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15. P2P proteomics - Data sharing for enhanced protein identification

Author

Schorlemmer, M, Abián, J, Sierra, C, De La Cruz, D, Bernacchioni, L, Jaén, E, Perreau De Pinninck, A, Atencia, M, Schorlemmer, M, Abián, J, Sierra, C, De La Cruz, D, Bernacchioni, L, Jaén, E, Perreau De Pinninck, A, and Atencia, M

Abstract

Background: In order to tackle the important and challenging problem in proteomics of identifying known and new protein sequences using high-throughput methods, we propose a data-sharing platform that uses fully distributed P2P technologies to share specifications of peer-interaction protocols and service components. By using such a platform, information to be searched is no longer centralised in a few repositories but gathered from experiments in peer proteomics laboratories, which can subsequently be searched by fellow researchers. Methods. The system distributively runs a data-sharing protocol specified in the Lightweight Communication Calculus underlying the system through which researchers interact via message passing. For this, researchers interact with the system through particular components that link to database querying systems based on BLAST and/or OMSSA and GUI-based visualisation environments. We have tested the proposed platform with data drawn from preexisting MS/MS data reservoirs from the 2006 ABRF (Association of Biomolecular Resource Facilities) test sample, which was extensively tested during the ABRF Proteomics Standards Research Group 2006 worldwide survey. In particular we have taken the data available from a subset of proteomics laboratories of Spain's National Institute for Proteomics, ProteoRed, a network for the coordination, integration and development of the Spanish proteomics facilities. Results and Discussion. We performed queries against nine databases including seven ProteoRed proteomics laboratories, the NCBI Swiss-Prot database and the local database of the CSIC/UAB Proteomics Laboratory. A detailed analysis of the results indicated the presence of a protein that was supported by other NCBI matches and highly scored matches in several proteomics labs. The analysis clearly indicated that the protein was a relatively high concentrated contaminant that could be present in the ABRF sample. This fact is evident from the information that

Published
2012

33. Differential expression of proteins from cultured endothelial cells exposed to uremic versus normal serum.

Author

Carbó C, Arderiu G, Escolar G, Fusté B, Cases A, Carrascal M, Abián J, and Díaz-Ricart M

Abstract

BACKGROUND: Deficient hemostasis and accelerated atherosclerosis coexist in patients with chronic kidney disease. Endothelial dysfunction may be involved in the high incidence of atherothrombotic events in these patients. We established an in vitro model of endothelial dysfunction by exposing endothelial cells to uremic media and applied a proteomic approach to characterize endothelial cell dysfunction in uremia. STUDY DESIGN: Cross-sectional study. SETTING AND PARTICIPANTS: Serum samples from 8 patients with chronic kidney disease on hemodialysis treatment were collected. PREDICTOR: Exposure of cultured endothelial cells to normal and uremic serum. OUTCOME AND MEASUREMENTS: Proteins from lysed cells were characterized by isoelectric point and molecular weight by using 2-dimensional gel electrophoresis. Spots were visualized by means of silver staining and identified by using mass spectrometry. RESULTS: Identification of the most prominent proteins showed molecules related to inflammation (high mobility group box 1, aldose reductase, and proteasome components) and oxidative stress (superoxide dismutase and glutathione peroxidase), both associated with chronic kidney disease. These changes may be caused by activation of the nuclear factor-kappaB transcription factor. Changes in expression of cytoskeletal proteins (destrin and vimentin) also were detected. LIMITATIONS: In vitro study. CONCLUSION: Proteomic techniques proved to be a powerful tool to investigate endothelial dysfunction in uremia. A more exhaustive analysis will provide answers and potential therapeutic targets in the near future. Copyright © 2008 by the National Kidney Foundation, Inc. [ABSTRACT FROM AUTHOR]

Published
2008
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35. On the origin of some controversial ions (m/z59, 60, 77, and 119) in the thermospray reagent plasma from ammonium acetate

Author

Abián, J., Sáchez-Baeza, F., Gelpí, E., and Barceló, D.

