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Recent Research Papers of Note in Proteomics: May 15, 2008

Journal: Rapid Communications in Mass Spectrometry, May 9 [Epub ahead of print]
Title: Lys Tag: an easy and robust chemical modification for improved de novo sequencing with a matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometer.
Authors: P Conrotto; U Hellman
Authors describe the methodology and experimental applications of “a fast, efficient, and cheap lysine derivatization” that improves the signals from lysine-terminated peptides. The method, they say, can be used as a lysine-blocking agent in combination with other derivatization techniques, and upon peptide fragmentation generates a series of predominantly y-ions “allowing the determination of unambiguous amino acid sequences,” according to the abstract.

Journal: Bioinformatics, May 3 [Epub ahead of print]
Title: DAnTE: a statistical tool for quantitative analysis of -omics data.
Authors: AD Polpitiya; WJ Qian; N Jaitly; VA Petyuk; JN Adkins; DG Camp; GA Anderson; RD Smith
DAnTE, which stands for Data analysis Tool Extension, is designed to address challenges associated with quantitative bottom-up, shotgun proteomics data. It features selected normalization methods, missing value-imputation algorithms, peptide-to-protein rollup methods, plotting functions, and a hypothesis testing scheme that can handle “unbalanced data and random effects,” according to the abstract.

Journal: Bioinformatics, May 3 [Epub ahead of print]
Title: A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
Authors: BJ Webb-Robertson; WR Cannon; CS Oehmen; AR Shah; V Gurumoorthi; MS Lipton; KM Waters
Authors present a SVM model using a simple descriptor space based on 35 properties of amino acid content, charge, hydrophilicity, and polarity for quantitatively predicting proteotypic peptides.

Journal: Proteomics, May 2 [Epub ahead of print]
Title: The HUPO Brain Proteome Project wish list summary of the 9th HUPO BPP Workshop 9-10 January 2008, Barbados
Authors: M Hamacher; M Eisenacher; F Tribl; C Stephan; K Marcus; T Hardt; J Wiltfang; L Martens; D Desiderio; H Gutstein; YM Park; HE Meyer
Project group members have drafted a so-called HUPO BPP wish list containing timelines, suggestions and missions, to be updated regularly, serving as a guideline for the next phase of the project.

Journal: EMBO Reports, May
Title: PeptideAtlas; a resource for target selection for emerging targeted proteomics workflows
Authors: EW Deutsch; H Lam; R Aebersold
Authors describe the PeptideAtlas Project, its contents and components, and show they provide “a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics,” according to the abstract.

Journal: Proteomics, May
Title: Technical strategies to reduce the amount of "false significant" results in quantitative proteomics.
Authors: S Fuxius; M Eravci; O Broedel; S Weist; U Mansmann; S Eravci; A Baumgartner
By controlling for running samples in two different 2 DE runs; running 2D gels produced in two different gel casters; normalizing the entire gel rather than normalizing several different gel zones; using IPG strips from different packages; and dividing the whole sample into subgroups during software analysis, the authors say they were able to reduce the false positive rates in experiments to about 5 percent.

Journal: Proteomics, May
Title: Applications in brain proteomics: 8(th) HUPO Brain Proteome Project Workshop 7 October 2007, Seoul, Korea
Authors: : M Hamacher; M Eisenacher; C Stephan; K Marcus; T Hardt; J Wiltfang; YM Park; HE Meyer; A Henkel; CR Jimenez
About 100 researchers met before the HUPO World Congress in the fall to discuss the latest results and strategies concerning Huntington’s disease, glioblastoma, and standardization.

Journal: Proteomics, May
Title: Enhanced nuclear proteomics
Authors: M Barthéléry; U Salli; KE Vrana
Authors report a nuclear-isolation and protein-extraction procedure which “effectively isolates intact nuclei and then depletes the sample of histones by taking advantage of their ability to form an insoluble complex with DNA at lower pH,” according to the abstract. The method “greatly” improves electrofocusing efficacy and nearly doubles the number of protein spots detected.

Journal: Journal of Dental Research, May
Title: Proteome of human minor salivary gland secretion
Authors: WL Siqueira; E Salih; DL Wan; EJ Helmerhorst; FG Oppenheim
Using LC-ESI-MS-MS, authors identified 56 proteins, including 12 that had never been identified in any salivary secretion. While other research has focused on the proteomes of major human salivary secretions and whole saliva, this study is the first looking into the proteome of minor salivary gland secretion, the authors say in the abstract. The differences in the salivary proteome may be important with respect to specific oral functions, they add.

Journal: Journal of Proteome Research, April 29 [Epub ahead of print]
Title: A Computational Strategy to Analyze Label-Free Temporal Bottom-Up Proteomics Data
Authors: X Du; SJ Callister; NP Manes; JN Adkins; RA Alexandridis; X Zeng; JH Roh; WE Smith; TJ Donohue; S Kaplan; RD Smith; MS Lipton
Described is a strategy to address challenges related to extracting biological information from dynamic proteomics data, including extraneous variability, missing abundance values, and the identification of significant temporal patterns. The paper also demonstrates its values for analyzing temporal bottom-up proteomics data using data from a Rhodobacter sphaeroides 2.4.1 time-course study.

Journal: BMC Bioinformatics, April 25
Title: PARPST: a PARallel algorithm to find peptide sequence tags
Authors: S Brunetti; E Lodi; E Mori; M Stella
Described is a work-efficient parallel algorithm for protein identification by tandem mass spectrometry. The algorithm can find all the sequence tags having “score greater than a parameter or all the sequence tags of maximum length,” according to the abstract. On tests of 1,507 spectra in the Open Proteomics Database, the algorithm is demonstrated to be efficient and effective with results comparable to other methods.

Journal: BMC Medical Genomics, April 25 [Epub ahead of print]
Title: HIP2: An online database of human plasma proteins from healthy individuals
Authors: S Saha; SH Harrison; C Shen; H Tang; P Radivojac; RJ Arnold; X Zhang; JY Chen
The current version of HIP2 contains 12,787 protein entries linked to 86,831 peptide entries identified using different MS platforms. The web-based database was developed to be the comprehensive collection of healthy human plasma proteins, the authors say in the abstract. Users can search for plasma protein/peptide annotations, peptide/protein alignments, and experimental/sample conditions with options for filter-based retrieval.

Journal: Nucleic Acids Research, April 25 [Epub ahead of print]
Title: ISPIDER Central; an integrated database web-server for proteomics
Authors: JA Siepen; K Belhajjame; JN Selley; SM Embury; NW Paton; CA Goble; SG Oliver; R Stevens; Zamboulis; N Martin; A Poulovassillis; P Jones; R Côté; H Hermjakob; MM Pentony; DT Jones; CA Orengo; SJ Hubbard
According to the authors, ISPIDER offers more search capabilities than other, mature proteomic repositories including PRIDE, PepSeeker, PeptideAtlas, and the Global Proteome Machine. Users can search for proteins and peptides that have been characterized in MS-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers or clients. The European Bioinformatics institute’s Protein Identifier Cross-Reference service is used “to resolve accessions from different sequence repositories,” according to the abstract.

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