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Lipid rafts are membrane microdomains that have been proposed to play an important role in several platelet-signalling cascades, including those mediated by the receptors Glycoprotein VI (GPVI), and C-type lectin domain family 1 member B (CLEC-2), both involved in thrombus formation. We have performed a LC-MS/MS proteomic analysis of lipid rafts isolated from platelets activated through GPVI and CLEC-2 as well as from resting platelets. Our aim was to determine the magnitude of changes in lipid rafts protein composition and to elucidate the relevance of these alterations in platelet function. A number of relevant signalling proteins were found enriched in lipid rafts following platelet activation (such as the tyrosine protein kinases Fyn, Lyn and Yes; the G proteins G(i) and G(z); and cAMP protein kinase). Interestingly, our results indicate that the relative enrichment of lipid rafts in these signalling proteins may not be a consequence of protein translocation to these domains upon platelet stimulation, but the result of a massive loss in cytoskeletal proteins after platelet activation. Thus, this study may help to better understand the effects of platelet activation in the reorganization of lipid rafts and set the basis for further proteomic studies of these membrane microdomains in platelets. SIGNIFICANCE: We performed the first proteomic comparative analysis of lipid rafts- protein composition in platelets activated through GPVI and CLEC-2 receptors and in resting state. We identified a number of signalling proteins essential for platelet activation relatively enriched in platelets activated through both receptors, and we show that lipid rafts reorganization upon platelet activation leads to a loss in cytoskeletal proteins, highly associated to these domains in resting platelets., (Copyright © 2019 Elsevier B.V. All rights reserved.)

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., (Copyright © 2015 Elsevier B.V. All rights reserved.)

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., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Candida albicans public proteomic datasets, though growing steadily in the last few years, still have a very limited presence in online repositories. We report here the creation of a C. albicans PeptideAtlas comprising near 22,000 distinct peptides at a 0.24% False Discovery Rate (FDR) that account for over 2500 canonical proteins at a 1.2% FDR. Based on data from 16 experiments, we attained coverage of 41% of the C. albicans open reading frame sequences (ORFs) in the database used for the searches. This PeptideAtlas provides several useful features, including comprehensive protein and peptide-centered search capabilities and visualization tools that establish a solid basis for the study of basic biological mechanisms key to virulence and pathogenesis such as dimorphism, adherence, and apoptosis. Further, it is a valuable resource for the selection of candidate proteotypic peptides for targeted proteomic experiments via Selected Reaction Monitoring (SRM) or SWATH-MS., Biological Significance: This C. albicans PeptideAtlas resolves the previous absence of fungal pathogens in the PeptideAtlas project. It represents the most extensive characterization of the proteome of this fungus that exists up to the current date, including evidence for uncharacterized ORFs. Through its web interface, PeptideAtlas supports the study of interesting proteins related to basic biological mechanisms key to virulence such as apoptosis, dimorphism and adherence. It also provides a valuable resource to select candidate proteotypic peptides for future (SRM) targeted proteomic experiments. This article is part of a Special Issue entitled: Trends in Microbial Proteomics., (© 2013.)

