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Modern scientific research produces datasets of increasing size and complexity that require dedicated numerical methods to be processed. In many cases, the analysis of spectroscopic data involves the denoising of raw data before any further processing. Current efficient denoising algorithms require the singular value decomposition of a matrix with a size that scales up as the square of the data length, preventing their use on very large datasets. Taking advantage of recent progress on random projection and probabilistic algorithms, we developed a simple and efficient method for the denoising of very large datasets. Based on the QR decomposition of a matrix randomly sampled from the data, this approach allows a gain of nearly three orders of magnitude in processing time compared with classical singular value decomposition denoising. This procedure, called urQRd (uncoiled random QR denoising), strongly reduces the computer memory footprint and allows the denoising algorithm to be applied to virtually unlimited data size. The efficiency of these numerical tools is demonstrated on experimental data from high-resolution broadband Fourier transform ion cyclotron resonance mass spectrometry, which has applications in proteomics and metabolomics. We show that robust denoising is achieved in 2D spectra whose interpretation is severely impaired by scintillation noise. These denoising procedures can be adapted to many other data analysis domains where the size and/or the processing time are crucial. [ABSTRACT FROM AUTHOR]

This work provides the first identification of fish glue from a few micrograms of a 17th century artwork sample using an adapted proteomics approach. Fish glue has been widely used as a binder in various art objects such as paintings, manuscripts or polychrome objects however its authentication remains particularly challenging. The lack of information on fish species in genomic and proteomic databases represents a major drawback. A supplementary difficulty is provided by the historical sample features, i.e. a few micrograms of a 17th century polychrome object with a multilayered structure. SYPRO® Ruby staining was used as a screening technique to probe the presence of proteins in the sample cross-section. Results revealed the presence of several layers containing proteins among which a thin proteinaceous layer located between the silver leaf and the glaze. This thin layer is described as fish glue coating by historical sources but its composition has not been identified yet. The optimized methodology, based on high resolution mass spectrometry and adapted bioinformatic tools, was successfully applied to 50 μg of a polychromy sample and resulted in the identification of several collagen proteins. Extensive interpretation of data generated by tandem mass spectrometry allowed the identification of proteins from different biological origins. In particular, seven peptides specific to fish collagen proteins were identified for the first time proving the presence of fish glue in the sample and corroborating information found in historical texts dealing with the polychromy technique. [ABSTRACT FROM AUTHOR]

Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) achieves high resolution and mass accuracy, allowing the identification of the raw chemical formulae of ions in complex samples. Using ion isolation and fragmentation (MS/MS), we can obtain more structural information, but MS/MS is time- and sample-consuming because each ion must be isolated before fragmentation. In 1987, Pfändler et al. proposed an experiment for 2D FT-ICR MS in order to fragment ions without isolating them and to visualize the fragmentations of complex samples in a single 2D mass spectrum, like 2D NMR spectroscopy. Because of limitations of electronics and computers, few studies have been conducted with this technique. The improvement of modern computers and the use of digital electronics for FT-ICR hardware now make it possible to acquire 2D mass spectra over a broad mass range. The original experiments used in-cell collision-induced dissociation, which caused a loss of resolution. Gas-free fragmentation modes such as infrared multiphoton dissociation and electron capture dissociation allow one to measure high-resolution 2D mass spectra. Consequently, there is renewed interest to develop 2D FT-ICR MS into an efficient analytical method. Improvements introduced in 2D NMR spectroscopy can also be transposed to 2D FT-ICR MS. We describe the history of 2D FT-ICR MS, introduce recent improvements, and present analytical applications to map the fragmentation of peptides. Finally, we provide a glossary which defines a few keywords for the 2D FT-ICR MS field. [ABSTRACT FROM AUTHOR]

