Publications (13)50.1 Total impact
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Article: Reproducibility of combinatorial peptide ligand libraries for proteome capture evaluated by selected reaction monitoring.
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ABSTRACT: Systems biology studies require the capability to quantify with high precision proteins spanning a broad range of abundances across multiple samples. However, the broad range of protein expression in cells often precludes the detection of low-abundance proteins. Different sample processing techniques can be applied to increase proteome coverage. Among these, combinatorial (hexa)peptide ligand libraries bound to solid matrices (CPLLs) have been used to specifically capture and detect low-abundance proteins in complex samples. To assess whether CPLL capture can be applied in systems biology studies involving the precise quantitation of proteins across a multitude of samples, we evaluated its performance across the whole range of protein abundance of S. cerevisiae. We used selected reaction monitoring assays for a set of target proteins covering a broad abundance range to quantitatively evaluate the precision of the approach and its capability to detect low-abundance proteins. Replicated CPLL-isolates showed an average variability of ~10% in the amount of the isolated proteins. The high reproducibility of the technique was not dependent on the abundance of the protein or the amount of beads used for the capture. However, the protein-to-bead ratio affected the enrichment of specific proteins. We did not observe a normalization effect of CPLL beads on protein abundances. However, CPLLs enriched for and depleted specific sets of proteins and thus changed the abundances of proteins from a whole proteome extract. This allowed the identification of ~400 proteins otherwise undetected in an untreated sample, under the experimental conditions used. CPLL capture is thus a useful tool to increase protein identifications in proteomic experiments, but it should be coupled to the analysis of untreated samples, to maximize proteome coverage. Our data also confirms that CPLL capture is reproducible and can be confidently used in quantitative proteomic experiments. Biological Significance Combinatorial hexapeptide ligand libraries (CPLLs) bound to solid matrices have been proposed to specifically capture and detect low-abundance proteins in complex samples. To assess whether the CPLL capture can be confidently applied in systems biology studies involving the precise quantitation of proteins across a broad range of abundances and a multitude of samples, we evaluated its reproducibility and performance features. Using selected reaction monitoring assays for proteins covering the whole range of abundances we show that the average variability of replicated CPLL-isolates is ~10% in the amount of the isolated proteins. CPLL reproducibility is not dependent on the abundance of the protein or the amount of beads used for the capture, however, the protein-to-bead ratio affects the enrichment of specific proteins. CPLLs enriched for and depleted specific sets of proteins from a whole proteome extract. Our results suggest that CPLL-based analyses should be coupled to the analysis of untreated samples, to maximize proteome coverage. Overall, our data confirms that CPLL capture can be used in quantitative proteomic experiments and guides the correct use of this technique.Journal of proteomics 06/2013; · 5.07 Impact Factor -
Article: Assessment of the floral origin of honey via proteomic tools.
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ABSTRACT: The honey from chestnut, acacia, sunflower, eucalyptus and orange was analysed for its proteome content, in order to see if any plant proteins present would allow the proteo-typing of these different varieties. Since the total protein content turned out to be minute, 200g of each honey type were diluted to 1L and then added with ProteoMiner to enhance the visibility of the proteinaceous material. All bands visible in the SDS-PAGE profile of each type of honey were eluted, digested and identified by mass spectrometry in a LTQ-XL instrument. It turned out that all proteins identified (except one, the enzyme glyceraldehyde-3-phosphate dehydrogenase from Mesembryanthemum crystallinum) were not of plant origin but belonged to the Apis mellifera proteome. Among the total proteins identified (eight, but only seven as basic constituents of all types of honey) five belonged to the family of major royal jelly proteins 1-5, and were also the most abundant ones in any type of honey, together with α-glucosidase and defensin-1. It thus appears that honey has a proteome resembling the royal jelly proteome (but with considerably fewer species), except that its protein concentration is lower by three to four orders of magnitude as compared to royal jelly. Attempts at identifying additional plant (pollen, nectar) proteins via peptidome analysis were unsuccessful.Journal of proteomics 04/2012; 75(12):3688-93. · 5.07 Impact Factor -
Article: Plasma proteomics for biomarker discovery: a study in blue.