Proteins differentially expressed in peripheral blood mononuclear cells (PBMCs) from systemic lupus erythematosus (SLE) patients versus Normal controls were identified by 2-DE and MALDI-MS. Thus, S100A9 expression was significantly increased in SLE PBMCs relative to Normal PBMCs at both mRNA and protein levels. Increased S100A9 levels in SLE PBMCs correlated positively with the abnormal presence of low-density granulocytes (LDGs) detected by flow-cytometry in the mononuclear cell fractions. Another set of proteins that were differentially expressed in SLE PBMCs formed S100A9-independent clusters, suggesting that these differences in protein expression are in fact reflecting changes in the abundance of specific cell types. In SLE PBMCs spots of the two S100A9 isoforms, S100A9-l and S100A9-s, and their phosphorylated counterparts were identified and confirmed to be phosphorylated at Thr(113) by MS/MS analyses. In addition, the phorbol ester PMA alone or in combination with ionomycin induced a stronger increase in threonine phosphorylation of S100A9 in SLE than in Normal PBMCs, while the same stimuli caused the opposite effect on phosphorylation and activation of Erk1/2, suggesting the existence of an abnormal S100A9 signaling in SLE PBMCs. Therefore, the expansion and activation of LDGs in SLE seems to underlie this prominent S100A9 signature., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Lipoprotein lipase (LPL) plays a pivotal role in lipid metabolism and is implicated in several pathophysiological conditions. A large number of LPL studies have been performed in rat, although the amount of information derived from direct study of the protein in this species is limited. Here we attempted to examine possible modifications of LPL using proteomic tools. By combining high-resolution two-dimensional gel electrophoresis and Western blot with biological mass spectrometry we demonstrate the coexistence of multiple LPL pI isoforms in rat heart. We studied the origin of this pI heterogeneity by: (1) comparison with the 2D pattern of LPL from post-heparin rat plasma (as a source of mature LPL); (2) protein dephosphorylation; (3) protein deglycosylation; and (4) partial sequencing of LPL isoforms. The results reveal that LPL pI heterogeneity does not correspond to different stages of intracellular maturation or protein phosphorylation. It can be partially explained by glycosylation, although other post-translational modifications must also be involved. We also report the first partial sequence to be obtained from direct study of rat LPL protein. These findings should be the basis for further research aimed at identifying the molecular differences between LPL isoforms and exploring their potential functional implications.

Epidemiological studies have shown that cigarette smoke, an oxidant agent, is a risk factor for the development of diabetic nephropathy (DN), in which pathogenesis transforming growth factor beta(1) (TGFbeta(1)) plays a key role. In our experimental model we exposed mesangial cell cultures to cigarette smoke concentrate (CSC) to study the effect of smoking on the pathogenesis of DN. Thus, we analyzed the effect of CSC on TGFbeta(1) and lipid peroxidation (8-epi-PGF(2alpha)) in rat mesangial cells. Furthermore, since the protein kinase C (PKC) pathway appears to be a key factor for the enhanced production of TGFbeta(1), we also analyzed the effect of the selective PKCbeta inhibitor LY379196 on TGFbeta(1) response to CSC. CSC induced an increase of both TGFbeta(1) and 8-epi-PGF(2) compared to basal conditions (5 mM glucose). The CSC-induced increase in TGFbeta(1) secretion was significantly suppressed by LY379196. These data suggest that smoking could increase TGFbeta(1) production, probably due to oxidative stress and PKCbeta activation. This finding supports the concept that smoking is a risk factor for DN development.

Condensed sister chromatids possess a protein scaffold or axial core to which loops of chromatin are attached. The sister cores are believed to be dynamic frameworks that function in the organization and condensation of chromatids. Chromosome structural proteins are implicated in the establishment of sister chromatid cohesion and in the maintenance of epigenetic phenomena. Both processes of templating are tightly linked to DNA replication itself. It is a question whether the structural basis of sister chromatid cores is templated during S phase. As cells proceed through the cell cycle, chromatid cores undergo changes in their protein composition. Cytologically, cores are first visualized at the start of prometaphase. Still, core assembly can be induced in G1 and G2 when interphase cells are fused with mitotic cells. In this study, we asked if chromatid cores are similarly able to assemble in S-phase cells. We find that the ability to assemble cores is transiently lost during local replication, then regained in chromosome regions shortly after they have been replicated. We propose that core templating occurs coincident with DNA replication and that the competence for the assembly of the sister chromatid cores is acquired shortly after passage of replication forks.

N-Phenyllinoleamide (NPLA), the anilide of linoleic acid, has been associated with the epidemiology of toxic oil syndrome, but its contribution to the illness is still undetermined. Because it has been suggested that fatty acid anilides were absorbed via the hepatic portal vein, this study has been aimed at determining the hepatic metabolism of NPLA by rat liver. For this purpose, isolated liver was perfused with NPLA (0.1 mM) spiked with either aniline- or fatty acid-labelled NPLA. Gas chromatographic-mass spectrometric analysis of the peaks appearing in the radiochromatographic metabolic profiles shows that metabolism of NPLA in the liver results in formation of aniline and linoleic acid, both biologically active metabolites whose expected direct effects were not observed in patients suffering toxic oil syndrome.

