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Recent Research Papers of Note : Aug 3, 2006

Journal: Bioinformatics, July 15, 2006 [Epub ahead of print]
Title: A computational approach toward label-free protein quantification using predicted peptide detectability
Authors: H. Tang; R.J. Arnold; P. Alves; Z. Xun; D.E. Clemmer; M.V. Novotny; J.P. Reilly; P. Radivojac
Authors propose a new concept of peptide predictability to help explain the relationship between a protein’s quantity and the peptides identified from it in a high-throughput proteomics experiment.

Journal: BMC Bioinformatics, July 26, 2006, [Epub ahead of print]
Title: Identification of biomarkers from mass spectrometry data using a “common” peak approach
Authors: T. Fushiki; H. Fujisawa; S. Eguchi
Authors propose using “common” peaks in data as biomarkers. Analysis is conducted by preprocessing data, identifying biomarkers and applying AdaBoost to construct a classification function. AdaBoost selects informative “common” peaks. AsymBoost is examined to balance false positives and negatives.

Journal: Bioinformatics, July 15, 2006
Title: Semi-supervised LC/MS alignment for differential proteomics
Authors: B. Fischer; J. Grossmann; V. Roth; W. Gruissem; S. Baginsky; J.M. Buhmann
Authors propose a label-free environment where correspondence between elements of two samples must be established prior to comparative analysis. Alignment between samples is achieved by nonlinear robust ridge regression.

Journal: Journal of Pharmaceutical and Biomedical Analysis, July 19, 2006 [Epub ahead of print]
Title: A sensitive liquid chromatography and mass spectrometry method for the determination of posaconazole in human plasma
Authors: J.X. Shen; G. Krishna; R.N. Hayes
Authors propose using LC/MS method to quantitate plasma levels of posaconazole in certain patients. The method uses semi-automated 96-well protein precipitation with gradient chromatographic separation of analytes using a Varian Polaris C-18A column.

Journal: The Journal of Biological Chemistry, July 21, 2006 [Epub ahead of print]
Title: Antigen processing of a short viral antigen by proteasomes
Authors: D. Lopez; Ol Calero; M. Jimenez; M. Garcia-Calvo; M. Del Val
Authors propose using microLC-MS/MS to focus on each short peptide generated by proteasomes that are closely related and overlapping or identical in retention times and masses to optimize identification of generated peptides.

Journal: Blood, Aug. 1, 2006
Title: In-depth analysis of the membrane and cytosolic proteome red blood cells
Authors: E.M. Pasini; M. Kirkegaard; P. Mortensen; H.U. Lutz; A.W. Thomas; M. Mann
Authors use MS-based proteomics to characterize the normal RBC protein profile to obtain the most complete RBC proteome possible by combining high-accuracy, high-sensitivity protein identification technology with selected biochemical procedures for sample preparation.

Journal: Rapid Communications in Mass Spectrometry, July 24, 2006 [Epub ahead of print]
Title: In vacuo isotope coded alkylation technique (IVICAT); an N-terminal stable isotopic label for quantitative liquid chromatography/mass spectrometry proteomics
Authors: B.L. Simons; G. Wang; R.F. Shen; M.A. Knepper
Authors present a new isotopic labeling strategy to modify the N-terminal amino group of peptides in a quantifiable reaction without the use of expensive reagents or solvents.

Journal: Annali di Chimica, May-June 2006
Title: Hollow-fiber flow field-flow fractionation: a gentle separation method for mass spectrometry of native proteins
Authors: P. Reschiglian; A. Zattoni; B. Roda; A. Roda; D. Parisi; M.H. Moon; B.R. Min
Low-impact ionization sources like electrospray ionization (ESI) and matrix-assisted, laser desorption/ionization (MALDI) equipped with time-of-flight (TOF) mass analyzers provide intact protein analysis over a very wide molar mass range. ESI/TOFMS provides also indications on the higher-order structure of intact proteins and non-covalent protein complexes. However, direct analysis of intact protein mixtures in real samples shows limited success, mainly because spectra become very complex to interpret.

Journal: Molecular & Cellular Proteomics: MCP, July 19, 2006 [Epub ahead of print]
Title: Evaluation of multi-protein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry
Authors: T. Liu; W.J. Qian; H.M. Mottaz; M.A. Gritsenko; A.D. Norbeck; R.J. Moore; S.O. Purvine; D.G. Camp; R.D. Smith
Authors report a detailed evaluation of immunoaffinity subtraction performed by applying the ProteomeLab IgY-12 system.

