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Recent Research Papers of Note in Proteomics: Mar 15, 2007

Journal: Molecular Systems Biology, Mar 13
Title Large-scale mapping of human protein-protein interactions by mass spectrometry
Authors: RM Ewing; P Chu; F Elisma; H Li; P Taylor; S Climie; L McBroom-Cerajewski; MD Robinson; L O’Connor; M Li; R Taylor; M Dharsee; Y Ho; A Heilbut; L Moore; S Zhang; O Ornatsky; YV Bukhman; M Ethier; Y Sheng; J Vasilescu; M Abu-Farha; JP Lambert; HS Duewel; II Stewart; B Kuehl; K Hogue; K Colwill; K Gladwish; R Kinach; SL Adams; MF Moran; GB Morin; T Topaloglou; D Figeys
Authors report the first large-scale study of protein-protein interactions in human cells by mass spectrometry. The interactions for 338 bait proteins were mapped. The proteins were selected based on known or suspected disease and functional associations.

Journal: Electrophoresis, March 9 [Epub ahead of print]
Title: Online coupling of SPE and CE-MS for peptide analysis
Authors: FW Tempels; WJ Underberg; GW Somsen; GJ de Jong
Authors describe an online SPE-CE-MS system they devised for the analysis of peptides. Analytes were preconcentrated using a C18 microcolumn and introduced into the CE system via a valve interface. The CE system with a polybrenepoly(vinlysulfonate) bilayer coated capillary is combined with an ion-trap MS via ESI using a coaxial sheath-liquid sprayer. “The online coupling of the SPE and CE step by the valve interface is advantageous because it allows an independent functioning of the system parts,” according to the abstract. The authors optimized the SPE-CE system using UV detection. The SPE-CE system was then coupled to the ion-trap MS, and test solutions with enkephalin peptides were used to evaluate its performance.

Journal: Physiological Genomics, March 6 [Epub ahead of print]
Title: An improved method for the analysis of membrane proteins by mass spectrometry
Authors: SP Mirza; BD Halligan; AS Greene; M Olivier
Authors present a detergent-free method for isolating membrane-bound and membrane-associated proteins, then identifying them by MS. They delipidate proteins from the membrane bilayer by chloroform extraction as a way to overcome dissolution and ionization problems during analysis. They say their method results in a higher number of identified membrane proteins and higher quality of MS data, compared to results obtained by direct tryptic digestion of insoluble membrane pellets.

Journal: RapidCommunications in Mass Spectrometry, March 5 [Epub ahead of print]
Title: Use of the arginine-specific butanedione/phenylboronic acid tag for analysis of peptides and protein digests using matrix-assisted laser desorption/ionization mass spectrometry
Authors: A Leitner; S Amon; A Rizzi; W Lindner
Authors applied an arginine-specific labeling technique to the study of peptides by MALDI-MS. The reaction converts the guanidine group of the arginine side chain by reacting it with 2.3-butanedione and an arylboronic acid. “After optimizing the method using arginine-containing model peptides — for which sensitivity down to the low fmol range was demonstrated — the procedure was applied to enzymatic digests of several model proteins in solution and to protein spots in gels obtained by two-dimensional electrophoretic separation of cell lysate samples,” according to the abstract.

Journal: Molecular & Cellular Proteomics, March 5 [Epub ahead of print]
Title: Compositional protein analysis of high-density lipoproteins in hypercholesterolemia by shotgun LC-MS/MS and probabilistic peptide scoring
Authors: M Heller; E Schlappritzi; D Stalder; JM Nuoffer; A Haeberli
Authors evaluated peptide match score summation index (PMSSI) “based on probabilistic peptide scores calculated by the PHENYX protein identification engine for absolute protein quantification, in accordance with protein abundance index [PAI] as proposed by [Matthias] Mann and colleagues,” according to the abstract. The authors say that applied to high-density lipoproteins, the approach compares favorably to alternative protein quantitation methods and is complementary to HDL lipid analysis while not relying on complicated sample treatment.

Journal: Analytical Chemistry, March 1
Title: Bidimensional tandem mass spectrometry for selective identification of nitration sites in proteins
Authors: A Amoresano; G Chiappetta; P Pucci; M D’Ischia; G Marino
Authors report a new approach involving dansyl chloride labeling of protein nitration sites that rely on the potential of MS analysis. The tryptic digest from the entire protein mixture is analyzed by a linear ion trap MS while discrimination between nitro- and unmodified peptides is based on two selectivity criteria obtained by combining a precursor ion scan and an multi-stage MS/MS analysis.

