Split before search
When on a search for biomarkers, especially in a high-abundance or high-frequency system, such as serum albumin or immunoglobulins, the order of any sub-fractionating can be critical. This is demonstrated here with a search for serum albumin-derived liver cancer markers in urine by Broodman et al. Markers for liver diagnosis are relatively rare as they are normally found as IgGs from which they must be extracted. The complementarity determining regions (CDRs) are easier to examine if they are divided into their components: Fab, κ, λ, Fab-κ, and Fab λ are further purified (molecular dissociation). This substantially reduces the complexity of sequences to search and yields twice as many CDRs (and twice the chance of finding cancer precursors).
Riding through the Zodiac on a cricket
I'm not sure what it means, but over the past several years of writing this column, I've worked my way through much of the living Zodiac: lions (cats), twins, virgins (presumed), water bearer, archer, fish, etc. And today, Scorpio (Pandinus caviminus) joins the list, courtesy of Diego-Garcia et al., University of Leuven. Interesting toxin activity assay unit: μg extract per oocyte or per cricket. The toxins function by blocking Na+ and K+ conductance channels. Toxins are extracted from the telson (stinger) by applying a 15–20 V pulse to “milk” the stinger. These workers also constructed a telson expression library from transcripts of one telson. This species is not normally fatal to humans. Potential source of drugs. Native to southern Africa, it is traded as an exotic pet in Europe, Japan and North America.
Clear as MUDpit
The more quickly a biomarker can be identified and verified, the better the patient's chance of survival (at least in theory). The current state of the art puts Multidimensional Protein Identification technology (MudPIT) in the lead over 2DE-based methods. Not satisfied, Weng et al. have been looking for improved methods of discovery of human urinary exosome biomarkers, lots of them. Optimizing the method against previously published methods led to the use of trifluoroethanol solution-phase digestion over the more commonly used in-gel digestion, adoption of a high-efficiency ion trap MS, and a smaller starting volume of urine that was much easier to handle. The number of proteins identified per sample ranged from 1462 old MS to 12 388 on the new MS. A side benefit: two new well-characterized data sets.