One of my favorite types of blog posts are ones that list articles with brief descriptions so I can either bookmark a single site or remember the name of the blog without having to recall the names of the articles (or publications that featured the articles).
Therefore, when Christian Ravnsborg (Product Manager for our proteomics solutions in Odense, Denmark) sent out a list of 14 articles focusing on proteomics research published in a 30-day span in Nature magazine, I was thrilled and immediately set to writing blog posts listing the articles for the convenience of our readers!
In case you are wondering why the focus on articles published in Nature magazine when there are so many other distinguished publications featuring articles on this subject, here is why. Having an article published inNature is not only very prestigious but such articles are often highly cited leading to grant funding and attention from the mainstream media. Also, many of the most significant scientific breakthroughs in modern history have been first published inNature. While most journals tend to be specialized, Nature tends to span across different fields, so the criteria for acceptance is tougher. It is indeed the number one ranked journal in science. Research scientists are the primary audience for the journal, but summaries and accompanying articles are intended to make many of the most important papers understandable to scientists in other fields and the public.
Here are the first four from Christian’s list. Happy reading!
Synopsis: In this paper, the authors report on an empirically driven approach for generating both optimal proteotypic peptides and their fragmentation patterns in a scalable, economical and generalizable fashion. Rather than relying on sparsely populated spectral databases, prediction algorithms, peptide synthesis, or purchase of full-length proteins, the authors have leveraged the collection of tagged cDNA clones that are currently available for most human and model-organism proteins to generate in vitro–synthesized full-length protein samples, followed by tryptic digestion and MS analysis using SRM.
Like what you are learning?
Synopsis: The authors of this article rather than selecting a precursor ion and subjecting it to HCD, yielding fragment ions (MS2 ions) for quantification and identification, used an additional round of fragmentation (MS3). The rationale for this approach is that an additional round of ion selection considerably reduces interference because the likelihood of other MS2 ions having similar m/z values and being selected together is minimal.
Synopsis: The authors describe using the approach called QuantMode in which a precursor ion is selected and undergoes charge reduction using ETD. Assuming that the co-selected ions of identical m/z have different charge states, the reduction in charge means that the resulting ions no longer have overlapping m/z and thus precursor selection can be carried out more precisely. The selected charge-reduced ion is fragmented by HCD and a second trapping of the same precursor is fragmented in the linear trap of the mass spectrometer by CID. This results in the generation of two sets of fragment ions under optimal collision energies from the same precursor: those generated by HCD containing the uncontaminated reporter ions and those generated by CID, which only correspond to sequence-specific ions. Both sets of ions are then combined in the C-trap of the instrument and analyzed together in the Orbitrap. The advantage of this approach is that it increases accuracy of measurement.
Synopsis: The authors describe using a four-dimensional separation system (two-dimensional liquid electrophoresis, LC and MS) to identify 1,043 gene products from human cells that are dispersed into more than 3,000 protein species created by PTMs, RNA splicing and proteolysis. The overall system produced greater than 20-fold increases in both separation power and proteome coverage. This level of proteome coverage represents the most comprehensive implementation of top-down mass spectrometry so far.
Look for the next blog post listing more of these great articles. Also, do tell us if you have read any others in the comments field below.