An integrated cross-linking-MS approach to investigate cell penetrating peptides interacting partners
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): Séverine Clavier , Xiuxia Du , Sandrine Sagan , Gérard Bolbach , Emmanuelle Sachon Cell penetrating peptides (CPPs) are attracting attention because of their ability to deliver biologically active molecules into cells. On their way they can interact with membrane and intracellular proteins. To fully understand and improve CPP efficiency as drug delivery tools, their partners need to be identified. To investigate CPP-protein complexes, chemical cross-linking coupled to mass spectrometry is a relevant method. With this aim, we developed a...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Proteome of cell wall-extracts from pathogenic Paracoccidioides brasiliensis: Comparison among morphological phases, isolates, and reported fungal extracellular vesicle proteins
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): Larissa V.G. Longo , Júlia P.C. da Cunha , Tiago J.P. Sobreira , Rosana Puccia We identified non-covalently linked cell wall proteins from Paracoccidioides brasiliensis yeasts and mycelia, with focus on the yeast pathogenic phase, and correlated them with reported fungal extracellular vesicle proteins. We studied isolates Pb3 and Pb18, which evoke distinct patterns of experimental paracoccidioidomycosis and represent two phylogenetic groups. Proteins were extracted mildly with dithiothreitol, trypsinized, and peptides analyzed by liquid c...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Human tear peptide/protein profiling study of ocular surface diseases by SPE-MALDI-TOF mass spectrometry analyses
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): Nerea González , Ibon Iloro , Javier Soria , Juan A. Duran , Alaitz Santamaría , Felix Elortza , Tatiana Suárez The goal of this study was to investigate differences in tear peptidome/proteome profiles of aqueous-deficient dry eye, Meibomian gland dysfunction and control individuals. Tears from 93 individuals were collected by capillary and subjected to solid-phase extraction followed by MALDI-TOF for profiling analysis. Obtained spectra were aligned by variable penalty dynamic time warping (VPdtw) and the resulting data analyzed usi...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Proteomic and meta-transcriptomic study on lymph node metastasis in gastric cancer
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): Hiroshi Ichikawa , Tatsuo Kanda , Shin-ichi Kosugi , Yasuyuki Kawachi , Toshifumi Wakai , Tadashi Kondo To examine the proteomic background of lymph node metastasis (LNM) in gastric cancer, we performed protein expression profiling of paired non-tumor, primary tumor, and LNM tissues. Using a label-free proteomic approach, we generated protein expression profiles of 3894 unique proteins and identified 109 differentially expressed proteins. Functional pathway analysis of the differentially expressed proteins showed that members of the beta...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Impact of high glucose concentration on aspirin-induced acetylation of human serum albumin: An in vitro study
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): Francesco Finamore , Feliciano Priego-Capote , Florent Gluck , Anne Zufferey , Pierre Fontana , Jean-Charles Sanchez Aspirin (ASA) plays a key role in protecting high risk cardiovascular patients from ischaemic events. The modifications underlying its effects are the results of the trans-acetylation that occurs between ASA and the amino groups made up of lysine and N-terminal residues. ASA's effects have also been demonstrated on several plasma proteins, including human serum albumin (HSA). However, its beneficial effects seem to be lowe...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
In vitro biomarker discovery in the parasitic flatworm Fasciola hepatica for monitoring chemotherapeutic treatment
This study provides candidate protein/peptide biomarkers to validate for detection of TCBZ failure and resistance. Graphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Inflammatory markers in Huntington's disease plasma—A robust nanoLC–MRM-MS assay development
We report a robust and sensitive quantitative assay with a relative standard deviation of <15% that accounts for the entire sample processing. The assay has a dynamic range with 4 orders of magnitude and the LOQs are in the attomolar range. We used plasma from Huntington's disease gene carriers and healthy controls to compare our MRM method with antibody based methods. Importantly, we found a good agreement between assays for the measurement of C-reactive protein, in contrast to complement component 3 and complement factor H. Graphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Serum protein profiling of early and advanced stage Crohn's disease
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): C. Piras , A. Soggiu , V. Greco , A. Cassinotti , G. Maconi , S. Ardizzone , A. Amoresano , G. Bianchi Porro , L. Bonizzi , P. Roncada Crohn's disease (CD) represents a highly debilitating disease of difficult diagnosis and increasing incidence. Serum protein profiling of early stage Crohn's disease (ES) CD was investigated in order to improve the comprehension of the very early pathologic mechanisms and to support the difficult diagnostic procedures currently available. Inflammatory proteins and complement 3 chain C (C3c) were over-...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
