Showing papers in "Journal of Proteomics in 2008"

TL;DR: A relationship between ROS and HSP also seems to exist, corroborating the hypothesis that during the course of evolution, plants were able to achieve a high degree of control over ROS toxicity and are now using ROS as signalling molecules to induce HSPs.

TL;DR: By exploring baits ranging from single, individual amino acids, to di-, tri-, tetra- penta- and hexapeptides, it was demonstrated that the 6-mer baits are the ones with the most promising length for capturing the largest possible population of proteins and that probably longer lengths would hardly be needed.

TL;DR: The need to put technologies and methods in affinity subtraction or enrichment into a context of proteomic and systems biology as "Separomics" is discussed and a prospective of affinity-mediated proteomics is provided.

TL;DR: Saliva samples from eight individuals with non-malignant conditions of the head and neck region were employed as a control group and compared to saliva from eight patients with HNSCC using 2D DIGE analysis and subsequent mass spectrometry identification of candidate proteins, finding the increased abundance of one of the proteins identified.

TL;DR: This work assessed the utility of lectin-based and HILIC-based affinity enrichment techniques, alone or in combination, for preparation of glycoproteins and glycopeptides for subsequent analysis by MALDI and ESI mass spectrometry.

TL;DR: Special emphasis is placed on quantification techniques: gel-based, and label-free techniques are briefly discussed whereas stable-isotope coding and internal peptide standards are extensively reviewed.

TL;DR: In this article, the authors report the proteomic characterization of the venoms of two closely related pit vipers of the genus Lachesis, L. muta and L. stenophrys, and compare the toxin repertoire of the former revealed through a proteomic versus a transcriptomic approach.

TL;DR: Venoms from the Armenian mountain vipers Macrovipera lebetina obtusa and Vipera raddei were analyzed by RP-HPLC, N-terminal sequencing, MALDI-TOF mass fingerprinting and CID-MS/MS, and it is estimated that the similarity of venom proteins between M.l. obTusa and M. l.

TL;DR: The results indicate that each genus of hematophagous arthropods studied to date evolved unique protein families that assist blood feeding, thus characterizing potentially new pharmacologically active components or antimicrobial agents.

TL;DR: Each extraction protocol for 2-DE proteomic analysis using Arabidopsis leaf tissue had its main features, and the TCA-acetone-phenol protocol provided the best results in terms of spot focusing, resolved spots, spot intensity, unique spots detected, and reproducibility.

TL;DR: The methodology of quantitative proteomics as it applies to the analysis of complex biological model systems is discussed, and a special attention will be given to model systems that are suitable for functional genomic studies, where the potential of quantitative protein characterization can be effectively demonstrated.

TL;DR: This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ Orbitrap mass spectrometer.

TL;DR: Compositional differences between their venoms can be employed as a taxonomy signature for unambiguous species identification independently of geographic origin and morphological characteristics.

TL;DR: The pilot study presented here demonstrates that mass spectrometry combined with linear discriminant analysis (LDA) may provide valuable data for identifying and studying the pathophysiology of malignant diseases.

TL;DR: In practice, the experimental results do not always mirror the theoretical basis and therefore optimal solubilization conditions for each membrane and membrane protein complex should be investigated individually to tap the full potential of BN-PAGE analysis.

TL;DR: Flow field-flow fractionation (F4) is introduced as a complementary pre-analytical separation method for protein separation/isolation, which can be effectively utilized for proteomic research and on selected applications based on size-dependent proteome separation.

TL;DR: Integration of proteomic, immunohistochemical, and parallel gene expression datasets demonstrate the coordinated manner in which intestinal cell maturation is regulated.

TL;DR: It is demonstrated that the constitutive expression of the tomato prosystemin gene highly affected host protein synthesis, and engineered plants showed a number of differentially synthesized proteins that were identified by PMF MALDI-TOF and microLC-ESI-IT-MS/MS experiments as polypeptide species involved in protection from pathogens and oxidative stress, or in carbon/energy metabolism.

TL;DR: The latest contribution to the expansion of the pool of on-line proteomics data is the World-2DPAGE Constellation, accessible at http://world-2dpage.expasy.org/.

TL;DR: The first sequence analysis of membrane-bound class III peroxidases was reported, and predictions of hydrophobic domains in comparison with solubilization experiments suggest an N-terminal transmembrane domain for the isoenzymes.

TL;DR: MITICS image ensures image reconstruction, files are first converted to XML files before being loaded in a database, and three different data representations and calculations for image reconstruction are implemented.

TL;DR: Stable isotope labeling with amino acids in cell culture and quantitative mass spectrometry-based proteomics are used to identify the host targets of the SPI-1 effector, SopB/SigD and find no evidence that SopB alone can alter Cdc42 activity.

TL;DR: This is the first attempt to design and validate a pathway search engine using as input expression proteomics data and it is demonstrated that different dominant pathways can be correctly identified even from limited datasets.

TL;DR: A high-throughput approach for biomolecule analysis is demonstrated for a mixture of peptides from tryptic digest of four proteins as well as a tryptic digests of human plasma to achieve rapid sample analysis.

TL;DR: Proteomic technology was applied to the study of EBC samples collected from single patients with pulmonary emphysema associated to alpha(1)-antitrypsin deficiency and a number of cytokines and cytokeratins were found to be higher in patients than in controls.

TL;DR: Analysis of proteomic maps of long-term grown and fresh clinical Trichomonas vaginalis isolates exhibiting low and high virulence phenotypes demonstrates that expression of specific proteins by high and low virulence parasites could be associated with the ability of each isolate to undergo morphological transformation and interact with host cells.

TL;DR: The goal of this review is to evaluate the use of the most common non-covalent and covalent staining techniques in 2D electrophoresis gels, in order to obtain maximal information per electrophoreis gel and for an identification of potential biomarkers.

TL;DR: Two-DE DIGE revealed a complex protein pattern of readily labeled thiols and di-sulphide and/or oxidized proteins in frontal cortex autopsy tissue of a subject with mild Alzheimer's disease and may provide an additional tool for an identification of oxidation susceptible proteins.

TL;DR: Proteomics can play a potentially relevant role in transfusion medicine (TM) to assess the protein composition of blood-derived therapeutics, particularly for identifying modified proteins.