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Recent Research Papers of Note : Feb 19, 2009


Journal: Molecular & Cellular Proteomics, Feb. 9 [Epub ahead of print]
Title: MitoMiner: an integrated database for the storage and analysis of mitochondrial proteomics data
Authors: AC Smith; AJ Robinson

The many experiments that have been conducted to define the mitochondrial proteome have resulted in large and difficult datasets that are difficult to analyze, the authors said in the abstract. They seek to address this by developing a new public resource for the storage and investigation of this data. They call the database MitoMiner, which uses a model to describe the proteomic data and associated biological information.

Journal: Nature Methods, Feb. 8 [Epub ahead of print]
Title: Quantitative interaction proteomics using mass spectrometry
Authors: A Wepf; T Glatter; A Schmidt; R Aebersold; M Gstaiger

Presented is a mass spec-based strategy for the absolute quantification of protein complex components isolated through affinity purification. Bait proteins were quantified via isotope-labeled reference peptides corresponding to an affinity tag sequence while prey proteins were quantified by label-free correlational quantification using the precursor ion signal intensities of proteotypic peptides generated in reciprocal purifications. The authors used their method to quantitatively analyze interaction stoichiometries in the human protein phosphatase 2A network.

Journal: Journal of Proteome Research, Feb. 6 [Epub ahead of print]
Title: Pathway-based biomarker search by high-throughput proteomics profiling of secretomes
Authors: K Lawlor; A Nazarian; L Lacomis; P Tempst; J Villanueva

A secretome, a biological fluid that may be enriched with secreted or shed proteins from adjacent disease-relevant cancer cells, has recently been targeted for biomarker discovery. In the paper, authors describe a method for secretome analysis using “stacking gels,” label-free relative quantitation, and pathway analysis. The protocol presented increases the throughput of secretome analysis by about one order of magnitude compared to earlier methods, according to the abstract.

Journal: Journal of Proteome Research, Feb. 6
Title: Evaluation of archival time on shotgun proteomics of formalin-fixed and paraffin-embedded tissues
Authors: BM Balgley; T Guo; K Zhao; X Fang; FA Tavassoli; CS Lee

According to the abstract, access to archived FFPE tissue specimens via shotgun-based proteomics analyses may “open new avenues for both prospective and retrospective translational research.” One issue in performing comparative proteomics measurements with FFPE tissue relates to potential variability in protein composition and retrieval based on storage time. Authors seek to address this by coupling capillary isotachophoresis-based proteome technology with optimized protein extraction and digestion procedures for handling FFPE tissues to evaluate the effects of storage time on archival-tissue proteome analysis across 10 archived uterin mesenchymal tumor tissue blocks, including nine uterine leiomyomas dating to between 1990 and 2002 and a single case of alveolar soft part sarcoma from 1980.

Journal: Molecular & Cellular Proteomics, Feb. 4 [Epub ahead of print]
Title: SISCAPA peptide enrichment on magnetic beads using an inline beadtrap device
Authors: NL Anderson; A Jackson; D Smith; D Hardie; C Borchers; TW Pearson

SISCAPA, or stable isotope standards and capture by anti-peptide antibodies, is used for specific antibody-based capture of individual tryptic peptides from a digest of whole human plasma using a simplified magnetic bead protocol and a novel rotary magnetic beadtrap device. “A large majority of the peptides that are bound non-specifically in SISCAPA reactions were shown to bind to components other than the antibody (e.g., the magnetic beads), suggesting that substantial improvement in enrichment could be achieved by development of improved inert bead surfaces,” according to the abstract.

Journal: Journal of the American Chemical Society, Feb. 4
Title: Chaperonin complexes monitored by ion mobility mass spectrometry
Authors: E van Duijn; A Barendregt; S Synowsky; C Versluis; AJ Heck

Authors highlight native mass spectrometry in combination with ion mobility mass spectrometry as a new method to generate structural information from macromolecular functional protein assemblies. According to the abstract, IM-MS “allows the assessment of gas phase ion collision cross sections of protein complex ions, which can be related to overall shapes/volumes of protein assemblies, and thus be used to monitor changes in structure.” They applied IM-MS to study intermediate chaperonin complexes that may be present during substrate folding. Their results, they said, reveal that the protein assemblies retain their solution phase structural properties in the gas phase, "addressing a long standing issue in mass spectrometry.”

Journal: Chembiochem : A European Journal of Chemical Biology, Feb. 3 [Epub ahead of print]
Title: Particle-based synthesis of peptide arrays
Authors: F Breitling; T Felgenhauer; A Nesterov; V Lindenstruth; V Stadler; FR Bischoff

While lithographic methods have revolutionized genomics, an issue that has dragged down the field of high-density peptide arrays has been the monomer-by-monomer repeated consecutive coupling of 20 different amino acids associated with lithography because this can result in an excessive number of coupling cycles, according to the authors. They said that “combinatorial synthesis based on electrically charged solid amino acid particles resolves this problem.” The method proposed “should allow for the translation of entire genomes into sets of overlapping peptides to be used in proteome research,” the authors reported.

Journal: Journal of Proteome Research, February
Title: High-throughput liquid-liquid fractionation of multiple protein post-translational modifications
Authors: JH Deford, JE Nuss; J Amaning; RD English; D Tjernlund; J Papaconstantinou

Authors modified a two-dimensional HPLC system, Beckman Coulter’s PF2D ProteomeLab, to create proteome maps of PTMs. The system, they said in the abstract, resolves complex protein mixtures by anion exchange chromatofocusing in the first dimension and hydrophobicity in the second dimension. “The simultaneous identification of multiple protein modifications, accomplished by incorporating a photo diode array (PDA) detector into the PF2D system, facilitates the simultaneous production of three-dimensional proteome maps and visualization of both unmodified and post-translationally modified (PTM) proteins at their signature wavelengths within the proteome,” according to the abstract.

