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Recent Research Papers of Note: Apr 30, 2009

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Journal: Biomedical Chromatography: BMC, May
Title: Limitation of immunoaffinity column for the removal of abundant proteins from plasma in quantitative plasma proteomics
Authors: T Ichibangase; K Moriya; K Koike; K Imai
In plasma proteomics, it is "essential" to prepare protein samples without high-abundance proteins with preparation techniques such as immunoaffinity capture, according to the abstract. Preliminary experiments by the authors suggest that functional changes resulting from usage alter the ability of the immunoaffinity column. In this study, they assess changes in the ability of immunoaffinity columns to remove abundant proteins from plasma. The reproducibility of the affinity column was tested by fluorogenic derivatization-liquid chromatography-tandem mass spectrometry combined with an IgY column. Their results, they said, suggests that "in quantitative plasma proteomics studies, it is important to keep in mind the risk of not only the nonselective loss but also the changes in the adsorption ability of the immunoaffinity column," according to the abstract.


Journal: Amino Acids, April 24 [Epub ahead of print]
Title: Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset
Authors: MG Shi; JF Xia; XL Li; DS Huang

Because protein-protein interaction data derived from high-throughput technologies are often incomplete and noisy, it is important to develop computational methods and high-quality interaction datasets for predicting PPIs, the authors stated in the abstract. They propose a sequence-based method that combines correlation coefficient transformation and a support vector machine.


Journal: Analytical Chemistry, April 21, [Epub ahead of print]
Title: Two-dimensional mass mapping as a general method of data representation in comprehensive analysis of complex molecular mixtures
Authors: KA Artemenko; AR Zubarev; TY Samgina; AT Lebedev; MM Savitski; RA Zubarev

In the abstract, the authors said that a new high-throughput, de novo sequencing method combining collision-activated dissociation and electron-capture dissociation utilizes the benefits of high resolution and high mass-accuracy. The technique, however, also has a new bottleneck, "which occurs in data representation," they said. They suggest a new method of data analysis and visualization "that represents a comprehensive picture of the peptide content, including relative abundances and grouping into families." Molecular masses are put onto a 2D bubble plot, "with the relative monoisotopic mass defect and isotopic shift being the axes, and with the bubbled area proportional to the peptide abundance." On such a plot, peptides that belong to the same family form a compact group, "so that the family identity can in many cases be determined from the molecular mass alone."


Journal: Journal of Proteome Research, April 21 [Epub ahead of print]
Title: Characterization of human skeletal muscle biopsy samples using shotgun proteomics
Authors: KC Parker; R Walsh; M Salajegheh; A Amato; B Krastins; D Sarracino; SA Greenberg

Authors characterized the human muscle proteome, using four different workflows to study biopsy specimens: 1D and 2D peptide separation, SDS gels, and differential solubilization. They performed MS/MS analyses of 178 four-hour LC separations derived from 31 patients and identified more than 2,000 proteins. They also determined how 370 "very abundant" proteins behave upon differential solubilization.


Journal: Electrophoresis, April 20 [Epub ahead of print]
Title: Introducing a new parameter for quality control of proteome profiles: Consideration of commonly expressed proteins
Authors: A Slany; VJ Haudek; NC Gundacker; J Griss; T Mohr; H Wimmer; M Eisenbauer; L Elbling; C Gerner

Authors present a strategy to generate a list of commonly expressed proteins to serve as a positive control in order to facilitate "quality assessment of proteome profiling experiments," according to the abstract. They compared the cytoplasmic fractions of four different cells — human dendritic cells, endothelial cells, fibroblasts, and keratinocytes. 2D PAGE and shotgun analyses were done to profile the proteomes, resulting in the identification of 360 proteins by the first method and 665 proteins by the latter. All proteins were considered to be common proteins by the authors.

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Journal: BMC Genomics, April 16 [Epub ahead of print]
Title: Estimating accuracy of RNA-Seq and microarrays with proteomics
Authors: X Fu; N Fu; S Guo; Z Yan; H Hu; C Menzel; W Chen; Y Li; R Zeng; P Khaitovich

Authors evaluated the relative accuracy of microarrays, transcriptome sequencing, and proteomics, determining that RNA-seq provides "a better estimate of absolute expression levels," according to the abstract. "Our result shows that in terms of overall technical performance, RNA-seq is the technique of choice for studies that require accurate estimation of absolute transcript levels."


Journal: Journal of Proteome Research, April 16 [Epub ahead of print]
Title: Software platform for rapidly creating computational tools for mass spectrometry-based proteomics
Authors: D May; W Law; M Fitzgibbon; Q Fang; M McIntosh

Authors describe and demonstrate the proteomics toolkit provided in the open-source msInspect software distribution. They show the toolkit's ability to "rapidly develop new computational tools" by presenting an example application, Qurate, a graphical tool for manually curating isotopically labeled peptide quantitative events.


Journal: Molecular & Cellular Proteomics, April 15 [Epub ahead of print]
Title: Large-scale proteomics analysis of the human kinome
Authors: FS Oppermann; F Gnad; JV Olsen; R Hornberger; Z Greff; G Kéri; M Mann; H Daub

"Members of the human protein kinase superfamily are the major regulatory enzymes involved in the activity control of eukaryotic signal-transduction pathways," according to the abstract. Protein kinases are located at the nodes of phosphorylation-based signal transmission, so analysis of their cellular expression and site-specific phosphorylation "can provide important insights into the architecture and functionality of signaling networks," the authors said. In global proteome studies, low protein-kinase abundance levels lead to "rather minor peptide species that are occluded by a vast excess of peptides from other cellular proteins," they added. In their study, they employed SILAC to compare the binding characteristics of three kinase-selective affinity resins by quantitative MS.


Journal: Molecular & Cellular Proteomics, April 14 [Epub ahead of print]
Title: SysPTM – a systematic resource for proteomic research of post-translational modifications
Authors: H Li; X Xing; G Ding; Q Li; C Wang; L Xie; R Zeng; Y Li

Presented is a curated, web-accessible PTM dataset, SysPTM. According to the abstract, the database provides a "systematic and sophisticated platform for proteomic PTM research, equipped not only with a knowledgebase of manually curated multi-type modification data, but also with four fully developed, in-depth data-mining tools." SysPTM currently contains data detailing 117,349 experimentally determined PTM sites on 33,421 proteins involving almost 50 PTM types.


Journal: Journal of Proteome Research, April 8 [Epub ahead of print]
Title: A new probabilistic database search algorithm for ETD spectra
Authors: R Sadygov

Author reports a database search engine using ETD spectra and protein sequence databases to identify peptides. The search engine is based on probability modeling of shared-peak count and shared-peak intensity between the spectra and the peptide sequences. The utility of the algorithm for real-world data is demonstrated with the presentation of applications of the model to two high-throughput datasets obtained from yeast whole cell lysates.


Journal: Journal of Proteome Research, April
Title: Post-analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures
Authors: MR Hoopmann; GE Merrihew; PD von Haller; MJ MacCoss

Though peptide identification by microcapillary LC-MS/MS is now routine, many peptides within the detection limit of the MS remain unidentified due to limitations in MS/MS sampling speed "despite the dynamic range and peak capacity of the instrument," the authors said in the abstract. They developed an automated approach using mass spectra from high resolution muLC-MS data "to define the molecular species present in the mixture and direct the acquisition of MS/Ms spectra to precursors that were missed in prior analyses," according to the abstract. The approach increases the coverage of the molecular species sample by MS/MS and the number of peptides and proteins identified during the acquisition of technical or biological replicates using 1D chromatographic separation, the authors said.

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