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Recent Research Papers of Note in Proteomics: Jul 26, 2007

Journal: Laboratory Investigation: A Journal of Technical Methods and Pathology, August
Title: ‘Tissue surrogates’ as a model for archival formalin-fixed paraffin-embedded tissues
Authors: CB Fowler; RE Cunningham; TJ O’Leary; JT Mason
Authors have developed a procedure for the formation of ‘tissue surrogates’ to model FFPE tissues. They fixed cytoplasmic protein at concentrations approaching the protein content in whole cells. In the study, they used tissue surrogates from at least one protein to evaluate extraction protocols “for the ability to quantitatively extract proteins from the surrogates,” according to the abstract.

Journal: Molecular BioSystems, August
Title: Proteomics data validation: Why we all must provide data
Authors: L Martens; H Hermjakob
Authors share their views about the issue surrounding the sharing of proteomic data and propose guidelines on how to do so.

Journal: Molecular & Cellular Proteomics, July 23, 2007
Title: Shotgun protein sequencing: Assembly of peptide tandem mass spectra from mixtures of modified proteins
Authors: N Bandeira; KR Clauser; PA Pevzner
Authors demonstrate, for the first time, they say, “the feasibility of automated shotgun protein sequence of protein mixtures by utilizing MS/MS spectra of overlapping and possibly modified peptides generated via multiple proteases of different specificities,” according to the abstract.

Journal: Molecular & Cellular Proteomics, July 20 [Epub ahead of print]
Title: High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites
Authors: J Stahl-Zeng; V Lange; R Ossola; R Aebersold; B Domon
Authors describe a method for detecting plasma proteins at concentrations in the ng/mL or sub ng/mL range and accurate quantification over five orders of magnitude. Their method is based on the selective isolation of N-glycosites from the plasma proteome and the detection and quantification of targeted peptides in a quadrupole linear ion-trap instrument in MRM mode.

Journal: Proteomics, July 19 [Epub ahead of print]
Title: Applications of field-flow fractionation in proteomics: Present and future
Author: J Chmelik
According to the author, field-flow fractionation allows for the separation of analytes in a relatively short time and the collection of fractions for further characterization or investigation of properties. Only small samples are consumed during the process. These and other advantages make FFF “uniquely qualified for separation and purification of biological samples,” according to the abstract. The paper discusses selected applications of FFF and future trends in application of FFF to proteomics.

Journal: Analytical Chemistry, July 18 [Epub ahead of print]
Title: Noncompetitive detection of low molecular weight peptide by open sandwich immunoassay
Author: SL Lim; H Ichinose; T Shinoda; H Ueda
Authors attempted noncompetitive detection of small peptides by open sandwich enzyme-linked immunosorbent assay utilizing the antigen-induced enhancement of antibody VH/VL interaction. According to the authors, their approach “with a single monoclonal antibody with a short measurement time, may prove a useful tool in immunodiagnostic as well as in proteomics research.”

Journal: Biotechnology Journal, July 18 [Epub ahead of print]
Title: Affibody-mediated transferring depletion for proteomics applications
Authors: C Grönwall; A Sjöberg; M Ramström; I Höidén-Guthenberg; S Hober; P Jonasson; S Stähl
Authors selected an Affibody ligand with specific binding to human transferring by phage display technology from a combinatorial protein library based on the staphylococcal protein A-derived Z domain. They say that they were able to deplete 85 percent of the total transferrin content in plasma samples after only two cycles of transferrin removal using their approach. For cerebrospinal fluid, 78 percent efficiency was achieved in single-step depletion.

Journal: Journal of Proteome Research, July 18, [Epub ahead of print]
Title: An enzymatic deglycosylation scheme enabling identification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins
Authors: P Hägglund; R Matthiesen; F Elortza; P Højrup; P Roepstorff; ON Jensen; J Bunkenborg
Authors used two different enzymatic deglycosylation strategies for N-glycosylation site analysis — removal of entire N-glycan chains by peptide-N-glycosidase (PNGase) digestion with concomitant deamidation of the release asparagines residue, and digestion with two end-beta-N-acetylglucosaminidases that cleave the glycosidic bond between the two N-acetylglucosamine residues in the conserved N-glycan core structure. They applied their strategies to identify 103 N-glycosylation sites in the Cohn IV fraction of human plasma.

Journal: Rapid Communications in Mass Spectrometry: RCM, July 17 [Epub ahead of print]
Title: Electrospray-assisted laser desorption/ionization and tandem mass spectrometry of peptides and proteins
Authors: IX Peng; J Shiea; RR Loo; JA Loo
Authors constructed an electrospray-assisted laser desorption/ionization source utilizing a nitrogen laser pulse to desorb intact molecules from matrix-containing sample solution droplets, followed by electrospray ionization post-ionization. Their instrument and method, they say in their abstract, could be useful for protein sequencing analysis and top-down proteomics and may complement MALDI-based measurements.

Journal: Analytical Chemistry, July 15
Title: Dynamic collision-induced dissociation of peptides in a quadrupole ion trap mass spectrometer
Authors: OL Collin; M Beier; GP Jackson
Authors demonstrate dynamic collision-induced dissociation to fragment natural peptides. They used leucine enkephalin as a diagnostic molecule and compared fragmentation efficiencies and energetics of DCID with other methods of collisional activation in ion traps.

