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Recent Research Papers of Note: Jan 11, 2007

Journal: Molecular & Cell Proteomics: MCP, Jan. 5 [Epub ahead of print]
Authors: J Lee; Y Xu; Y Chen; R Sprung; SC Kim; S Xie; Y Zhao
Authors report optimization of the immobilized metal ion affinity chromatography procedure using 32P-labeled tryptic peptides and development of MS/MS/MS for the identification of phosphopeptide sequences and phosphorylation sites. The improved method allows recovery of phophorylated tryptic peptides up to 77 percent, the authors note in the abstract, with only minor retention of unphosphorylated peptides.

Journal: Chembiochem : A European Journal of Chemical Biology, Jan. 8 [Epub ahead of print]
Authors: NF Visser; A Scholten; RH van den Heuvel; AJ Heck
Authors explore the utility of combining suface planson resonance coupled with LC/MS/MS as an alternative in chemical proteomics for efficient specific extraction and quantitative identification of small-molecule-binding proteins from complex mixtures.

Journal: Journal of Proteome Research, Jan. 6
Authors: EL Huttlin; AD Hegeman; AC Harms; MR Sussman
Authors have created a method for calculating the expected uncertainty associated with false-positive rates in peptide identifications from large-scale proteomics experiments. The method involves using concatenated reverse and forward protein sequence databases.

Journal: Journal of Proteome Research, Jan. 6
Authors: J Vasilescu; DR Zweitzig; NJ Denis; JC Smith; M Ethier; DS Haines; D Figeys
Authors demonstrate an application of a microfluidic processing device, the Proteomic Reactor, for enzymatic digestion of affinity-purified proteins for LC/MS/MS analysis. The authors say in the abstract that the Proteomic Reactor “enabled the identification of numerous ubiquitinated proteins in a human cell line expressing reduced amounts of the ubiquitin-dependent chaperone, valosin-containing protein.”

Journal: Journal of Proteome Research, Jan. 6
Authors: J Dai; WH Jin; QH Sheng; CH Shieh; JR Wu; R Zeng
Authors use a system consisting of multi-dimensional liquid chromatography (yin-yang MLDC) coupled with mass spectrometry for identifying peptides and phosphopeptides.

Journal: Journal of Proteome Research, Jan. 6
Authors: F Zhou, J Galan; RL Geahlen; WA Tao
Authors report a strategy for rapid analysis of peptide-protein interactions with more than one phosphorylation site involved. The strategy is based on quantitative proteomics.

Journal: Journal of Proteome Research, Jan. 6
Authors: AM Frank; MM Savitski; ML Nielsen; RA Zubarev; PA Pevzner
Authors evaluate peptide de novo sequencing by precision mass spectrometry and explore differences when compared to analysis of low-precision data. “We demonstrate how the dramatically improved performance of de novo sequencing with precision mass spectrometry paves the way for novel approaches to peptide identification that are based on direct sequence lookups, rather than comparisons of spectra to a database,” they say in the abstract.

Journal: Journal of Proteome Research, Jan. 6
Authors: RF Kemperman; PL Horvatovich; B Hoekman; TH Reijmers; FA Muskiet; R Bischoff
Authors describe a platform for the comparative profiling of urine. Reversed-phase LC/MS and multivariate statistical data analysis were used. Urinary compounds were separated by gradient elution and detected by electrospray ion-trap MS.

Journal: Methods in Molecular Biology, 2006
Authors describe methods for affinity isolation of PP1C-dontining protein complexes in the yeast Saccaharomyces cerevisiae. They also describe ways of using MS to identify associated polypeptides. Authors say in the abstract that the basic method they describe can be “easily adapted to study PP1C-associated proteins in other lower or higher eukaryotes and for characterizing the protein-protein interactions of other protein phosphatases in yeast.”

Journal: Nature Biotechnology, Dec. 31 [Epub ahead of print]
Authors: P Mallick; M Schirle; SS Chen; MR Flory; H Lee; D Martin; J Ranish; B Raught; R Schmitt; T Werner; B Kuster; R Aebersold
Authors used more than 600,000 peptide identifications generated by four proteomic platforms, they empirically identified more than 16,000 proteotypic peptides for 4,030 distinct yeast proteins. They say possible applications of proteotypic peptides include validation of protein identifications, absolute quantification of proteins, and annotation of coding sequences in genomes.

Journal: Molecular & Cellular Proteomics: MCP, Dec. 27 [Epub ahead of print]
Authors: J Wissing; L Jansch; M Nimtz; G Dieterich; R Hornberger; G Keri; J Wehland; H Daub
To more characterize protein kinases more comprehensively biochemically, authors describe a pre-fractionation strategy employing a combination of immobilized low-molecular-weight inhibitors for the selective affinity capture of protein kinases.

Journal: Journal of American Chemical Society, Jan. 10
Authors: KD Green; MK Pflum
Authors describe what they say is the first enzymatic phosphorylation-dependent biotinylation reaction of proteins. They coupled kinase enzymes with ATP-biotin conjugate to biotinylate substrate peptides and proteins after phosphate transfer. The reaction enables detection of phosphoproteins in cell lysates or phosphopeptides after trypsin proteolysis. “Importantly, the studies reveal the cosubstrate promiscuity of kinase enzymes, laying the foundation for development of new chemical tools targeting the phosphoproteome,” the authors say in the abstract.

Journal: Pancreas, January
Authors: R Chen; S Pan; K Cooke; KW Moyes; MP Bronner; DR Goodlett; R Aebersold; TA Brentnall
Authors used quantitative proteomics to identify and quantify proteins from pancreatitis juice. They identified and quantified 72 proteins found in the pancreatic juice of pancreatitis patients but not found in healthy ones. Of that, 27 proteins were found to be differentially expressed. Authors say that identification of these proteins could provide useful information for studies of specific pancreatitis-associated proteins and to eliminate potential false-positive biomarkers for pancreatic cancer.

Journal: Electrophoresis, Dec. 27 [Epub ahead of print]
Authors: LL Lv; BC Liu; CX Zhang; ZM Tang; L Zhang; ZH Lu
Authors describe strategies for optimizing the condition of antibody microarray building based on agarose-coated slides

Journal: Journal of chromatography. B, Analytical technologies in the biomedical and life sciences, Dec. 21 [Epub ahead of print]
Authors: T Linke; S Doraiswamy; EH Harrison
Authors describe the depletion of seven abundant rat plasma proteins with an immunoaffinity column with couple antibodies directed against albumin, IgG, transferrin, IgM, haptoglobin, fibrinogen, and alpha1-anti-trypsin. Although they were able to reduce the dynamic range of the plasma proteome by about two to three orders of magnitude, “the difference between medium-abundant and low abundant plasma proteins is still in the range of 7-8 orders of magnitude and beyond the dynamic range of current proteomic technologies. Thus, exploring the plasma proteome in greater detail remains a daunting task,” they say in the abstract.

Journal: Methods in Molecular Biology, 2006
Authors: S Pan; R Aebersold
Authors describe methods for introducing mass tags to proteins and peptides for MS-based quantitative proteomic analysis, including isotope-coded affinity tags, stable isotope labeling by amino acids in cell culture, global internal standard technology, and mass-coded abundance tagging.

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