Journal: Molecular & Cellular Proteomics: MCP, July 19, 2006 [Epub ahead of print]
Title: PEPPeR: A platform for experimental proteomic pattern recognition
Authors: J.D. Jaffe; D.R. Mani K.C. Leptos; G.M. Church; M.A. Gillette; S.A. Carr
Authors describe a new algorithm, “Landmark Matching,” and “Peak Matching” that reduce the over-reliance on identification-based quantitative methods and problems associated with chromatographic separation reproducibility.

Journal: Proteomics, July 21, 2006 [Epub ahead of print]
Title: Quantification of change in phosphorylation of BCR-ABL kinase and its substrates in response to Imatinib treatment inhuman chronic myelogenous leukemia cells
Authors: X. Liang; M. Hajivandi; D. Veach; D. Wisniewski; B. Clarkson; M.D. Resh; R.M. Pope
Authors observed that BCR-ABL kinase is phosphorylated at tyrosine 393 and 644 and that SH2-domain containing inositol phosphatase (SHIP)-2 and downstream kinase (Dok)-2 are phosphorylated at tyrosine 1135 and 299. Based on the relative intensity of isotopic peptide pairs, authors demonstrate that the level of phosphorylation of BCR-ABL kinase as well as SHIP-2 and Dok-2 is reduced by about 90 percent upon treatment with Imatinib, a specific inhibitor of BCR-ABL kinase.

Journal: Proteomics, July 21, 2006 [Epub ahead of print]
Title: Comprehensive quantitative proteome analysis of 20S proteasome subtypes from rat liver by isotope coded affinity tag and 2D gel-based approaches
Authors: F. Schmidt; B. Dahlmann; K. Janek; A. Kloss; M. Wacker; R. Ackermann; B. Thiede; P.R. Jungblut
Authors compared 20S proteasome subtypes isolated from rat with four approaches based on the combination of isotope-coded affinity tag (ICAT), 2-DE, LC and ESI and MALDI MS.

Journal: Amino Acids, July 2006
Title: Near infrared spectroscopy, cluster and multivariate analysis hyphenated to thin layer chromatography for the analysis of amino acids.
Authors: N. Heigl; C.W. Huck; M. Rainer; M. Najam-Ul-Haq; G.K. Bonn
Authors developed a method based on near-infrared spectroscopy for the rapid and non-destructive determination and quantification of solid and dissolved amino acids.

Journal: Methods, July 15, 2006 [Epub ahead of print]
Title: Lipidomics: An analysis of cellular lipids by ESI-MS
Authors: S. Milne; P. Ivanova; J. Forrester; H. Alex Brown
Using lipidomics, authors can identify about 450 phospholipid species from total membrane extracts and qualitatively measure pattern response changes initiated by cell surface receptors. This approach facilitates the elucidation of the metabolic changes induced by a perturbation in the cell and recognition of patterns of signaling.

Journal: Bioconjugate Chemistry, July-Aug. 2006
Title: Site-specific, covalent attachment of proteins to a solid surface
Authors: B.P. Duckworth; T.A. Taton; A. Guo; M.D. Distefano
Authors describe a strategy to attach a desired protein to a solid surface in a covalent, site-specific manner using an enzymatic posttranslational modification method to site-specifically label a target protein with an azide; an alternative substrate for protein farnesyl transferase containing an azide group was developed for this purpose.

Journal: Molecular & Cellular Proteomics, July 15, 2006 [Epub ahead of print]
Title: The identification of nucleic acid-interacting proteins using a simple proteomics approach that directly incorporates the electrophoretic mobility shift assay
Authors: J.A. stead; J.N. Keen; K.J. McDowall
Authors describe a simple proteomics-based approach for the identification of MS of proteins in crude extracts that interact with nucleic acids.

Journal: Combinatorial Chemistry & High Throughput Screening, July 2006
Title: A method for rapid protease substrate evaluation and optimization
Authors: I.A. Kozlov; P.C. Melnyk; C. Zhao; J.P. Hachmann; V. Shevchenko; A. Srinivasan; D.L. Barker; M. Lebl
Authors have developed a high throughput assay for measuring protease activity in a solution.

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.