Newly designed gels for electrophoresis protein separation were synthesized from acrylamide, N, N′-methylenebis (acrylamide) and dextran mixtures. Radical polymerization was initiated by ammonium persulfate and N, N, N′, N′-tetramethylethylenediamine. The time dependence of absorbance during polymerization was monitored using UV-visible spectroscopy. The exothermic polymerization process exhibited a sharp rise of temperature reminiscent of the Trommsdorff effect. The swelling kinetics of the synthesized gels was examined in deionized water and buffer solutions. One of the challenges was to find an alternative to commercial products, sold as mixtures with no detailed chemical contents, commonly used in sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) for protein separation. For this reason, a systematic comparison was made of the properties of one of the most commonly used commercial gels, Duracryl from Genomics Solution Inc., and those of the synthesized polyacrylamide/dextran gels. Copyright © 2011 Society of Chemical Industry Fergusson plots show that newly designed gels synthesized from acrylamide, N, N′-methylenebis(acrylamide) and dextran mixtures exhibited superior protein separation capabilities compared to commercial Duracryl gels. [ABSTRACT FROM AUTHOR]

Abstract: Quercetin, the polyphenolic compound, which has the highest daily intake, is well known for its protective effects against aging diseases and has received a lot of attention for this reason. Both quercetin 3-O-β-d-glucuronide and quercetin 3′-O-β-d-glucuronide are human metabolites, which, together with their regioisomers, are required for biological as well as physical chemistry studies. We present here a novel synthetic route based on the sequential and selective protections of the hydroxyl functions of quercetin allowing selective glycosylation, followed by TEMPO-mediated oxidation to the glucuronide. This methodology enabled us to synthesize the five O-β-d-glucosides and four O-β-d-glucuronides of quercetin, including the major human metabolite, quercetin 3-O-β-d-glucuronide. [Copyright &y& Elsevier]

This manuscript deals with the identification of protein residues in amphorae, including particularly identification of protein species. The work described was performed on fishes, the anchovy ( Engraulis encrasicolus) and bonito ( Sarda sarda) species frequently found in the Mediterranean area. Based on proteomic techniques, the analytical strategy was adapted to analysis of protein residues from tiny ceramic fragments. The major difficulty was to extract proteins and limit their hydrolysis during the sample preparation; consequently, multiple soft extraction techniques were evaluated. The most valuable results were obtained using a solution containing high amounts of denaturing agents, urea and thiourea, reducing agent, dithiothreitol, and detergent, 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate. The analysis using nano liquid chromatography-nano electrospray ionization double quadrupole time-of-flight mass spectrometry resulted in the identification of up to 200 proteins for the anchovy and bonito species, among which 73 peptides were found to be fish-specific. Because bonito and anchovy species are not documented and fully sequenced in genomic databases, the preliminary protein identification was realized via sequence homology to other fish sequenced species. Amino acid substitutions of peptides were assigned on the basis of the interpretation of tandem mass spectrometry spectra using de novo sequencing; these peptides, not reported up to now in databases, constitute species-specific markers. The method developed was finally applied to an archaeological sample replica impregnated with a mixture of fish tissue from both species; this experiment successfully led to the identification of 17 fish proteins, including 33 fish-specific peptides. This work shows that the analytical method developed has great potential for the identification of protein species in complex archaeological samples. [ABSTRACT FROM AUTHOR]

Abstract: This work presents the precise identification of triacylglycerols (TAGs) extracted from archaeological samples using a methodology based on nanoelectrospray and Fourier transform mass spectrometry. The archaeological TAG identification needs adapted sample preparation protocols to trace samples in advanced degradation state. More precisely, the proposed preparation procedure includes extraction of the lipid components from finely grinded ceramic using dichloromethane/methanol mixture with additional ultrasonication treatment, and TAG purification by solid phase extraction on a diol cartridge. Focusing on the analytical approach, the implementation of “in-house” species-dependent TAG database was investigated using MS and InfraRed Multiphoton Dissociation (IRMPD) MS/MS spectra; several vegetal oils, dairy products and animal fats were studied. The high mass accuracy of the Fourier transform analyzer (Δm below 2.5ppm) provides easier data interpretation, and allows distinction between products of different origins. In details, the IRMPD spectra of the lithiated TAGs reveal fragmentation reactions including loss of free neutral fatty acid and loss of fatty acid as α,β-unsaturated moieties. Based on the developed preparation procedure and on the constituted database, TAG extracts from 5th century BC to 4th century AD Olbia lamps were analyzed. The structural information obtained succeeds in identifying that bovine/ovine fats were used as fuel used in these archaeological Olbia lamps. [Copyright &y& Elsevier]