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ABSTRACT: The performance of Cibacron Blue dye (HiTrapBlue or Affigel Blue) in depleting albumin from plasma, as a pre-treatment for biomarker searching in the low-abundance proteome, is here assessed. It is shown that (i) co-depletion of non-albumin species is an ever-present hazard; (ii) the only proper eluant able to release quantitatively the proteins bound to the dye is boiling 4% SDS-25 mM DTT, an ion shock (2 M NaCl) being quite ineffective in releasing the low-abundance species tightly bound to the dye moiety; (iii) the mechanism of dye-protein interaction, after an initial ion-ion docking, is a robust hydrophobic interaction, which progressively augments at lower and lower pH values; (iv) at pH 2.2 in the presence of 0.1% TFA, the blue resin behaves, for all practical purposes, just as a reverse-phase chromatography column, since all residual proteins present in plasma are completely harvested. However Cibacron Blue technology should not necessarily be discarded: As long as also the plasma fraction adsorbed is properly released and analyzed, together with the flow through, one should be able to perform a viable analysis of the low-abundance proteome.Electrophoresis 12/2011; 32(24):3638-44. · 3.30 Impact Factor -
Article: Horam nonam exclamavit: sitio. The trace proteome of your daily vinegar.
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ABSTRACT: The trace proteome of white-wine vinegar has been identified via capture with home-made combinatorial peptide ligand libraries under conditions mimicking reverse-phase capture, i.e. at pH 2.2 in presence of 0.1% trifluoroacetic acid. A total of 27 unique gene products have been identified, of which 10 specific of the database Vitis vinifera, 13 found in the general database Uniprot_viridiplantae and 4 in Swiss Prot_all entries. The most abundant species detected, on the basis of spectral counts, appears to be the whole genome shotgun sequence of line PN40024, scaffold_22 (a protein of the glycosyl hydrolase family). Curiously, up to the present, no information had been available on vinegar proteome.Journal of proteomics 08/2011; 75(2):718-24. · 5.07 Impact Factor -
Article: Cibacron Blue and proteomics: the mystery of the platoon missing in action.
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ABSTRACT: The use of Cibacron Blue columns (HiTrapBlue) in proteome analysis for removal of plasma albumin, for facilitating biomarker discovery, has not borne any fruit. In fact, the visibility of low-abundance proteins was obscured. It is here reported that, upon albumin sequestering from plasma, there is adsorption, via hydrophobic interaction, of a substantial number of plasma proteins, which are lost for subsequent analysis if the blue resin is eluted via an ion shock (2 M NaCl) or with a somewhat more robust eluant (5 M urea, 2 M thiourea, 2% CHAPS, 2% sulphobetain 3-10) as recommended by manufacturers. Such treatments, in fact, release at most 25 to 30 unique gene products, including albumin. If, however, the Affigel-Blue resin, after elution with either of the two above eluants, is further eluted with boiling 4% SDS in 25 mM DTT, all the missing proteins (amounting to at least 112 unique species) are desorbed and biomarker analysis can be conducted in a correct way. It is also suggested that such blue-resin treatment could be coupled to ProteoMiner adsorption, this coupled treatment further enhancing the chances of success for discovery of low-abundance proteins.Journal of proteomics 07/2011; 74(12):2856-65. · 5.07 Impact Factor -
Article: "Proteomineering" serum biomarkers. A study in scarlet.
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ABSTRACT: The performance of sera pre-treatment for biomarker searching via combinatorial peptide ligand libraries (CPLL) has recently been challenged (Proteomics 2010, 10, 1416-1425) and stated to allow discovery of only medium to high-abundance proteins. We have thus investigated four elution protocols, as published in recent reports: (i) in 4 M urea+1% CHAPS; (ii) in 4 M urea+1% CHAPS+5% acetic acid; (iii) in 8 M urea+2% CHAPS+5% acetic acid; (iv) in boiling 4% SDS+25 mM DTT. One milliliter of serum, in all cases, was captured with 50 μL of CPLL beads, which were then eluted with the four eluants described above. In the first three cases, after the first elution, the beads were re-eluted with cocktail (iv), known to offer maximal release of proteins adsorbed by the CPLL ligands. Eluant (i) released only ca. 20% of the species adsorbed, eluant (ii) ca. 60%, eluant (iii) ca. 80%. Thus, the poor performance of the CPLL methodology, as reported in (i) is not due to any fault of the capture technique, but simply to the adoption of a very poor elution protocol. Even those using eluants (ii) and (iii) should know that a substantial fraction of the captured species still remains bound to the beads and is thus not available to biomarker discovery. Once more, eluant (iv) is recognized as the only one able to offer optimal recovery from the CPLL baits.Electrophoresis 03/2011; 32(9):976-80. · 3.30 Impact Factor -
Article: "Proteomineering" or not? The debate on biomarker discovery in sera continues.
