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Recent Research Papers of Note: Nov 22, 2006

Journal: Pacific Symposium on Biocomputing, 2006
Title:High-accuracy peak picking of proteomics data using wavelet techniques
Authors: E Lange; C Gropl; K Reinert; O Kohlbacher; A Hildebrandt
Authors present a new peak-picking algorithm for the analysis of mass spectrometric data. “The method uses the multiscale nature of spectrometric data by first detecting the mass peaks in the wavelet-transformed signal before a given asymmetric peak function is fitted to the raw data. In an optional third stage, the resulting fit can be further improved using techniques from nonlinear optimization,” the authors say in their abstract.

Journal: Journal of immunological methods, Nov. 2 [Epub ahead of print]
Title: Quantitative detection of therapeutic proteins and their metabolites in serum using antibody-coupled ProteinChip Arrays and SELDI-TOF-MS
Authors: L Favre-Kontula; Z Johnson; T Steinhoff; A Frauenschuh; F Vilbois; AE Proudfoot
Authors propose an alternative to ELISA for the quantitative detection of protein therapeutics in serum. Polyclonal antibodies immobilized in ProteinChip arrays and SELDI-TOF MS are used.

Journal: Methods in Molecular Biology, 2006
Title: Identification of phosphorylated proteins
Authors: MV Turkina, AV Vener
Authors describe a method of revealing and characterizing the dynamic protein phosphorylation networks in plants.

Journal: Journal of Proteome Research, Nov. 3
Title: Capillary array reversed-phase liquid chromatography-based multidimensional separation system coupled with MALDI-TOF-TOF-MS detection for high-throughput proteome analysis
Authors: X Gu; C Deng; X Zhang
“A high-throughput on-line capillary array-based two-dimensional liquid chromatography (2D-LC) system coupled with MALDI-TOF-TOF-MS proteomics analyzer for comprehensive proteomic analyses has been developed, in which one capillary strong-cation exchange (SCX) chromatographic column was used as the first separation dimension and 18 parallel capillary reversed-phase liquid chromatographic (RPLC) columns were integrated as the second separation dimension,” the authors say in their abstract.

Journal: Journal of Proteome Research, Nov. 3
Title: Detecting differential and correlated protein expression in label-free shotgun proteomics
Authors: B Zhang; NC Verberkmoes; MA Langston; E Uberbacher; RL Hettich; NF Samatova
Authors performed a systematic analysis of different approaches to quantify differential protein expression in eukaryotic Saccharomyces cerevisiae and prokaryotic Rhodopseudomonas palustris label-free LC-MS/MS data.

Journal: Molecular & Cellular Proteomics, Oct. 29 [Epub ahead of print]
Title: Shotgun glycopeptide-capture approach coupled with mass spectrometry for comprehensive glycoproteomics
Authors: B Sun; JA Ranish; AG Uleg; JT White; X Yan; B Lin; L Hood
Authors present a general shotgun glycoproteomics approach to profile glycoproteins comprehensively in complex biological mixtures. Glycopeptides derived from glycoproteins are enriched by selective capture onto a solid support using hydrazide chemistry. Enzymatic release of the peptides followed, then analysis by tandem mass spectrometry. Validation was done with standard protein mixtures resulting in a capture efficiency of almost 100 percent.

Journal: Methods, November
Title:Quantitative proteomics to study mitogen-activated protein kinases
Authors: B Blagoev; M Mann
Authors “describe the SILAC labeling procedure and explain how to design SILAC experiments to examine the level and duration of phosphorylation of endogenous MAP kinases and their substrates in cell culture systems,” according to the paper’s abstract.

Journal:Brain: A Journal of Neurology, November
Title: Proteome-based plasma biomarkers for Alzheimer's disease
Authors: A Hye; S Lynham; M Thambisetty; M Causevic; J Campbell; HL Byers; C Hooper; F Rijsdijk; SJ Tabrizi; S Banner; CE Shaw; C Foy; M Poppe; N Archer; G Hamilton; J Powell; RG Brown; P Sham; M Ward; S Lovestone
Authors performed a case-control study of plasma using 2D-gel electrophoresis and mass spectrometry to seek biomarkers in peripheral tissue.

Journal: Molecular & Cellular Proteomics, Oct. 23 [Epub ahead of print]
Title: Determination of binding specificities in highly multiplexed bead-based assays for antibody proteomics

Authors: JM Schwenk; J Lindberg; M Sundberg; M Uhlen; P Nilsson

Authors describe a single-tube multiplex approach to simultaneously analyze the binding of antibodies to a large number of different antigens.

Journal: Nature Methods, Oct. 22 [Epub ahead of print]
Title: An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells
Authors: T Burckstummer; KL Bennett; A Preradovic; G Schutze; O Hantschel; G Superti-Furga; A Bauch
Authors designed dual-affinity tags optimized for use in mammalian cells and compared the efficiency of each tag with conventional tandem affinity purification tag. Authors found that a tag based on protein G and streptavidin-binding peptide “resulted in a ten-fold increase in protein complex yield and improved the specificity of the procedure,” according to the paper’s abstract.

The Scan

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.

Estonian Biobank Team Digs into Results Return Strategies, Experiences

Researchers in the European Journal of Human Genetics outline a procedure developed for individual return of results for the population biobank, along with participant experiences conveyed in survey data.

Rare Recessive Disease Insights Found in Individual Genomes

Researchers predict in Genome Medicine cross-population deletions and autosomal recessive disease impacts by analyzing recurrent nonallelic homologous recombination-related deletions.

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.