Ten sulfonamide antibiotics including sulfanilamide (SNL), sulfamethazine (SMZ), sulfamethizole (SMTZ), sulfachloropyridazine and sulfaquinoxaline (SQX), were analyzed by thermospray (TSP) mass spectrometry on-line with a high-performance liquid chromatography-UV detection system. Except for the pairs SMZ-SMTZ and sulfadimethoxine-SQX, the standards were resolved in both the UV and TSP profiles. Co-eluting compounds could be differentiated in TSP by their different relative molecular masses. The [M+H]+ ion was the base peak for all the standards except SNL, which showed an [M+NH4]+ ion. Collision-induced dissociation of the [M+H]+ ions afforded daughter ion spectra characterized by common ions at m/z 92, 108 and 156, and ions derived from the amine substituent ([MH-155]+). TSP detection limits [signal-to-noise ratio (S/N) > 3] were below 20 ng (scan mode), 2 ng (selected reaction monitoring, daughter ions from [M+H]+) and 400 pg (selected ion monitoring). UV detection limits were ca. 2 ng (S/N > 5). Results obtained from the multi-residue analysis of spiked cow milk samples at the low ng/ml level are presented.

Cyclo- and lipo-oxygenase metabolites of arachidonic acid have been reported to have very simple thermospray mass spectra. However, thromboxane B2 (TXB) in ammonium acetate-methanol and at interface temperatures below the point of total vaporization shows a mass spectral pattern characterized by abundant ions at low masses. The more abundant TXB fragment ions have been characterized as adducts from four principal fragments with molecular masses of 156, 170, 196 and 326. Positive- and negative-ion mass spectra, and mass spectra obtained with an alternative thermospray buffer (butylammonium acetate) support the molecular masses of these fragments. A tentative assignment of the fragments can be made by comparison of the thermospray mass spectra of TXB, 2,3-dinor-TXB and some of their methyl ester and methyl oxime derivatives. Interface temperature and solvent composition effects on the fragmentation, as well as in the electron-capture processes observed when working in the filament-on mode, are discussed. Fragmentation mechanisms can be related to those observed for monosaccharides, and imply retro-Diels-Alder as well as retroaldolic condensation-type rearrangements.

Thermospray high-performance liquid chromatography-mass spectrometry (HPLC-MS) can be a powerful tool for characterizing eicosanoids in complex biological samples. The positive ion spectra obtained from primary prostaglandins such as PGE1 PGE2, 19-OHPGE1, 19-OHPGE2, PGF2 alpha, PGD2, 6-keto-PGF1 alpha and from leukotriene B4 are very simple, with base peaks corresponding to ions arising from the loss of H2O from the (M + H)+ and (M + NH4)+ ions, except for PGB2 and PGF2, where the latter two ions predominate. The application of this technique to the concurrent determination of the E1 and E2 prostaglandins and their 19-hydroxylated derivatives in human semen is described. The technique affords a moderate level of sensitivity (5-20 ng on-column) and excellent specificity so that virtually no sample manipulation is required other than dilution in acetone and centrifugation. The clear supernatant is injected directly into the HPLC-MS system. A similar analysis by either gas chromatography (GC) or GC-MS would need multi-step derivatization, thus increasing the sample manipulation required and the total analysis time.

The early identification of fatty acid anilides in suspect oils directed attention to their possible role in the Spanish toxic oil syndrome. These anilides or their oxidized derivatives could have been spontaneously formed during the handling and/or storage of the oil. The exact cause of the intoxication is still unknown but free radical and peroxidative mechanisms have been implicated in its etiology. Epoxy-hydroxylated derivatives from linoleic acid anilide were obtained using a model of accelerated oxidation. Their mass spectral patterns agree with the trimethylsilyl ethers of N-phenyl-9,10-epoxy-11-hydroxy-12-octadecenamide and N-phenyl-12,13-epoxy-11-hydroxy-9-octadecenamide, respectively. These compounds were also identified is rapeseed oil samples supplemented with N-phenyl-linoleamide and submitted to the reported accelerated oxidation method.