Journal: Journal of chromatography. B, Analytical technologies in the biomedical and life sciences, March 1
Title: Two dimensional liquid phase separations of proteins using online fractionation and concentration between chromatographic dimensions
Authors: JA Karty; WE Running; JP Reilly
Authors present a 2D LC system they say employs online fractionation of proteins into a series of small reversed phase trapping columns that decouple the two separation dimensions and “avoid problems associated with off-line fraction collection,” according to the abstract.

Journal: Analytical Chemistry, March 1
Title: Proteomic complex detection using sedimentation
Authors: NT Hartman; F Sicilia; KS Lilley; P Dupree
Authors present a quantitative proteomics technique called Proteomic Complex Detection using Sedimentation to profile the sedimentation of large numbers of proteins through a rate zonal centrifugation gradient. According to the abstract, ProCoDeS is useful in screening extracts of tissues, cells, or organelle fractions to identify specific proteins in stable complexes “that can be characterized by subsequent targeted techniques such as affinity tagging.”

Journal: Journal of Proteome Research, March
Title: Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy
Authors: PJ Boersema; N Divecha; AJ Heck; S Mohammed
The authors assess the potential of zwitterionic hydrophilic interaction liquid chromatography as a first dimension for the analysis of complex peptide mixtures. They developed a 2D-LC system that hyphenates ZIC-HILIC offline with reversed-phase. The authors say the two dimension are “fairly orthogonal, and the system performs very well in the analysis of minute amounts of complex peptide mixtures.”

Journal: Electrophoresis, March
Title: Development and assessment of scoring functions for protein identification using PMF data
Authors: Z Song; L Chen; A Ganapathy; XF Wan; L Brechenmacher; N Tao; D Emerich; G Stacey; D Xu
Authors say they developed new probability-based scoring functions for Peptide Mass Fingerprinting protein identification based on the Mowse algorithm. Their computational methods are assessed and compared with other methods using PMF data of 52 gel spots of known protein standards, the abstract says, and the comparison shows that the new scoring schemes have “higher or comparable accuracies for protein identification in comparison to the existing methods.”

Journal: Journal of Proteome Research, March
Title: Isolation of phosphopeptides by pI-difference-based electrophoresis
Authors: Y Xu; R Sprung; SW Kwon; SC Kim; Y Zhao
Authors describe the discovery of pI differences between methylated phosphopeptides and methylated nonphosphorylated peptides. The pI difference allows isolation of methylated phosphopeptides from the methylated nonphosphopeptides by in-solution isoelectric focusing. They say that the principle of the approach is proven by isolating a phosphorylated peptide from a nonphosphorylated tryptic digest of myoglobin.

Journal: Nature Biotechnology, Feb. 25 [Epub ahead of print]
Title: An integrated mass spectrometric and computational framework for the analysis of protein interaction networks
Authors: O Rinner; LN Mueller; M Hubalek; M Muller; M Gstaiger; R Aebersold
Authors describe a method of analyzing protein complexes through integrating label-free, quantitative MS and computational analysis. Their system, MasterMap, evaluates peptide intensity profiles throughout the sequential dilution of samples, and identifies specific interaction partners and changes in the composition of protein complexes, the authors say. It also reveals variations in the phosphorylation states of components of protein complexes. “Our analysis identifies previously known and unknown interactions of FoxO3A with 14-3-3 proteins, in addition to identifying FoxO3A phosphorylation sites and detecting reduced 14-3-3 binding following inhibition of phosphoinositide-3 kinase,” according to the abstract.

Journal: Molecular & Cellular Proteomics: MCP, Feb. 23 [Epub ahead of print]
Title: Improved method for differential expression proteomics using trypsin-catalyzed 18O labeling with a correction for labeling efficiency
Authors: A Ramos-Fernandez; D Lopez-Ferrer; J Vazquez
As a way of addressing computation problems associated with post-digestion 18O labeling, authors analyze the behavior of large collections of peptides that are subjected to post-digestion labeling. Saying the behavior can be explained by a universal kinetic model, authors developed an advanced quantification algorithm for this kind of labeling. “Our method fits the entire isotopic envelope to parameters related with the kinetic exchange model, allowing at the same time an accurate calculation of the relative proportion of peptides in the original samples and of the specific labeling efficiency of each one of the peptides,” the authors say in the abstract.

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