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ABSTRACT: The performance of sera pre-treatments for biomarker discovery has been recently assessed as very poor not only for immuno-subtraction, in turn evaluated as a tool unable to look deep into the low-abundance proteome (LAP) and thus incapable to lead to any novel biomarker discovery (J Proteome Res 2010;9:4982-4991), but also for combinatorial peptide ligand libraries (CPLL) (Proteomics 2010;10:1416-1425). The performance of both tools has been given as enabling to barely detect a meagre 25% more as compared to control, untreated sera. Meanwhile, other studies indicated the extreme effectiveness of peptide libraries to enlarge the knowledge of proteome compositions. In this contradictory situation we are here re-evaluating some protocol aspects and report that indeed CPLL is an excellent tool, able to dig really deep into the low-abundance proteome. The problem is that in those reports under-optimized capture and elution protocols had been adopted. With the protocols here reported, namely (a) abandoning the step of adding 150mM salt to the sample; (b) capture at three different pH values (pH 4.0, 7.0 and 9.3) and (c), most importantly, eluting from CPLL beads in 4% boiling SDS in the presence of 25mM DTT, we can largely expand the windows of visibility. In particular, it is here shown that a common elution protocol adopted in several reports, in 4M urea and 1% CHAP, barely elutes about 15% of the captured species. Nevertheless if the CPLL beads thus treated are further eluted with boiling SDS-DTT, an additional 80% is recovered.Journal of proteomics 02/2011; 74(5):589-94. · 5.07 Impact Factor -
Article: A simple and effective method to analyze membrane proteins by SDS-PAGE and MALDI mass spectrometry.
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ABSTRACT: Identification and characterization of membrane proteins is a crucial challenge in proteomics research. Thus, we designed a novel method to prepare proteins possessing extensive hydrophobic stretches for mass spectrometry studies, without sacrificing other classes of proteins. This method uses sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) separation and relies solely on a matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) instrument, the most common and easiest to use mass spectrometer. Using this analytical procedure, a significant number of hydrophobic peptides were recovered, with no reduction in overall sequence coverage and with a good identification of transmembrane proteins sequence. Applying this method to the systematic identification of proteins located in lipid rafts, up to 47% of identified proteins were obtained with an improvement of sequence coverage. The procedure presented here is suitable for both identifying purified hydrophobic proteins and systematically investigating hydrophobic protein mixtures. It can be easily applied even in non-dedicated laboratories, such as those mostly devoted to clinical chemistry.Anticancer research 04/2010; 30(4):1121-9. · 1.73 Impact Factor -
Article: Pre-analytical operating procedures for serum Low Molecular Weight protein profiling.
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ABSTRACT: Biological specimen collection and storage are an integral component of serum proteomics research. Although many efforts have been posed to address the effects of pre-analytical procedures, standardized protocols for collection and storage of samples for Low Molecular Weight (LMW) proteome profiling are still needed. Here we report a systematic analysis on the influence of pre-analytical factors [clotting times, temperature and time storage, addition of protease inhibitor (PI)] on serum LMW proteome profiling. Moreover, a comparison between manual versus automated peptide purification by functionalized magnetic bead-based MALDI-MS approach was performed. The results demonstrated best serum LMW proteins recovery and stability using a clotting time between 1 and 2h, with serum stored up to 2h either at room temperature or at 4 degrees C, independently of PI addition. PI addition to whole blood resulted in a lower number of LMW peaks detected. Finally, minimal effects on serum proteome profiles were observed after 1-month storage at -80 degrees C, independently of PI addition on whole blood and/or serum. In conclusion, the use of standardized pre-analytical and storage procedures together with an automated peptide purification might minimize potential bias on serum LMW profiling results, thus allowing a better homogeneity and reproducibility in future proteomics studies.Journal of proteomics 09/2009; 73(3):667-77. · 5.07 Impact Factor -
Article: Mass spectrometric identification of hemoglobin modifications induced by nitrosobenzene.
