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Recent Research Papers of Note: May 21, 2009


Journal: Journal of Agricultural and Food Chemistry, May 18 [Epub ahead of print]
Title: Functional proteomic analysis predicts beef tenderness and the tenderness differential
Authors: Zapata I; Zerby HN; Wick M

Authors performed functional proteomics to associate electrophoretic bands from the myofibrallar muscle fraction to meat tenderness, which they said is one of the most detrimental factors of meat quality. They used SDS-PAGE to analyze the myofibrillar muscle fraction of the Longissimus dorsi from 22 Angus cross steers. They then characterized six "significant" electrophoretic bands by electrophoretic and statistical analysis. The bands were sequenced by nano-LC-MS/MS. "The protein(s)/peptide(s) identified in these bands encompass a wide array of cellular pathways related to structural, metabolic, chaperone, and developmental functions," according to the abstract. The study, the authors added, begins to assemble information reported elsewhere separately into a complete picture "that will lead to the establishment of a coherent mechanism accounting for meat tenderness."

Journal: Nature Methods, May 17 [Epub ahead of print]
Title: A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
Authors: Bell AW; Deutsch EW; Au CE; Kearney RE; R Beavis; Sechi S; Nilsson T; Bergeron JJ; HUPO Test Sample Working Group, et al.

A test-sample study was conducted by HUPO to determine researcher errors leading to irreproducibility. Twenty out of 27 labs were unable to identify 20 proteins comprising the test sample, and only one lab identified all 22 tryptic peptides of 1,250 Da. Centralized analysis of the raw data indicated that all 20 proteins and 22 peptides of 1,250 Da had been detected by the participants [see accompanying story this issue].

Journal: Nature Methods, May 17 [Epub ahead of print]
Title: A stress test for mass spectrometry-based proteomics
Author: Aebersold, R

In the commentary accompany the study detailing HUPO's test-sample study, the author addresses the results of the test and what still needs to be done to achieve reproducibility in proteomics.

Journal: Analytical Chemistry, May 15
Title: Two-dimensional mass mapping as a general method of data representation in comprehensive analysis of complex molecular mixtures
Authors: Artemenko KA; Zubarev AR; Samgina TY; Lebedev AT: Savitski MM: Zubarev RA

A recent proteomics-grade high-throughput de novo sequencing method utilizing high resolution, high mass accuracy, and collision-activated dissociation and electron capture dissociation has been described. While the approach enables the sequencing of hundreds of peptides in a single LC-MS/MS run, the technique presents a new bottleneck in data representation. The authors suggest a new method of data analysis and visualization "that presents a comprehensive picture of the peptide content, including relative abundances and grouping into families," according to the abstract. The 2D mass mapping calls for molecular masses onto a 2D bubble plot "with the relative monoisotopic mass defect and isotopic shift being the axes and with the bubble area proportional to the peptide abundance," the authors said in the abstract. Peptides in the same family form a compact group and the family identity can in many cases be determined from the molecular mass. The performance of the method is demonstrated on the high-throughput analysis of skin secretion of three frogs, Rana ridibunda, Rana arvalis, and Rana temporaria.

Journal: Analytical Chemistry, May 15
Title: Combined pulsed-Q dissociation and electron transfer dissociation for identification and quantification of iTRAQ-labeled phosphopeptides
Authors: Yang F; Wu S; Stenoien DL; Zhao R; Monroe ME; Gritsenko MA; Purvine SO; Polpitiya AD; Tolic N; Zhang Q; Norbeck AD; Orton DJ; Moore RJ; Tang K; Anderson GA; Pasa-Tolic L; Camp DG; Smith, RD

According to the abstract, the use of isobaric tags for relative and absolute quantification "enables a high-throughput quantification of peptides via reporter ion signals in the low m/z range of tandem mass spectra." PQD, a form of ion trap CID, enables detection of low m/z fragment ions, while ETC is useful for sequencing peptides that contain PTMs. Analysis of the phosphoproteome of human fibroblast cells with a sensitive linear ion trap MS showed the hybrid approach improves the identification and quantification of phosphopeptides.

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Journal: Journal of Proteome Research, May 12 [Epub ahead of print]
Title: A comparison of labeling and label-free mass spectrometry-based proteomics approaches
Authors: Patel VJ; Thalassinos K; Slade S; Connolly JB; Crombie A; Murrell JC; Scrivens J

Authors characterize the proteome of the recently discovered bacterium Methylocella silvestris using three profiling and comparative proteomics approaches. Results were compared based on the number of proteins identified, confidence in identification, sequence coverage, and agreement of regulated proteins. Also sample preparation, instrument time, and sample loading requirements of the different approaches were compared.

Journal: Journal of Proteome Research, May 11 [Epub ahead of print]
Title: In-gel 18O-labeling for improved identification of proteins fro 2-DE gel spots in comparative proteomic experiments
Authors: Broedel O; Krause E; Stephanowitz H; Schuemann M; Eravci M; Weist S; Brunkau C; Wittke J; Eravci S; Baumgartner A

Authors present a method to overcome the potential presence of overlapping proteins, which they said "severely" impairs the reliability of 2DE gel-based comparative proteomics. Corresponding protein spots from two experimental groups are digested in the presence of 16O and 18O, respectively. The samples are pooled and analyzed by mass spectrometry.