Abstract

The origin of ions at m/z60, 77, and 119 in the thermospray (TSP) reagent plasma is reconsidered. It is demonstrated that these major ions in the TSP spectrum of ammonium acetate are not due to dehydration processes in the gas or liquid phase, as is generally accepted, but to the preexistence of acetamide as an impurity in the commercial salts. Acetamide, characterized by TSP/tandem mass spectrometry, gas chromatography-electron impact ionization mass spectrometry, 1H-NMR, and 13C-NMR, is responsible for the [M +60]+and [M + 77]+adducts observed in some spectra. The buffer ion at m/z59 is also due to impurities in the ammonium acetate salts. Washing the solid salt with chloroform eliminates most of these impurities. Examples using the pesticides linuron, monuron, and carbaryl show that the ions observed at m/zMr+ 60 and Mr+ 59 disappear when a buffer obtained from acetic acid and ammonia is used instead of the commercial salts.

Published
1994
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40. Characterization of arachidonic acid metabolites through the 12-lipoxygenase pathway in human epidermis by high-performance liquid chromatography and gas chromatography/mass spectrometry

Author

Rosa Antón, Abián J, and Vila L

Subjects
Adult, Humans, Indicators and Reagents, Spectrophotometry, Ultraviolet, Arachidonic Acids, Epidermis, In Vitro Techniques, Arachidonate 12-Lipoxygenase, Chromatography, High Pressure Liquid, Gas Chromatography-Mass Spectrometry
Abstract

Fragments of human epidermis were incubated in the presence of exogenous arachidonic acid. The incubates were subjected to reversed-phase and straight-phase high-performance liquid chromatography and finally the identity of the arachidonic acid metabolites of the 12-lipoxygenase pathway was determined by means of gas chromatography/mass spectrometry. It was found that human epidermis produces 8-hydroxy-11,12-epoxy- and 10-hydroxy-11,12-epoxyeicosatrienoic acid, 8,9,12-, 8,11,12- and 10,11,12-trihydroxyeicosatrienoic acid, 12-keto-eicosatetraenoic acid and 12-hydroxy-eicosatetraenoic acid derived from arachidonic acid via the 12-lipoxygenase pathway. As far as is known, this is the first time that a systematic and complete characterization of arachidonic acid metabolism through the 12-lipoxygenase pathway in human epidermis has been reported. Some of the eicosanoids characterized have potent biological activities that suggest their role in the inflammatory response on human skin.

45. Assessment of power output in jump tests for applicants to a sports sciences degree

Author

Aj, Lara, Abián J, Luis M. Alegre, Jiménez L, and Aguado X

Subjects
Adult, Male, Adolescent, Movement, Physical Exertion, Faculty, Weight-Bearing, Spain, Task Performance and Analysis, Humans, Regression Analysis, Muscle Strength, Muscle, Skeletal, Sports
Abstract

Our study aimed: 1) to describe the jump performance in a population of male applicants to a Faculty of Sports Sciences, 2) to apply different power equations from the literature to assess their accuracy, and 3) to develop a new regression equation from this population.The push off phases of the counter-movement jumps (CMJ) on a force platform of 161 applicants (age: 19+/-2.9 years; weight: 70.4+/-8.3 kg) to a Spanish Faculty of Sports Sciences were recorded and subsequently analyzed. Their hands had to be placed on the hips and the knee angle during the counter movement was not controlled. Each subject had 2 trials to reach a minimum of 29 cm of jump height, and when 2 jumps were performed the best trial was analyzed. Multiple regression analysis was performed to develop a new regression equation.Mean jump height was 34.6+/-4.3 cm, peak vertical force 1 663.9+/-291.1 N and peak power 3524.4+/-562 W. All the equations underestimated power, from 74% (Lewis) to 8% (Sayers). However, there were high and significant correlations between peak power measured on the force platform, and those assessed by the equations.The results of the present study support the development of power equations for specific populations, to achieve more accurate assessments. The power equation from this study [Power = (62.5 x jump height (cm)) + (50.3 x body mass (kg)) 2184.7] can be used accurately in populations of male physical education students.

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