aggregates etc,...), as occurs in processes as different as the production of human therapeutic monoclonals or the generation of a standard collection of specific quality protein-binding molecules to study the human proteome, Proteomining with its large (>= 6 10^7) combinatorial hexapeptide sequence space is THE solution.

  • Sep 28, 2009
  • Posted by: Alain MILLER

• The interesting idea of using "peptide-library" was presented a few years ago.In brief, this approach addresses the so-called "dynamic range" of biological proteomes that represents a universal challenge in all proteomics. Clearly, a method that could solve fundamental problem would be of great value. However, so far, peptide/chemical libraries have in my opinion NOT fullfilled their promises. I have seen no studies demonstrating superior senstivity ("proteome coverage") with this approach as compared to, say, for example multi-dimensional LC-MS/MS; to be fair: it is very difficult to compare studies in this research line. Secondly, I have seen no critical evaluation of the reproducibility of this approach. Surely, the presented method is one (relatviely efficient) way to fractionate tissue/cells (and personally I dont have a better suggestion for a one-step fractionation procedure), but I do not see how this, at the present state, can be called Natures Method of the Year!?

  • Sep 30, 2009
  • Posted by: John Adams

• This paper fills a gap in our knowledge of human erythrocytes. A necessary paper. Darja Kanduc

  • Oct 12, 2009
  • Posted by: Darja Kanduc

• Out of curiosity, I have performed a simple literature search on this method. It turns out that, in addition to the paper here reported on RBC cytoplasmic proteome (where the capture has been outstanding!), it has been applied to human serum (J. Proteome Res. 6, 2007, 4055 – 4062) and urine (J. Proteome Research 4, 2005, 1917-1930) analysis, to egg white (J. Proteome Res. 7, 2008, 3461-3474) and yolk (J. Chromatogr. A 1216, 2009, 1241-1252) proteomes, to cow’s whey (J. Proteome Res. 8, 2009, 3925-3936) as well as to detection of trace host proteins in rDNA products (Proteomics 2007, 7, 1624-1633). In all cases, the detection of unique gene products was from 2 to five times higher than the best method available at the time of these studies. The technique has also been described in extenso in Nature Protocols (3, 2008, 883-890). Given these findings, should the peptide ligand library concept be considered for the contest on Nature’s Method of the year? I would be surprised if it were not! Rainer Barbieri

  • Nov 23, 2009
  • Posted by: Rainer Barbieri

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