Journal: Molecular & Cellular Proteomics, May 9 [Epub ahead of print]
Title: Systems-wide analysis of a phosphatase knock-down by quantitative proteomics and phosphoproteomics
Authors: Hilger M; Bonaldi T; Gnad F; Mann M

Signal transduction in metazoans regulates almost all aspects of biological function, and many diseases involve aberrant signaling, according to the abstract. Perturbations in phosphorylation-based signaling networks are often studied in a hypothesis-driven approach using phosphor-specific antibodies. In the study, the authors applied quantitative, high-resolution mass spectrometry to evaluate the systems' response to the elimination of one signaling component. They metabolically labeled Drosophila cells using SILAC. Phosphatase Ptp61F was knocked down by RNAi. They detected more than 10,000 phosphorylation sites in the phosphoproteome of Drosophila Schneider cells and trained a phosphosite predictor with the data.

Journal: Journal of Proteome Research, May 8 [Epub ahead of print]
Title: TOPPView - an open-source viewer for mass spectrometry data
Authors: Sturm M; Kohlbacher O

Presented is TOPPView, an integrated data visualization and analysis tool for mass spectrometric datasets. It allows for the visualization and comparison of individual mass spectra, 2D LC-MS datasets and their accompanying metadata, according to the abstract. Because it supports standardized XML-based data exchange formats, data exchange is possible with any mass spec, and the integrated analysis tools of the Open MS Proteomics Pipeline, TOPP, allow "efficient data analysis from within TOPPView through a convenient graphical user interface," according to the abstract.

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Journal: Journal of Proteome Research, May 6 [Epub ahead of print]
Title: A new probabilistic database search algorithm for ETD spectra
Authors: Sadygov RG; Good DM; Swaney DL; Coon JJ

Authors describe a database search engine using ETD spectra and protein sequence databases for the identification of peptides. The search engine is based on the probabilistic modeling of shared peaks count and shared peaks intensity between the spectra and peptide sequences. "The shared peaks count accounts for the cumulative variations from amino acid sequences, while shared peaks intensity models the variations between the candidate sequence and product ion intensities," according to the abstract. Results of the application of their model on two high-throughput datasets obtained from yeast whole cell lysates are presented to demonstrate the utility of the algorithm.

Journal: Molecular & Cellular Proteomics, May 1 [Epub ahead of print]
Title: MRM-based, multiplexed, absolute quantification of 45 proteins in human plasma
Authors: Kyzyk MA; Smith D; Yang J; Cross TJ; Jackson AM; Hardie DB; Anderson NL; Borchers CH

Authors created a cocktail of 45 peptides as a standard, "easily adaptable to common plasma proteomics workflows," according to the abstract, to enable the absolute quantitation of 45 endogenous proteins in human plasma trypsin digests. The experiments were performed on simple tryptic digests of human EDTA-plasma without affinity depletion or enrichment beforehand. SIS peptides were added immediately after tryptic digestion. Proteotypic tryptic peptides containing isotopically-coded amino acids were synthesized for all 45 proteins. Capillary zone electrophoresis was used to assess peptide purity, while amino acid analysis determined peptide quantity. "Concentrations of individual peptide standards in the cocktail were optimized to approximate endogenous concentrations of analytes, and to ensure the maximum linear dynamic range of the MRM assays," according to the abstract.

Journal: Journal of Proteome Research, April 30 [Epub ahead of print]
Title: An interative strategy for precursor ion selection for LC-MS/MS-based shotgun proteomics
Authors: Zerck A; Nordhoff E; Resemann A; Mirgorodskaya E; Suckau D; Reinert K; Lehrach H; Gobom J

Current precursor ion selection strategies for LC-MS mainly selects the most prominent peptide signals for MS/MS analysis, resulting in the identification of high abundant proteins while proteins of lower abundance may be missed, the authors said in the abstract. Here, they present a "novel, iterative, and result-driven approach for precursor ion selection that significantly increases the efficiency of an MS/MS analysis by decreasing data redundancy and analysis time."

Journal: Journal of Proteome Research, April 30 [Epub ahead of print]
Title: Mapping the lung proteome in cystic fibrosis
Authors: Gharib SA; Vaisar T; Aitkin ML; Park DR; Heinecke JW; Fu X

The pathophysiology of cystic fibrosis lung disease is "incompletely" understood, according to the abstract,and studying the patterns of protein expression in bronchoalveolar lavage fluid may reveal novel mechanisms in the pathogenesis of CF lung disease. Shotgun proteomics was used to analyze BALF samples from eight cystic fibrosis and four control subjects. Spectral counting and statistical analysis was used to determine differential protein expression between the two sample groups. The authors used Gene Ontology analysis to identify enriched biological modules and applied network analysis to build a protein interaction map in CF lung disease. Shotgun proteomics of BALF identified hundreds of proteins "whose differential enrichment of depletion robustly distinguished the CF phenotype from normal controls," the authors said. "Functional categorization and network analysis identified key processes, including the immune response and proteolytic activity, that are known contributors to CF lung disease," they added in the abstract.

The Scan

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.

Study Presents New Insights Into How Cancer Cells Overcome Telomere Shortening

Researchers report in Nucleic Acids Research that ATRX-deficient cancer cells have increased activity of the alternative lengthening of telomeres pathway.

Researchers Link Telomere Length With Alzheimer's Disease

Within UK Biobank participants, longer leukocyte telomere length is associated with a reduced risk of dementia, according to a new study in PLOS One.

Nucleotide Base Detected on Near-Earth Asteroid

Among other intriguing compounds, researchers find the nucleotide uracil, a component of RNA sequences, in samples collected from the near-Earth asteroid Ryugu, as they report in Nature Communications.