Journal: BMC Bioinformatics, July 15 [Epub ahead of print]
Title: The ElPeptiDI tool: Enhancing peptide discovery in ICAT-based LC MS/MS experiments
Authors: M Cannataro; G Cuda; M Gaspari; S Greco; G Tradigo; P Veltri
Authors have created a method they say improves the data processing and peptide identification in sample sets subjected to ICAT labeling and LC-MS/MS analysis. The method is based on cross MS/MS results. The method is implemented in a tool, called EIPeptiDi, “which boosts the ICAT data analysis software improving peptide identification throughout the input data set,” according to the abstract.

Journal: Molecular & Cellular Proteomics: MCP, July 11 [Epub ahead of print]
Title: A metal-coded affinity tag approach to quantitative proteomics
Authors: R Ahrends; S Pieper; A Kühn; H Weisshoff; M Hamester; T Lindemann; C Scheler; K Lehmann; K Taubner; MW Linscheid
Authors present proof-of-principle for the medal-coded affinity tag, or MeCAT, technique for quantitative determination of peptides and proteins. Based on their results, they say that MeCAT allows for quantification not only of peptides but also of proteins in an absolute fashion at low concentration and in complex mixtures.

Journal: Molecular & Cellular Proteomics: MCP, July 7 [Epub ahead of print]
Title: Assessing bias in experiment design for large-scale mass spectrometry-based quantitative proteomics
Authors: B Piening B; J Whiteaker: H Zhang; SA Schaffer; D Martin; L Hohmann; K Cooke; J Olson; S Hansen; MR Flory; H Lee H; J Watts; DR Goodlett DR; R Aebersold; A Paulovich; B Schwikowski; A Prakash
Authors have created Chaorder, a fully automatic software tool that can assess experimental reproducibility of sets of large-scale LC-MS experiments. When Chaorder was applied to data from multiple laboratories and a range of instruments, experimental protocols, and sample complexities, biases introduced by sample processing steps, experimental protocols, and instruments choices were revealed. “Moreover, we show that reducing bias by correcting for just a few steps, for example randomizing the run order, does not provide much gain in statistical power for biomarker discovery,” they said in the abstract.

Journal: Journal of the American Society for Mass Spectrometry, July
Title: Targeted tandem mass spectrometry for high-throughput comparative proteomics employing nanoLC-FTICR MS with external ion dissociation
Authors: H Kang; L Pasa-Tolic; RD Smith
Authors report on a targeted LC-MS/MS capability realized with a hybrid quadrupole-7 Tesla Fourier transform ion cyclotron resonance MS, providing data dependent ion selection, accumulation, and dissociation external to the ICR trap, and a control software that directs intelligent MS/MS target selection based on LC elution time and mass-to-charge ratio.

Journal: Journal of Proteome Research, July
Title: Identification of proteolytic cleavage sites by quantitative proteomics
Authors: M Enoksson; J Li; MM Ivancic; JC Timmer; E Wildfang; A Eroshkin; GS Salvesen; WA Tao
Authors report on a new strategy. Lysine residues in proteins are blocked by guanidination. They use iTRAQ reagents to distinguish N-terminals newly formed by proteolytic treatment from original N-terminals in proteins. The proteins are tryptically digested and analyzed using MALDI-TOF/TOF MS. Peptides labeled with iTRAQ reagents were distinguished from other peptides “by exhibiting intense signature ions in tandem MS analysis,” authors say in the abstract. A corresponding data acquisition strategy was developed to specifically analyze iTRAQ tagged N-terminal peptides.

Journal: Journal of Separation Science, July
Title: HPLC-chip-mass spectrometry for protein signature identifications
Authors: J Hardouin; R Joubert-Caron; M Caron
Authors evaluate the use of an HPLC-chip microfluidic device interfaced to an IT MS to search for biomarker signatures. The identification of autoantigens was chosen as a model.

Journal: Journal of Separation Science, July
Title: Assessing a novel microfluidic interface for shotgun proteome analysis
Authors: A Staes; E Timmerman; J Van Damme; K Helsens; J Vandekerckhove; M Vollmer; K Gevaert
Authors evaluate a new type of HPLC chip holding larger enrichment columns for gel-free proteome studies. A T-cell proteome was tryptically digested, then fractionated by strong cation exchange chromatography. Selected fractions were analyzed by MS/MS on an IT MS using both the new chip and conventional nanoLC-MS/MS interface.

Journal: Proteomics, July
Title: Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing
Authors: P Waridel; A Frank; H Thomas; V Surendranath; S Sunyaev; P Pevzner; A Shevchenko
Authors combined LC-MS/MS analysis on a linear ion trap LTQ MS with data processing, stringent, and sequence-similarity database searching tools to identify proteins in organisms with unsequenced genomes. Highly specific stringent searchers were done as a first layer screen for the identification of either known proteins, or unknown proteins sharing identical peptides with related database sequences. Matched spectra were removed, and the remainder was filtered against a non-annotated library of background spectra that cleaned up the dataset from spectra of common protein and chemical contaminants. The dataset was then subjected to rapid batch de novo interpretation by PepNovo software, followed by MS Blast sequence-similarity search. A single dataset was acquired at the uncompromised sensitivity with no need of manual selection of MS/MS spectra for subsequent de novo interpretation.

Journal: Nature reviews. Molecular Cell Biology, June 27 [Epub ahead of print]
Title: Analysis of protein complexes using mass spectrometry
Authors: AC Gingras; M Gstaiger; B Raught; R Aebersold
Authors say that the combination of affinity purification and mass spectrometry with other techniques such as biochemical fractionation, intact mass measurement, and chemical crosslinking can help to decipher the supramolecular organization of protein complexes. Combined with other quantitative proteomics approaches, AP-MS can result in a better understanding of the dynamics of protein-complex assembly.

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