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ABSTRACT: Aniline and nitrobenzene (NB) are widely used industrial chemicals. Early effects of aniline toxicity include methemoglobin formation and damage to erythrocytes (Jenkins, F.P., 1972. The no-effect dose of anilne in human subjects and a comparison of aniline toxicity in man and rat. Food Cosmet. Toxicol. 10, 671-679; Bus, J.S., Popp, J.A., 1987. Perspectives on the mechanism of action of the splenic toxicity of aniline and structurally-related. Food Chem. Toxicol. 25, 619-627). In this report, we describe an analytical method, based on LC techniques and mass spectrometry, which could help in monitoring the exposure to aniline and NB. In particular, we describe and characterize the formation of specific adducts during an in vitro reaction of nitrosobenzene (NOB), the main metabolite of aniline and NB, and human hemoglobin.Ecotoxicology and Environmental Safety 11/2008; 72(5):1601-8. · 2.29 Impact Factor -
Article: Plasmodium lipid rafts contain proteins implicated in vesicular trafficking and signalling as well as members of the PIR superfamily, potentially implicated in host immune system interactions.
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ABSTRACT: Plasmodium parasites, the causal agents of malaria, dramatically modify the infected erythrocyte by exporting parasite proteins into one or multiple erythrocyte compartments, the cytoplasm and the plasma membrane or beyond. Despite advances in defining signals and specific cellular compartments implicated in protein trafficking in Plasmodium-infected erythrocytes, the contribution of lipid-mediated sorting to this cellular process has been poorly investigated. In this study, we examined the proteome of cholesterol-rich membrane microdomains or lipid rafts, purified from erythrocytes infected by the rodent parasite Plasmodium berghei. Besides structural proteins associated with invasive forms, we detected chaperones, proteins implicated in vesicular trafficking, membrane fusion events and signalling. Interestingly, the raft proteome of mixed P. berghei blood stages included proteins encoded by members of a large family (bir) of putative variant antigens potentially implicated in host immune system interactions and targeted to the surface of the host erythrocytes. The generation of transgenic parasites expressing BIR/GFP fusions confirmed the dynamic association of members of this protein family with membrane microdomains. Our results indicated that lipid rafts in Plasmodium-infected erythrocytes might constitute a route to sort and fold parasite proteins directed to various host cell compartments including the cell surface.Proteomics 07/2008; 8(12):2500-13. · 4.43 Impact Factor -
Article: Biochemical characterization of MLC1 protein in astrocytes and its association with the dystrophin-glycoprotein complex.
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ABSTRACT: MLC1 gene mutations have been associated with megalencephalic leukoencephalopathy with subcortical cysts (MLC), a rare neurologic disorder in children. The MLC1 gene encodes a membrane protein (MLC1) with unknown function which is mainly expressed in astrocytes. Using a newly developed anti-human MLC1 polyclonal antibody, we have investigated the biochemical properties and localization of MLC1 in cultured astrocytes and brain tissue and searched for evidence of a relationship between MLC1 and proteins of the dystrophin-glycoprotein complex (DGC). Cultured astrocytes express two MLC1 components showing different solubilisation properties and subcellular distribution. Most importantly, we show that the membrane-associated component of MLC1 (60-64 kDa) localizes in astrocytic lipid rafts together with dystroglycan, syntrophin and caveolin-1, and co-fractionates with the DGC in whole rat brain tissue. In the human brain, MLC1 protein is expressed in astrocyte processes and ependymal cells, where it colocalizes with dystroglycan and syntrophin. These data indicate that the DGC may be involved in the organization and function of the MLC1 protein in astrocyte membranes.Molecular and Cellular Neuroscience 04/2008; 37(3):480-93. · 3.66 Impact Factor -
Article: Functional genomics, new tools in malaria research.
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ABSTRACT: The mosquito-transmitted unicellular parasite Plasmodium falciparum, the agent of malaria disease, still causes more than one million deaths every year in the tropical and subtropical areas of the world. New intervention strategies are needed to contrast the insurgence of resistance to effective drugs and insecticides. The complete annotated genomes of the human parasite P. falciparum and the rodent model P. yoelii is now available thus providing a prediction of their possible gene products. This makes feasible the application of functional genomics to malaria research with the final goal of providing a complete survey of Plasmodium life cycle. Genome-wide approaches to the study of transcriptome or proteome were successfully applied to malaria parasite with the promise for new drug and vaccine candidates in the next future.Annali dell'Istituto superiore di sanita 02/2005; 41(4):469-77. · 0.94 Impact Factor
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Institutions
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2009
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Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Pisana
Roma, Latium, Italy
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2005–2008
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Istituto Superiore di Sanità
- Department of Infectious, Parasitic and Immune-mediated Diseases
Roma, Latium, Italy
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