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Recent Research Papers of Note in Proteomics : Jul 10, 2008

Journal: Bioinformatics, July 7 [Epub ahead of print]
Title: ProteoWizard: Open source software for rapid proteomics tools development
Authors: D Kessner; M Chambers; R Burke; D Agus; P Mallick
The software project provides a modular and extensive set of open-source, cross-platform tools and libraries for proteomics data analysis. It is specifically released under the Apache v2 license so it can be used in both academic and commercial projects.

Journal: BMC Bioinformatics, July 7 [Epub ahead of print]
Title: 2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments
Authors: J Allmer; S Kuhlgert; M Hippler
To facilitate the handling of the large amount of data from mass spectrometric analysis, automatic import strips are available and the need to manually import data into the database has been minimized. The software can store and cross-analyze results from many algorithms, the authors said in the abstract.

Journal: Journal of Proteome Research, July 1 [Epub ahead of print]
Title: An immuno-chemo-proteomics method for drug target deconvolution
Authors: C Saxena, E Zhen; RE Higgs; JE Hale
Authors developed a soluble probe in which a small molecule is coupled with a peptide epitope and used it to affinity isolate binding proteins from cell lysate. They report the probe allowed direct verification that the compound “after coupling with peptide epitope retained its binding characteristics,” according to the paper’s abstract. The approach allowed them to identify the known Bisindolylmaleimide-III targets, PKC-alpha, GSK3-beta, CaMKII, adenosine kinase, CDK2, and quinine reductase type 2, and previously unidentified targets PKAC-alpha, prohibitin, VDAC and heme-binding proteins.

Journal: Analytical Chemistry, June 26 [Epub ahead of print]
Title: Mass spectrometry analysis of proteome-wide proteolytic post-translational degradation of proteins
Authors: Y Shen; KK Hixson; N Toliæ, DG Camp; SO Purvine; RJ Moore; RD Smith
Authors studied the protein degradation in yeast S. cerevisiae on a proteome-wide scale by using sequencing-based MS/MS to detect intermediate peptides produced from the intracellular degradation of proteins. They detected 1,100 peptides and their 200 protein-substrate origins, obtaining “new evidence for new insights into the proteome-wide protein-selective degradation in yeast cells,” they said in the paper’s abstract. “This evidence shows that the yeast cytoplasm is the largest pool for the degradation of proteins with both biochemical and geometric specificities, whereas the yeast nucleus seems to be a proteolysis-inert organelle under the condition studied.”

Journal: Analytical Chemistry, June 18 [Epub ahead of print]
Title: Dynamically multiplexed ion mobility time-of-flight mass spectrometry
Authors: ME Belov; B H Clowers; DC Prior; WF Danielson; AV Liyu; BO Petritis; RD Smith
Described are three technologies to make ion mobility spectrometry time-of-flight spectrometry a high-sensitivity, high-throughput platform. They include efficient ion accumulation in an ion funnel trap prior to IMS separation; multiplexing of ion packet introduction into the IMS drift tube; and signal detection with an analog-to-digital converter, into the IMS-TOF-MS system for the “high-throughput analysis of highly complex proteolytic digests of , for example, blood plasma,” according to the paper’s abstract.

Journal: Journal of Proteome Research, June 18 [Epub ahead of print]
Title: Enhancing peptide identification confidence by combining search methods
Authors: G Alves; WW Wu; G Wang; RF Shen; YK Yu
A method is described to combine the results from different database search methods to improve the accuracy of peptide identifications. Included in the authors’ analysis are Sequest (v27, rev12), ProbID (v1.0), InsPecT (v20060505), Mascot (v2.1), X! Tandem (v2007.07.01.2), OMSSA (v2.0), and RAId Dbs. They used two data sets, one in profile mode, the other collected in centroid mode, and tested search performance of all 21 combinations of two search methods and 35 possible combinations of three search methods. Their results suggest that properly combining search methods improves retrieval accuracy. In addition, the authors describe a theoretical framework that could allow a researcher to combine many independent scoring methods including de novo sequencing and spectral library searches.

Journal: Journal of Proteomics, June 14 [Epub ahead of print]
Title: MIAPEGelDB, a web-based submission tool and public repository of MIAPE gel electrophoresis documents
Authors: X Robin; C Hoogland: RD Appel; F Lisacek
MIAPEGelDB, a public repository and web-based data entry tool for storage of data from the Human Proteome Organization’s MIAPE project creating standards for data representation, is described.

Journal: Journal of Proteome Research, June 13 [Epub ahead of print]
Title: iTRAQ experimental design for plasma biomarker discovery
Authors: X Song; J Bandow; J Sherman; JD Baker; PW Brown; MT McDowell; MP Molloy
Using iTRAQ reagents, authors investigated aspects of experimental design for large studies requiring analysis of multiple sample sets. They compared immunodepleted plasma samples from health volunteers with patients with osteoarthritis in eight separate iTRAQ experiments. They used ProteinPilot software for analysis and found that the methodology resulted in “excellent” reproducibility from run to run for determining protein ratios, according to the paper’s abstract.

Journal: Proteomics, June 10 [Epub ahead of print]
Title: Infrared-assisted tryptic proteolysis for peptide mapping
Authors: S Wang; L Zhang; P Yang; G Chen
Authors allowed protein solutions containing trypsin in sealed Eppendorf tubes to digest under an infrared lamp at 37 masculineC. BSA and myoglobin were digested. Digests were identified by MALDI-TOF MS with sequence coverages of 69 percent (BSA) and 90 percent (MYO). The strategy, the authors say in the paper’s abstract, “is simple and efficient, offering great promise for high-throughput protein identification.”

Journal: Proteomics, June 10 [Epub ahead of print]
Title: Matrix layer sample preparation: An improved MALDI-MS peptide analysis method for proteomic studies
Authors: I Garaguso; J Borlak
Saying that the performance of MALDI-MS is “highly influenced” by sample preparation and the choice of matrix, the authors presented MALDI-MS sample prep methods for peptide mass mapping and peptide analysis. The method is based on the use of 2.5-dihydroxybenxoic acid matrix and prestructured sample supports they termed matrix layer.

Journal: Journal of Proteome Research, June 7 [Epub ahead of print]
Title: A shotgun proteomic method for the identification of membrane-embedded proteins and peptides
Authors: AR Blackler; AE Speers; MS Ladinsky; CC Wu
Because of the hydrophobic nature of their membrane-embedded domains, membrane proteins are difficult to work with. The authors propose a shotgun method for the high-throughput analysis of the membrane embedded transmembrane domains of integral membrane proteins, which extends the depth of coverage of the membrane proteome.

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