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Ponce J.,Fundacio Institute Dinvestigacio En Ciencies Of La Salut Germans Trias I Pujol | Brea D.,University of Santiago de Compostela | Carrascal M.,CSIC UAB Proteomics Laboratory | Guirao V.,Fundacio Institute Dinvestigacio En Ciencies Of La Salut Germans Trias I Pujol | And 5 more authors.
Proteomics | Year: 2010

Cell death induced by over-activation of glutamate receptors occurs in different neuropathologies. Cholesterol depletors protect from neurotoxic over-activation of glutamate receptors, and we have recently reported that this neuroprotection is associated with a reduction of the N-methyl-D-aspartate subtype of glutamate receptors in detergent-resistant membrane domains (DRM). In the present study we used comparative proteomics to further identify which proteins, besides the N-methyl-D-aspartate receptor, change its percentage of association to DRM after treatment of neurons with simvastatin. We detected 338 spots in neuronal DRM subjected to 2-DE; eleven of these spots changed its intensity after treatment with simvastatin. All 11 differential spots showed reduced intensity in simvastatin-treated samples and were identified as adipocyte plasma membrane associated protein, enolase, calretinin, coronin 1a, f-actin capping protein α1, f-actin capping protein α2, heat shock cognate protein 71, malate dehydrogenase, n-myc downregulated gene 1, prohibitin 2, Rab GDP dissociation inhibitor, translationally controlled tumor protein and voltage dependent anion selective channel protein 1. The proteins tested colocalized with the lipid raft marker caveolin-1. Interestingly, the proteins we have identified in the present study had been previously reported to play a role in cell fate and, thus, they might represent novel targets for neuroprotection. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA. Source

Schorlemmer M.,Artificial Intelligence Research Institute | Abian J.,CSIC UAB Proteomics Laboratory | Sierra C.,Artificial Intelligence Research Institute | De La Cruz D.,Artificial Intelligence Research Institute | And 4 more authors.
Automated Experimentation | Year: 2012

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 could be derived from the proposed P2P proteomics system, however it is not straightforward to arrive to the same conclusion by conventional means as it is difficult to discard organic contamination of samples. The actual presence of this contaminant was only stated after the ABRF study of all the identifications reported by the laboratories. © 2012 Schorlemmer et al.; licensee BioMed Central Ltd. Source

Badia-Villanueva M.,University of Barcelona | Carulla P.,University of Barcelona | Carrascal M.,CSIC UAB Proteomics Laboratory | Abian J.,CSIC UAB Proteomics Laboratory | And 3 more authors.
Biochemical and Biophysical Research Communications | Year: 2014

Lipoprotein lipase (LPL) hydrolyzes circulating triacylglycerols (TAG) into free fatty acids and glycerol. It is present in almost all tissues and its tissue-specific regulation directs the flow of circulating TAG in the body. We demonstrated in a previous study that, in rat heart and post-heparin plasma (PHP), LPL consists of a pattern of more than 8 forms of the same apparent molecular weight, but different isoelectric point (pI). In the present study we describe, for the first time, the existence of at least nine LPL pI isoforms in human PHP, with apparent pI between 6.8 and 8.6. Separation and characterization of these forms was carried out by 2DE combined with Western blotting and mass spectrometry (MALDI-TOF/MS and LC-MS/MS). Further studies are needed to discover their molecular origin, the pattern of pI isoforms in human tissues, their possible physiological functions and possible modifications of their pattern in different pathologies. © 2014 Elsevier Inc. All rights reserved. Source

Vialas V.,Complutense University of Madrid | Vialas V.,Instituto Ramon Y Cajal Of Investigacion Sanitaria Irycis | Sun Z.,Institute for Systems Biology | Reales-Calderon J.A.,Complutense University of Madrid | And 11 more authors.
Journal of Proteomics | Year: 2016

To provide new and expanded proteome documentation of the opportunistically pathogen Candida albicans, we have developed new protein extraction and analysis routines to provide a new, extended and enhanced version of the C. albicans PeptideAtlas. Two new datasets, resulting from experiments consisting of exhaustive subcellular fractionations and different growing conditions, plus two additional datasets from previous experiments on the surface and the secreted proteomes, have been incorporated to increase the coverage of the proteome. High resolution precursor mass spectrometry (MS) and ion trap tandem MS spectra were analyzed with three different search engines using a database containing allele-specific sequences. This approach, novel for a large-scale C. albicans proteomics project, was combined with the post-processing and filtering implemented in the Trans Proteomic Pipeline consistently used in the PeptideAtlas project and resulted in 49,372 additional peptides (3-fold increase) and 1630 more proteins (1.6-fold increase) identified in the new C. albicans PeptideAtlas with respect to the previous build. A total of 71,310 peptides and 4174 canonical (minimal non-redundant set) proteins (4115 if one protein per pair of alleles is considered) were identified representing 66% of the 6218 proteins in the predicted proteome. This makes the new PeptideAtlas build the most comprehensive C. albicans proteomics resource available and the only large-scale one with detections of individual alleles. © 2015 Elsevier B.V. Source

Villanueva J.,CSIC UAB Proteomics Laboratory | Carrascal M.,CSIC UAB Proteomics Laboratory | Abian J.,CSIC UAB Proteomics Laboratory
Journal of Proteomics | Year: 2014

Isotope dilution mass spectrometry is a reference technique for quantitative analysis, given that it combines the sensitivity and selectivity of MS instruments with the precision and accuracy associated with the use of internal standards. Isotope-labeled proteins are the optimal internal standards for quantitative proteomics as they closely mimic the behavior of their natural counterparts during the analytical process. A major complication of isotope dilution mass spectrometry proteomics is the technical difficulty of obtaining these internal standards, especially in studies where a high number of proteins have to be quantified simultaneously. In this paper, we review some of the characteristics of the isotope dilution mass spectrometry approach, its benefits in terms of reliability and quality control in targeted proteomic analysis and the different strategies developed for its application in proteomics.© 2013 Elsevier B.V. Source

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