The use of multiplex platforms for absolute and relative protein quantification of clinical material
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): Lisa Christiansson , Satu Mustjoki , Bengt Simonsson , Ulla Olsson-Strömberg , Angelica S.I. Loskog , Sara M. Mangsbo When introducing multiplex platforms to measure protein content in precious clinical material there is an increased risk of cross reactivity, loss of sensitivity as well as accuracy. In this paper, four multiplex platforms and one singleplex platform were compared by running pre- and post-treatment plasma samples from CML patients. We found a variation of absolute protein concentrations between platforms. For some of the...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Evolutionary conservation of the mature oocyte proteome
This study provides the first catalog of cnidarian oocyte proteins, revealing highly conserved ancient organization of life processes for over 500 million years of evolution. Significance The current study provides the first proteomic profile of an oocyte of a cnidarian organism the starlet sea anemone N. vectensis and gives new insights on the ancient origin of an oocyte proteome template. The comparative analysis with a chordate oocyte suggests that the oocyte proteome predates the divergence of the cnidarian and bilaterian lineages. In addition, the data generated in the study will serve as a valuable resource for fur...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
2DGE and DIGE based proteomic study of malignant B-cells in B-cell acute lymphoblastic leukemia
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): Sutapa Saha , Subrata Banerjee , Debasis Banerjee , Sarmila Chandra , Abhijit Chakrabarti With an objective of defining potential diagnostic and/or therapeutic markers and the mechanism of cellular transformation, we present a comparative proteomic study of B-lymphocytes from B-cell acute lymphoblastic leukemia (B-ALL) patients and normal controls, using two-dimensional gel electrophoresis and MALDI ToF/ToF tandem mass spectrometry. Our study led to the identification of 79 differentially regulated proteins in the malignant cells includin...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Comparative proteomic analysis reveals characteristic molecular changes accompanying the transformation of nonmalignant to cancer lung cells
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): Daniela Cadinu , Jagmohan Hooda , Md Maksudul Alam , Parimaladevi Balamurugan , Robert M. Henke , Li Zhang To identify changes in proteins accompanying transformation of normal lung epithelial cells to cancer cells, we performed a comparative proteomic study using two cell lines representing matching normal and cancer cells. Strikingly, a good number of detected actin cytoskeletal proteins were preferentially downregulated in cancer cells, while similar numbers of proteins in other organelles were up or downregulated. We also found that ...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
The importance of recognizing and reporting sequence database contamination for proteomics
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): Olivier Pible , Erica M. Hartmann , Gilles Imbert , Jean Armengaud Advances in genome sequencing have made proteomic experiments more successful than ever. However, not all entries in a sequence database are of equal quality. Genome sequences are contaminated more frequently than is admitted. Contamination impacts homology-based proteomic, proteogenomic, and metaproteomic results. We highlight two examples in the National Center for Biotechnology Information non-redundant database (NCBInr) that are likely contaminated: the bacterium Entero...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Clinical measurement of Hepcidin-25 in human serum: Is quantitative mass spectrometry up to the job?
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): Constance Delaby , Jérôme Vialaret , Pauline Bros , Audrey Gabelle , Thibaud Lefebvre , Hervé Puy , Christophe Hirtz , Sylvain Lehmann From its discovery, hepcidin has generated many hopes in terms of diagnosis and management of a wide variety of iron-related diseases. However, in clinical use its accurate quantification remains a challenge due to the limited sensitivity, specificity or reproducibility of the techniques described. In this work, we adapted a highly specific and quantitative mass spectrometry method based on selected ...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Worm peptidomics
Publication date: June 2014 Source:EuPA Open Proteomics, Volume 3 Author(s): Steven J. Husson , Ank Reumer , Liesbet Temmerman , Wouter De Haes , Liliane Schoofs , Inge Mertens , Geert Baggerman Bioactive peptides are present in all metazoan species where they orchestrate diverse functions. In the last decade, high-throughput approaches based on mass spectrometry helped the identification of endogenously occurring peptides in different species. We here review biochemical strategies to obtain sequence information of natural (non-tryptic) peptides in Caenorhabditis elegans and in the related nematodes Caenorhabdit...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
