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Recent Research Papers of Note : Sep 28, 2006

Journal:Analytical Chemistry, Sept. 15
Title: Dynamic isoelectric focusing for proteomics
Authors: R. Montgomery; X. Jia; L. Tolley
The authors use dynamic isoelectric focusing to migrate proteins to a designated sampling point where they can be collected for analysis. The authors say that this ability to collect and isolate the protein bands while maintaining a high peak capacity demonstrates that dynamic isoelectric focusing has “great potential” as a first dimension in a multidimensional separation system.

Journal: Analytical Chemistry, Sept. 15
Title: Tandem parallel fragmentation of peptides for mass spectrometry
Authors: A.A. Ramos; H. Yang; L.E. Rosen; X. Yao
Authors developed a method of large peptides with labile amide bonds and peptides with C-terminal arginine. The method has “unique potential for de novo sequencing of peptides and proteome analysis, especially for affinity-enriched subproteomes,” according to the paper’s abstract.

Journal: Bioinformatics, Sept. 11 [Epub ahead of print]
Title: Augur – a computational pipeline for whole genome microbial surface protein prediction and classification
Authors: A. Billion; R. Ghai; T. Chakraborty; T. Hain
Authors present Augur, an automatic prediction pipeline that “integrates major surface prediction algorithms and enables comparative analysis, classification, and visualization for gram-positive bacteria on a genome scale,” according to the paper’s abstract.

Journal: Methods in Molecular Biology, 2006
Title: Prediction of protein-protein interaction based on structure
Authors: G. Fernandez-Ballester; L. Serrano
Authors have developed a method to construct position-specific scoring matrices for the prediction and identification of sequences with putative significant affinity. The method is based on the information contained in structural databases and takes into account conformational and sequence details characterizing different structures within a family.

Journal: Journal of Immunological Methods, Aug. 17 [Epub ahead of print]
Title: Multiplexed PrEST immunization for high-throughput affinity proteomics
Authors: K. Larsson; K. Wester; P. Nilsson; M. Uhlen; S. Hober; H. Wernerus
Authors describe a multiplex immunization strategy for generation of monospecific antibodies dfdfdfdf towards recombinantly produced human protein fragments, denoted PrESTs.

Journal: Journal of Proteome Research, Sept. 1
Title: A novel approach of protein immobilization for protein chips using an oligo-cystein tag
Authors: T. Ichihara; J.K. Akada; S. Kamei; S. Ohshiro; D. Sato; M. Fujimoto; Y. Kuramitsu; K. Nakamura
Authors developed a novel protein tag consisting of five tandem cysteine repeats at termini of proteins. According to the paper’s abstract, the tag “should be useful for developing a novel protein printing method for protein chips that requires very low amounts of protein and can be used for high-performance analysis of protein-ligand interactions.”

Journal: Journal of Proteome Research, Sept. 1
Title: Multi-Q: A Fully Automated Tool for Multiplexed Protein Quantitation
Authors: W.T. Lin; W.N. Hung; Y.H. Yian; K.P. Wu; C.L. Han; Y.R. Chen; Y.J. Chen; T.Y. Sung; W.L. Hsu
Authors present a fully automated software package, Multi-Q, for multiplexed iTRAQ-based quantitation in protein profiling. According to the paper’s abstract, the software expedites the analysis of vast amounts of spectral data.

Journal: Journal of Proteome Research, Sept. 1
Title: Optimized Peptide Separation and Identification for Mass Spectrometry Based Proteomics via Free-Flow Electrophoresis
Authors: J. Malmstrom; H. Lee; A.I. Nesvizhskii; D. Shteynberg; S. Mohanty; E. Brunner; M. Ye; G. Weber; C. Eckerskorn; R. Aebersold
Authors present a protocol for peptide separation by continuous free-flow electrophoresis as the first dimension in a two-dimensional peptide separation workflow. “By the use of a flat pI gradient and a mannitol and urea-based separation media, we were able to perform high-throughput proteome analysis with improved interfacing between FFE and RPLC-MS/MS,” authors said in the paper’s abstract.

Journal: Journal of Proteome Research, Sept. 1
Title: Protein Cross-Linking Analysis Using Mass Spectrometry, Isotope-Coded Cross-Linkers, and Integrated Computational Data Processing
Authors: J. Seebacher; P. Mallick; N. Zhang; J.S. Eddes; R. Aebersold; M.H. Gelb
Authors developed an integrative approach to identify and characterize protein-protein contact sites by analyzing proteolytic products derived from proteins chemically cross-linked by isotopically coded cross-linkers using LC-MALDI tandem mass spectrometry and computer software.

Journal: Journal of Chromatography. B, Analytical technologies in the biomedical and life sciences, Aug. 29, [Epub ahead of print]
Title: A method for the identification of glycoproteins from human serum by a combination of lectin affinity chromatography along with anion exchange and Cu-IMAC selection of tryptic peptides
Authors: R. Qui; X. Zhang; F.E. Regnier
Authors describe a method for identifying glycoproteins from human serum. “Glycoproteins were selected with a concanavalin A (Con A) lectin column and then tryptically digested prior to sequential chromatographic selection of acidic and histidine containing peptides. Acidic peptides were selected with a strong anion exchange (SAX) column. Peptides captured by the SAX columns were then released and histidine-containing peptides in the mixture selected with a copper loaded immobilized metal affinity chromatography (Cu-IMAC) column,” authors said in the paper’s abstract.

Journal: Rapid Communications in Mass Spectrometry: RCM, Aug. 30 [Epub ahead of print]
Title: A method for rapidly confirming protein N-terminal sequences by matrix-assisted laser desorption/ionization mass spectrometry
Authors: C. Zhou; Y. Zhang; P. Qin; X. Liu; L. Zhao; S. Yang; Y. Cai; X Qian
Authors describe a method of identifying and sequencing the N-terminal peptide of a protein based on specific sulfonation of terminal amino groups and selective monitoring of the sulfonated peptide.

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