Journal: Proteomics, February
Title: Improved protein sequence coverage by on-resin deglycosylation and cysteine modification for biomarker discovery
Authors: H Kamada; T Fugmann; D Neri; C Roesli

The method described is for protein modifications after in vivo or ex vivo biotinylation. Biotinylated proteins were captured on streptavidin resin and all modifications and proteolytic digestions yielding peptides for mass-spec analysis are performed on resin. Using biotinylated bovine fetuin-A as a test protein, the authors report an improvement in sequence coverage from 7.9 percent to 58.7 percent, including the identification of all three glycosylation sites. A complex mixture derived from the ex vivo biotinylation of vascular structures in human kidney with cancer obtained by perfusion after surgical resection showed almost double the sequence coverage for all checked proteins when analyzed by LC-MALDI TOF/TOF, according to the abstract.

Journal: Proteomics, February
Title: Multivariate analysis of single quadrupole LC-MS spectra for routing characterization and quantification of intact proteins
Authors: FT Michaud; A Garnier; L Lemieux; C Duchesne

A method is proposed for protein mixture resolution and identification. The method is based on detection of intact, nondigested proteins by LC coupled to single quadrupole MS, followed by the analysis of the resulting spectra by multivariate analysis. The method enables even large molecular weight proteins that generate complex spectra to be characterized “to a level that allows isoform discrimination,” the authors said in the abstract.

Journal: Journal of Integrative Plant Biology, February
Title: Analysis of the Arabidopsis floral proteome: detection of over 2,000 proteins and evidence for post-translational modifications
Authors: B Feng; X Zhou; B Stanley; H Ma

Using two-dimension electrophoresis, mass spectrometry, and multi-dimensional protein identification technology approaches, the authors reported identifying 2,446 proteins in the wild-type Arabadopsis flower. They said that they detected proteins that are annotated to function in protein synthesis, folding, modification, and degradation, “as well as the presence of regulatory proteins such as transcription factors and protein kinases,” according to the abstract. “Our results allow the formulation of hypotheses regarding post-translational regulation of proteins in the flower, providing new understanding about Arabidopsis flower development and physiology,” the authors add.

Journal: Rapid Communications in Mass Spectrometry: RCM, Jan. 30 [Epub ahead of print
Title: Top-down proteomics with a quadrupole time-of-flight mass spectrometer and collision-induced dissociation
Authors: A Armirotti; U Benatti; G Damonte

Authors said they demonstrated that top-down data can be obtained by CID MS-MS on a q-TOF instrument not originally designed for such purposes. Protein identification is achieved with both N- and C- terminal sequence tags and BLAST database searches. The authors said that PTMs can also be addressed.

Journal: Journal of Proteome Research, Jan. 29 [Epub ahead of print]
Title: Automated 2D peptide separation on a 1D nano-LC-MS system
Authors: P Taylor; PA Nielsen; MB Trelle; OB Hørning; MB Andersen; O Vorm; MF Moran; T Kislinger

Presented is a variation of the traditional MudPIT protocol, combining highly sensitive chromatography using a nano-LC system with a two-dimensional precolumn in a vented column setup. Their method demonstrated better first-phase separation "leading to more proteins being characterized while using rather simple instrumentation and a protocol that requires less time and very little technical expertise to perform," the authors said in the abstract.

Journal: Journal of Proteome Research, Jan. 21 [Epub ahead of print]
Title: Quantitative matrix-assisted laser desorption ionization-Fourier transform ion cyclotron resonance (MALDI-FT-ICR) peptide profiling and identification of multiple-sclerosis-related proteins
Authors: MP Stoop; LJ Dekker; MK Titulaer; RJ Lamers; PC Burgers; Pa Sillevis Smitt; AJ van Gool; TM Luider; RO Hintzen

Authors present a MALDI-FT-ICR method for quantitative peptide profiling that uses peak height as a measure for abundance. Relative standard deviation in peak height of peptides spiked over three orders of magnitude in concentration were below 10 percent, according to the abstract, and allowed for accurate comparisons between MS and controls.

Journal: Analytical Chemistry, Jan. 20 [Epub ahead of print]
Title: Peptide quantification using 8-plex isobaric tags and electron transfer dissociation tandem mass spectrometry
Authors: D Phanstiel; R Unwin; GC McAlister; JJ Coon

Authors demonstrated that upon ETD, peptides labeled in with 8-plex iTRAQ tags fragment "to produce unique reporter ions that allow for five channels of quantification," according to the abstract.

Journal: Journal of Proteome Research, Jan. 16 [Epub ahead of print]
Title: Stable isotope dilution multidimensional liquid chromatography-tandem mass spectrometry for pancreatic cancer serum biomarker discovery
Authors: KH Yu; CG Barry; D Austin; CM Busch; V Sangar; AK Rustgi; IA Blair

A novel approach is reported for pancreatic cancer biomarker discovery. The technique uses a stable isotope-labeled proteome standard coupled with extensive multidimensional separation and tandem mass spectrometry. According to the authors, the technique allows for the detection of low abundance proteins "and focuses only on biologically relevant proteins derived from pancreatic cancer cells."